Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

a1 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
a2 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
abbreviationToTimeUnit - Static variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
aborted() - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
aborted() - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the CPM is stopped abruptly due to errors.
aboutDialog - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
AboveLeftFragmentExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
AboveLeftFragmentExtractor(String, String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveLeftFragmentExtractor
AboveRightFragmentExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
AboveRightFragmentExtractor(String, String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveRightFragmentExtractor
AbstractBagOfWordsExporter - Class in org.apache.ctakes.ytex.kernel
AbstractBagOfWordsExporter() - Constructor for class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
AbstractBaseDictionary - Class in org.apache.ctakes.dictionary.lookup
AbstractBaseDictionary() - Constructor for class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary
AbstractBaseMetaDataHit - Class in org.apache.ctakes.dictionary.lookup: Base impl for a MetaDataHit implementation.
AbstractBaseMetaDataHit() - Constructor for class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit
AbstractClassifier - Class in org.apache.ctakes.coreference.util
AbstractClassifier(UimaContext, String, int) - Constructor for class org.apache.ctakes.coreference.util.AbstractClassifier
AbstractConceptFactory - Class in org.apache.ctakes.dictionary.lookup2.concept: Author: SPF Affiliation: CHIP-NLP Date: 9/4/2014
AbstractConceptFactory(String) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.AbstractConceptFactory
AbstractJCasTermAnnotator - Class in org.apache.ctakes.dictionary.lookup2.ae: Performs the basic initialization with uima context, including the parse of the dictionary specifications file.
AbstractJCasTermAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
AbstractJdbcWriter - Class in org.apache.ctakes.core.cc: Write cas to a database using jdbc
AbstractJdbcWriter() - Constructor for class org.apache.ctakes.core.cc.AbstractJdbcWriter
AbstractJdbcWriter.FieldInfo - Interface in org.apache.ctakes.core.cc
AbstractJdbcWriter.TableInfo - Interface in org.apache.ctakes.core.cc
AbstractJdbcWriter.TableSqlInfo - Class in org.apache.ctakes.core.cc
AbstractJdbcWriter.TableSqlInfo(Connection, AbstractJdbcWriter.TableInfo) - Constructor for class org.apache.ctakes.core.cc.AbstractJdbcWriter.TableSqlInfo
AbstractRareWordDictionary - Class in org.apache.ctakes.dictionary.lookup2.dictionary: Author: SPF Affiliation: CHIP-NLP Date: 11/25/13
AbstractRareWordDictionary(String) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.AbstractRareWordDictionary
AbstractTermConsumer - Class in org.apache.ctakes.dictionary.lookup2.consumer: Author: SPF Affiliation: CHIP-NLP Date: 2/5/14
AbstractTermConsumer(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
accept(File) - Method in class org.apache.ctakes.ytex.kernel.FileUtil.DirectoryFileFilter
accept(File) - Method in class org.apache.ctakes.ytex.kernel.FileUtil.PrefixFileFilter
accept(File) - Method in class org.apache.ctakes.ytex.kernel.FileUtil.SuffixFileFilter
accept(File, String) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog.InteractiveFilter
ACRONYM_PATTERN - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change split sentences periods that do not have this acronym preceding it
acronymPattern - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change
actionPerformed(ActionEvent) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
adaptToBaseToken(BaseToken) - Static method in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator: Adapts JCas objects to BaseToken interfaces expected by the Finite State Machines.
adaptToFSMBaseToken(BaseToken) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
add(Collection<? extends ANNOTATION_TYPE>, Collection<? extends ANNOTATION_TYPE>) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Update the statistics, comparing the reference annotations to the predicted annotations.
add(Collection<? extends ANNOTATION_TYPE>, Collection<? extends ANNOTATION_TYPE>, <any>, <any>) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Update the statistics, comparing the reference annotations to the predicted annotations.
add(TlinkType) - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
add(String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings
add(K) - Method in class org.apache.ctakes.utils.struct.CounterMap
add(K, Integer) - Method in class org.apache.ctakes.utils.struct.CounterMap
add(K) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap
add(K, Integer) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap
addAll(Iterable<AnnotationStatisticsCompact<OUTCOME_TYPE>>) - Static method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Add all statistics together.
addAll(AnnotationStatisticsCompact<OUTCOME_TYPE>) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Adds all the statistics collected by another AnnotationStatisticsCompact to this one.
addAllValues(K, C) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: adds everything from the given collection to the internal collection mapped with key
addAllValues(K, C) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: adds everything from the given collection to the internal collection mapped with key
addAllValues(K, C) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: adds everything from the given collection to the internal collection mapped with key
addAllValues(K, C) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: adds everything from the given collection to the internal collection mapped with key
addAllValues(K, C) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: adds everything from the given collection to the internal collection mapped with key
addAllValues(K, C) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: adds everything from the given collection to the internal collection mapped with key
addAnnoLinks(JCas, <any>, List<DocumentMapperServiceImpl.AnnoLink>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
addAnnoLinks(JCas, <any>, List<DocumentMapperServiceImpl.AnnoLink>, AnnoMappingInfo) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
addAnnotation(Annotation) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Adds a single annotation to the syntactic cue annotation list.
addAnnotation(int, XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Inserts a new annotation with the specified internal id to this XcasFile.
addAnnotation(int, XcasAnnotation, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Inserts a new annotation, along with its position in the file, to this XcasFile object.
addAnnotation(int, XcasAnnotation, int, int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Inserts a new annotation, along with its position in the file, to this XcasFile object.
addAnnotations(JCas, Set, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: used by executeFSMs to add annotations for features for DrugMention
addAnnotations(List) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Adds a list of annotations to the syntactic cue annotation list.
addCacheEntry(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Adds an entry to the dictionary lookup cache.
addChild(SimpleTree) - Method in class org.apache.ctakes.utils.tree.SimpleTree
addChildrenToNodes(Map<NodeKey, Node>, QueryMappingInfo) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
addCleartkAttributeAnnotatorsToAggregate(File, AggregateBuilder) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
addCollectionFilter(CollectionFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Adds a Collection filter to the engine.
addConcept(String) - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
addConcept(JCas, Map<String, OntologyConcept>, Annotation, Feature, Feature, boolean) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator: add a concept to the map of concepts for the current named entity.
addConcepts(ConceptGraph, String, Set<String>, Set<String>) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
addConcepts(Map<String, Integer>, Set<String>) - Method in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
addCuePhrase(JCas, String, int, int) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
addCuiTuiToMap(Map<String, Set<String>>, Map<String, String>, String, String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
addDocKey(JCas, Map<String, Object>) - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
addExcludeList(DictionaryEngine, Iterator<?>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
addExcludeList(DictionaryEngine, List<Element>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
addExternalAttributeAnnotatorsToAggregate(AggregateBuilder) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
addField(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow
addFilenameToDir(String, String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil
addGapSegment(JCas, int, int) - Method in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
addIdentifiedAnnotationFeatures(KnowtatorAnnotation, IdentifiedAnnotation, JCas, int, Map<String, String>, Map<String, Boolean>, Map<String, KnowtatorAnnotation>, Map<String, TOP>, List<MiPACQKnowtatorXMLReader.DelayedFeature>) - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
addIdentifiedAnnotationFeatures(KnowtatorAnnotation, IdentifiedAnnotation, JCas, int, Map<String, String>, Map<String, Boolean>, Map<String, KnowtatorAnnotation>, Map<String, TOP>, List<SHARPKnowtatorXMLReader.DelayedFeature>) - Static method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
addInstance(<any>) - Method in class org.apache.ctakes.temporal.utils.SMOTEplus
addLink(<any>, List<DocumentMapperServiceImpl.AnnoLink>, String, String, Integer, FeatureStructure) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: add a link.
addMedicationSpecificAttributes(JCas, DrugMentionAnnotation, MedicationMention) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
addMetaData(Object, Object) - Method in class org.apache.ctakes.necontexts.ContextHit
addMetaData(Object, Object) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Adds a meta data entry for the document.
addNamedEntity(JCas, int, int, Map<String, OntologyConcept>, boolean, Set<MetaMapToCTakesAnnotator.NegSpan>) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
addNominalAttribute(String, SortedSet<String>, boolean) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter: Add a nominal attribute to the list of attributes
addNominalWordToInstance(BagOfWordsData, int, String, String) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
addNominalWordToInstance(SparseData, long, String, String) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
addNumericAttribute(BufferedWriter, String) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter
addNumericWordToInstance(BagOfWordsData, int, String, double) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
addNumericWordToInstance(SparseData, long, String, double) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
addOptionPrefix(String[], String) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
addOtherTimes(JCas, TopTreebankNode, IdentifiedAnnotation, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
addOtherTimes(JCas, TopTreebankNode, IdentifiedAnnotation, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor
addPhraseHead(List<TerminalTreebankNode>, TerminalTreebankNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor
addPostLookupFilter(PostLookupFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Adds a Post-lookup filter to the engine.
addPreLookupFilter(PreLookupFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Adds a Pre-lookup filter to the engine.
addRelation(ArrayList<RelationInfo>, List<?>, HashMap<String, ArgumentInfo>, String) - Static method in class org.apache.ctakes.assertion.cr.XMLReader
addRelation(ArrayList<RelationInfo>, List<?>, HashMap<String, ArgumentInfo>, String) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader
addRelation(JCas, BinaryTextRelation, String, String, String, Map<String, Annotation>, String) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
addRelation(ConceptGraph, Set<String>, String, String, boolean, Set<String>) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: add the relationship to the concept map
addRow(StringTableRow) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable
addSegment(SegmentMetaData) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Adds a segment.
addSpan(int, int) - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: Create a new span and add it to the list (not publicly available)
addStringAttribute(String, String) - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter: Adds an attribute that may be used for filtering.
addStringAttribute(String, String) - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation: Adds an attribute that may be used for filtering.
addStringAttribute(String, String) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
addStringAttribute(String, String) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
addSubtree(Set<String>, ConcRel) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
addSubtree(Set<String>, ConcRel) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: recursively add children of cr to childConcepts
addTlinkType(BinaryTextRelation) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
addTlinkType(Annotation, Annotation, TlinkType) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
addTlinkTypes(int, int, TlinkTypeSet) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
addToIndexes(JCas, Map<String, TOP>) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
addToIndexes(JCas, ArrayList<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
addVectors(HashMap<String, Double>, HashMap<String, Double>) - Method in class org.apache.ctakes.utils.wiki.WikiIndex
addWordsToInstances(Instances, BagOfWordsData) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
addWordsToInstances(Instances, SparseData, SortedMap<Long, String>) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter: add sparse data to instances
ADJP - Class in org.apache.ctakes.typesystem.type.syntax: An adjective phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADJP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ADJP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP: Never called.
ADJP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP: Internal - constructor used by generator
ADJP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP
ADJP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP
ADJP_Type - Class in org.apache.ctakes.typesystem.type.syntax: An adjective phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADJP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ADJP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP_Type: initialize variables to correspond with Cas Type and Features
adjustAssertionAttributesByI2B2Convertion(IdentifiedAnnotation, org.mitre.medfacts.i2b2.annotation.AssertionAnnotation) - Static method in class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
adjustAttr(JudgeAttributeInstances.Selector, String, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
adjustOffsetToBestMatch(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
ADVP - Class in org.apache.ctakes.typesystem.type.syntax: An adverb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADVP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ADVP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP: Never called.
ADVP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP: Internal - constructor used by generator
ADVP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP
ADVP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP
ADVP_Type - Class in org.apache.ctakes.typesystem.type.syntax: An adverb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADVP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ADVP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP_Type: initialize variables to correspond with Cas Type and Features
ae - Variable in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
AEROSOL - Static variable in class org.apache.ctakes.drugner.elements.FormElement
AF - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
Affects - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
Affects() - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects: Never called.
Affects(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects: Internal - constructor used by generator
Affects(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects
Affects_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
Affects_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects_Type: initialize variables to correspond with Cas Type and Features
AffectsTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
AffectsTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation: Never called.
AffectsTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation: Internal - constructor used by generator
AffectsTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation
AffectsTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
AffectsTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation_Type: initialize variables to correspond with Cas Type and Features
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel: precompute the scaling factor - we will always divide by this
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: load the map of uima annotation class name to mapper class name from the database.
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
afterPropertiesSet() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
afterSet - Static variable in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
afterWord - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
al - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
algorithm - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
alias - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
alignDrugMentionAttributes(String, DrugMention, DrugMentionAnnotation, DrugMentionAnnotation, String, boolean, boolean, boolean, String, String, String) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
alignId2GoldId - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
ALL_SCOPE - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: The ALL_SCOPE scope provides the context annotation that are found in all three of the other scopes (LEFT, MIDDLE, and RIGHT).
allAnnotationTypes - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
allBagsParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
allBagsParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
allBagsParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
allBagsParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
allBagsParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
allDigits(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
allFieldsValues() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Returns a string representation of all the attributes and references.
ALLFILELOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
allFileNames - Variable in class org.apache.ctakes.relationextractor.data.Splitter
allowClassifierModelOnClasspath(UimaContext) - Static method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Workaround for https://code.google.com/p/cleartk/issues/detail?id=346 Not intended for external use
allowSmallerSystemArguments - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
allParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
allParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
allParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
allParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
allParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
allTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
alog(double) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath
alphaFunction - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
AlternateCuePhraseAnnotator - Class in org.apache.ctakes.assertion.medfacts.cleartk
AlternateCuePhraseAnnotator() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
anaforaDirectory - Variable in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
anaforaXMLSuffixes - Variable in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
analysisBatch - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
analysisBatch - Variable in class org.apache.ctakes.ytex.uima.model.Document
analyzeContext(List<? extends Annotation>, int) - Method in interface org.apache.ctakes.necontexts.ContextAnalyzer: This method is called by the ContextAnnotator.
analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.necontexts.ContextAnalyzerAdapter
analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.necontexts.negation.NegationContextAnalyzer: This method analyzes a list of tokens looking for a negation pattern as specified by the class NegationFSM.
analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.necontexts.status.StatusContextAnalyzer: Analyze a list of tokens looking for a status pattern as specified by the class StatusIndicatorFSM.
analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.smokingstatus.context.negation.NegationContextAnalyzer: This method analyzes a list of tokens looking for a negation pattern as specified by the class NegationFSM.
anaph_feats - Static variable in class org.apache.ctakes.coreference.util.FeatureVector
anaph_model - Variable in class org.apache.ctakes.coreference.util.SvmVectorCreator
AnaphoricityAttributeCalculator - Class in org.apache.ctakes.coreference.util
AnaphoricityAttributeCalculator(JCas, Markable) - Constructor for class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
ANAT - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
ANAT_TUIS - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
AnatomicalSite - Class in org.apache.ctakes.typesystem.type.refsem: A body part or area, corresponding to the UMLS semantic group of Anatomy.
AnatomicalSite() - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: Never called.
AnatomicalSite(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: Internal - constructor used by generator
AnatomicalSite(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite
AnatomicalSite_Type - Class in org.apache.ctakes.typesystem.type.refsem: A body part or area, corresponding to the UMLS semantic group of Anatomy.
AnatomicalSite_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type: initialize variables to correspond with Cas Type and Features
AnatomicalSiteMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (AnatomicalSite) Entity.
AnatomicalSiteMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: Never called.
AnatomicalSiteMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: Internal - constructor used by generator
AnatomicalSiteMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
AnatomicalSiteMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
AnatomicalSiteMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (AnatomicalSite) Entity.
AnatomicalSiteMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type: initialize variables to correspond with Cas Type and Features
anchorEndofline(int[][], int, int, MedicationMention) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
AND_RELATION - Static variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl
annoBaseId - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
annoClassName - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
annoFieldName - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
AnnoMappingInfo - Class in org.apache.ctakes.ytex.uima.mapper
AnnoMappingInfo() - Constructor for class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
annoMappingInfos - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
annotateNegation(JCas, Sentence, Annotation, NegexAnnotator.NegexToken, boolean, boolean) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator: set the certainty/confidence flag on a named entity, and add a negation context annotation.
annotateParagraph(JCas, String, int, int, int) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: split paragraphs.
annotatePSESentenceFeatures(JCas) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator: Annotate PSESentenceFeature to be used to classify SE sentences based on the previously trained model
annotateRange(JCas, int, int) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: A utility method that annotates a given range.
annotateRange(JCas, String, Segment, int) - Method in class org.apache.ctakes.core.ae.SentenceDetector: Detect sentences within a section of the text and add annotations to the CAS.
annotateRange(JCas, int, int) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotator: A utility method that tokenizes a range of text.
annotateRange(JCas, int, int) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB: Tokenizes a range of text, adding the tokens to the CAS Tokenizes one sentence at a time.
annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator: A utility method that annotates a given range.
annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: A utility method that annotates a given range.
annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster: A utility method that annotates a given range.
annotateRange(JCas, String, int, int, int) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: Detect sentences within a section of the text and add annotations to the CAS.
annotateSentence(JCas, Sentence) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster
annotateSideEffects(JCas, List<SideEffectAnnotator.SideEffect>) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Add side effect components to CAS
annotation - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
annotation - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
annotation - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
Annotation - Class in org.apache.ctakes.preprocessor
Annotation() - Constructor for class org.apache.ctakes.preprocessor.Annotation
annotationClass - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
annotationClasses - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyFromGold
AnnotationContainmentLink - Class in org.apache.ctakes.ytex.uima.model: represent a containment relationship between annotations, e.g.
AnnotationContainmentLink() - Constructor for class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
AnnotationCounter - Class in org.apache.ctakes.coreference.util
AnnotationCounter() - Constructor for class org.apache.ctakes.coreference.util.AnnotationCounter
AnnotationDepUtils - Class in org.apache.ctakes.dependency.parser.util
AnnotationDepUtils() - Constructor for class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
AnnotationIdCollection - Class in org.apache.ctakes.temporal.utils: Author: SPF Affiliation: CHIP-NLP Date: 6/17/13
AnnotationIdCollection(ArrayList<BinaryTextRelation>) - Constructor for class org.apache.ctakes.temporal.utils.AnnotationIdCollection
AnnotationIdCollection.ArgComparator - Enum in org.apache.ctakes.temporal.utils
AnnotationIdCollection.ArgComparator() - Constructor for enum org.apache.ctakes.temporal.utils.AnnotationIdCollection.ArgComparator
annotationNode(JCas, Annotation) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
annotationNode(JCas, int, int) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
annotations - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile
annotationsClone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile
AnnotationSelector - Class in org.apache.ctakes.coreference.util
AnnotationSelector() - Constructor for class org.apache.ctakes.coreference.util.AnnotationSelector
annotationSlots - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The annotation-valued annotation attributes (i.e.
AnnotationStatisticsCompact<OUTCOME_TYPE extends java.lang.Comparable<? super OUTCOME_TYPE>> - Class in org.apache.ctakes.assertion.eval: Stores statistics for comparing Annotations extracted by a system to gold Annotations.
AnnotationStatisticsCompact() - Constructor for class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Create an AnnotationStatisticsCompact that compares Annotations based on their begin and end offsets, plus a Feature of the Annotation that represents the outcome or label.
AnnotationStatisticsCompact.Span - Class in org.apache.ctakes.assertion.eval
AnnotationStatisticsCompact.Span(Annotation) - Constructor for class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact.Span
annotationToFeatureValue(String) - Static method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Creates a Function that extracts a feature value from a TOP.
annotationToNull() - Static method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Creates a Function that always returns null.
annotationToSpan() - Static method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Creates a Function that converts an Annotation into a hashable representation of its begin and end offsets.
AnnotationTreeUtils - Class in org.apache.ctakes.constituency.parser.util
AnnotationTreeUtils() - Constructor for class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
annotationTypes - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
annotationTypes - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
annotationViewGenerator - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
annotationViewGenerator - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
ANNOTATOR_CLASSES - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
annotatorClass - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
annotatorNames - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
AnnotOffsetComparator - Class in org.apache.ctakes.coreference.util
AnnotOffsetComparator() - Constructor for class org.apache.ctakes.coreference.util.AnnotOffsetComparator
annoToLookupToken(Annotation) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: vng use the constructor identified during initialization to create the lookup token
ANT_SITE_TUIS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
ANY_ADJECTIVE - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
ANY_DEPREL - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
ANY_NOUN - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
ANY_POS - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
ANY_TOKEN - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex: Static identifiers used to build Regex expressions
ANY_VERB - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
apiMacroHome - Variable in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
APOSTROPHE - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
App - Class in org.apache.ctakes.jdl: Hello world!
App() - Constructor for class org.apache.ctakes.jdl.App
append(DependencyRegex) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
append(DEPNode[]) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
appendOptional(DependencyRegex) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
appendOptional(DEPNode[]) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
appendString(String, String, Writer) - Method in class org.apache.ctakes.ytex.sparsematrix.InstanceDataExporterImpl
AppJdl - Class in org.apache.ctakes.jdl: Java data loader Application.
AppJdl(String, String, String) - Constructor for class org.apache.ctakes.jdl.AppJdl
ApplicationContextHolder - Class in org.apache.ctakes.ytex.uima: get the spring bean application context.
ApplicationContextHolder() - Constructor for class org.apache.ctakes.ytex.uima.ApplicationContextHolder
apply(Feature) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
apply(String) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
apply(Feature) - Method in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
apply(Feature) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.BrownClusterFeatureFunction
apply(Feature) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction
apply(String) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
apply(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
apply(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
apply(String) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
apply(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
apply(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
apply(String) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
applyCapitalizationRules(Token, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Applies capitalization rules to the given token.
applyFilter(Collection<MetaDataHit>) - Method in interface org.apache.ctakes.dictionary.lookup.filter.CollectionFilter: Prunes the Collection of MetaDataHit objects that meet the filter implementation's match criteria.
applyFilter(Collection<MetaDataHit>) - Method in class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl: Implementation
applyOp(int) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl: Checks the comparison value against the specified operation.
applyPunctSymbolRules(List<Token>, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Applies punctuation/symbol rules to the given list of tokens.
applyTextModifier(TextModifier, String, StringBuffer) - Static method in class org.apache.ctakes.core.ci.HyphenTextModifierImpl: Apply text modifier to the text
TODO - move this to TextModifier and take a Logger See HyphenTextModifierImpl
applyTextModifier(String, StringBuffer) - Method in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer: Apply text modifier to the text TODO - move this to TextModifier and take a Logger See HyphenTextModifierImpl
applyWordNumRules(Token, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
AppMain - Class in org.apache.ctakes.jdl: Java data loader Main.
AppMain() - Constructor for class org.apache.ctakes.jdl.AppMain
ApproximateMath - Class in org.apache.ctakes.utils.wiki
ApproximateMath() - Constructor for class org.apache.ctakes.utils.wiki.ApproximateMath
ApproximateSimilarity - Class in org.apache.ctakes.utils.wiki
ApproximateSimilarity() - Constructor for class org.apache.ctakes.utils.wiki.ApproximateSimilarity
arg1 - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
arg1 - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
arg1 - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
arg1begin - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
arg1Class - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
arg1Class - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
arg1end - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
arg2 - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
arg2 - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
arg2 - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
arg2begin - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
arg2Class - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
arg2Class - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
arg2end - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
ArgumentInfo - Class in org.apache.ctakes.assertion.cr: Information about a relation argument.
ArgumentInfo(String, String) - Constructor for class org.apache.ctakes.assertion.cr.ArgumentInfo
ArgumentInfo - Class in org.apache.ctakes.relationextractor.knowtator: Information about a relation argument.
ArgumentInfo(String, String) - Constructor for class org.apache.ctakes.relationextractor.knowtator.ArgumentInfo
ArgumentOrderFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that indicate the order of the arguments (e.g.
ArgumentOrderFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.ArgumentOrderFeatureExtractor
arrangeIntoRows(Annotation, List<Annotation>) - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer: Arranges the list of annotations into one or more rows.
ArrayListMap<K,V> - Class in org.apache.ctakes.dictionary.lookup2.util.collection: Author: SPF Affiliation: CHIP-NLP Date: 7/23/14
ArrayListMap() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
ArrayListMap(int) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
arrID - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
arrInd - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
asEvaluation - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
ASNEEDED - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
AspectualTextRelation - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
AspectualTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation: Never called.
AspectualTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation: Internal - constructor used by generator
AspectualTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation
AspectualTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
AspectualTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation_Type: initialize variables to correspond with Cas Type and Features
asqrt(int) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath
asqrt(double) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath
assemble(Serializable, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
assemble(Serializable, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
Assertion - Class in org.apache.ctakes.assertion.medfacts.types: Updated by JCasGen Wed Sep 30 11:06:05 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-assertion/target/jcasgen/typesystem.xml
Assertion() - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion: Never called.
Assertion(int, TOP_Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion: Internal - constructor used by generator
Assertion(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion
Assertion(JCas, int, int) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion
Assertion_Type - Class in org.apache.ctakes.assertion.medfacts.types: Updated by JCasGen Wed Sep 30 11:06:05 EDT 2015
Assertion_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion_Type: initialize variables to correspond with Cas Type and Features
AssertionAboveLeftTreeExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
AssertionAboveLeftTreeExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionAboveLeftTreeExtractor
AssertionAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts
AssertionAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
AssertionCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
AssertionCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
AssertionCleartkAnalysisEngine.FEATURE_CONFIG - Enum in org.apache.ctakes.assertion.medfacts.cleartk
AssertionCleartkAnalysisEngine.FEATURE_CONFIG() - Constructor for enum org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.FEATURE_CONFIG
AssertionComponents - Class in org.apache.ctakes.assertion.medfacts.cleartk: Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.
AssertionComponents() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents
AssertionConst - Class in org.apache.ctakes.assertion.util
AssertionConst() - Constructor for class org.apache.ctakes.assertion.util.AssertionConst
AssertionCuePhraseAnnotation - Class in org.apache.ctakes.typesystem.type.temporary.assertion: A cue phrase indicating potential negation, uncertainty, or conditional Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
AssertionCuePhraseAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: Never called.
AssertionCuePhraseAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: Internal - constructor used by generator
AssertionCuePhraseAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation
AssertionCuePhraseAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation
AssertionCuePhraseAnnotation_Type - Class in org.apache.ctakes.typesystem.type.temporary.assertion: A cue phrase indicating potential negation, uncertainty, or conditional Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
AssertionCuePhraseAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type: initialize variables to correspond with Cas Type and Features
AssertionCuePhraseConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: Implementation that takes Rxnorm dictionary lookup hits and stores only the ones that are also present in the Orange Book.
AssertionCuePhraseConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
AssertionCuePhraseConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
assertionDecoderConfiguration - Variable in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
AssertionDependencyTreeExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
AssertionDependencyTreeExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionDependencyTreeExtractor
AssertionDepUtils - Class in org.apache.ctakes.assertion.util
AssertionDepUtils() - Constructor for class org.apache.ctakes.assertion.util.AssertionDepUtils
AssertionEvaluation - Class in org.apache.ctakes.assertion.eval
AssertionEvaluation(File, File, ArrayList<String>, Class<? extends <any>>, String...) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation
AssertionEvaluation.Corpus - Enum in org.apache.ctakes.assertion.eval
AssertionEvaluation.Corpus() - Constructor for enum org.apache.ctakes.assertion.eval.AssertionEvaluation.Corpus
AssertionEvaluation.HashableAnnotation - Class in org.apache.ctakes.assertion.eval
AssertionEvaluation.HashableAnnotation(int, int) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
AssertionEvaluation.HashableAnnotation(Annotation) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
AssertionEvaluation.OnlyGoldAssertions - Class in org.apache.ctakes.assertion.eval: Class that copies the manual Modifier annotations to the default CAS.
AssertionEvaluation.OnlyGoldAssertions() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.OnlyGoldAssertions
AssertionEvaluation.Options - Class in org.apache.ctakes.assertion.eval
AssertionEvaluation.Options() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer - Class in org.apache.ctakes.assertion.eval: Class that copies the manual Modifier annotations to the default CAS.
AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer
AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier - Class in org.apache.ctakes.assertion.eval: Class that copies the manual Modifier annotations to the default CAS.
AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier
AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier - Class in org.apache.ctakes.assertion.eval: Class that copies the manual Modifier annotations to the default CAS.
AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier
AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold - Class in org.apache.ctakes.assertion.eval: Annotator that removes cTAKES EntityMentions and Modifiers from the system view, and copies over the manually annotated EntityMentions and Modifiers from the gold view.
AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold
AssertionEvaluation.StringInstanceDataWriter - Class in org.apache.ctakes.assertion.eval
AssertionEvaluation.StringInstanceDataWriter(File) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.StringInstanceDataWriter
AssertionSampleFeatureGenerator - Class in org.apache.ctakes.assertion.medfacts.cleartk
AssertionSampleFeatureGenerator() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AssertionSampleFeatureGenerator
AssertionTreeUtils - Class in org.apache.ctakes.assertion.util
AssertionTreeUtils() - Constructor for class org.apache.ctakes.assertion.util.AssertionTreeUtils
assertTypes(Annotation, Class<? extends Annotation>, Annotation, Class<? extends Annotation>) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
assignNamedEntityFeats(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator: Assigns OID and segmentID values to NamedEntities
assignNamedEntityFeats(CAS) - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel: Assigns typeID and segmentID values to Drug NamedEntities
assignPatientLevelSmokingStatus() - Static method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus: performs the patient-level smoking status classification based on document-level classification each patient is assigned only one final smoking status RULE: If exists only U assign U Else if exist N and there is no PCS assign N Else if exist S and there is no PC assign S Else if exist P or C (can be both) If exists either P or C assign P or C respectively Else if exist both P and C If(C freq >= P freq) assign C Else assign P
AssociatedCodeElement - Class in org.apache.ctakes.drugner.elements
AssociatedCodeElement() - Constructor for class org.apache.ctakes.drugner.elements.AssociatedCodeElement
AssociatedCodeElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.AssociatedCodeElement
associatedCodePrimary - Variable in class org.apache.ctakes.drugner.DrugMention
associatedCodeSecondary - Variable in class org.apache.ctakes.drugner.DrugMention: terminology unique identifier (e.g.
AssociatedCodeToken - Class in org.apache.ctakes.drugner.fsm.output.elements
AssociatedCodeToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.AssociatedCodeToken
AssociatedPrimaryCodeElement - Class in org.apache.ctakes.drugner.elements
AssociatedPrimaryCodeElement() - Constructor for class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
AssociatedPrimaryCodeElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
AssociatedSecondaryCodeElement - Class in org.apache.ctakes.drugner.elements
AssociatedSecondaryCodeElement() - Constructor for class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
AssociatedSecondaryCodeElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
astDir - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
astPatt - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
attr - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
attr - Variable in class org.apache.ctakes.temporal.ae.feature.TimeXExtractor
ATTR_BODYLATERALITY_DISTAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_DORSAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_INFERIOR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_LATERAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_MEDIAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_PROXIMAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_SUPERIOR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_UNMARKED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYLATERALITY_VENTRAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYSIDE_BILATERAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYSIDE_LEFT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYSIDE_RIGHT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_BODYSIDE_UNMARKED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_HISTORYOF_INDICATOR_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_HISTORYOF_INDICATOR_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_INSTANCE_ID - Static variable in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: value instance_id.
ATTR_LAB_ABNORMAL_TRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ABNORMAL_VERYTRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_DELTAFLAG_CHANGEDOWN - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_DELTAFLAG_CHANGEUP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_DELTAFLAG_NOCHANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ESTIMATED_FLAG_FALSE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ESTIMATED_FLAG_TRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_1ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_2ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_3ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_4ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_ANTICOMPLEMENTARYPRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_CYTOTOXICPRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_DETECTED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_INTERMEDIATE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_INTERMEDIATERESISTANCE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_MODERATELYSUSCEPTIBLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_NEGATIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_NO_OR_NA_RANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_NORMAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_NOTDETECTED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_POSITIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_QUALITYCONTROLFAIL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_REACTIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_RESISTANT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_SMALL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_SUSCEPTIBLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_TRACE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_VERYSUSCEPTIBLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_LAB_ORDINAL_WEAKLY_REACTIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ALLERGY_INDICATOR_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ALLERGY_INDICATOR_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_1 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_2 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_3 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_4 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_5 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_DOSAGE_UNDETERMINED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_AEROSOL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_CAPSULE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_CREAM - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_ELIXIR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_EMULSION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_ENEMA - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_GEL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_IMPLANT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_INHALANT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_INJECTION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_LIQUID - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_LOTION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_LOZENGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_OINTMENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_PATCH - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_PELLET - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_PILL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_POWDER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_SHAMPOO - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_SOAP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_SOLUTION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_SPRAY - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_SUPPOSITORY - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_SYRUP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_FORM_TABLET - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_ENTERAL_GASTRIC - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_ENTERAL_ORAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_ENTERAL_RECTAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAARTERIAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_INTRACARDIAC - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAMUSCULAR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAPERIOTONEAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_INTRATHECAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAVENOUS - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_SUBCUTANEOUS - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSDERMAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSMUCOSAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_TOPICAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_ROUTE_UNDETERMINED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_STATUSCHANGE_DECREASE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_STATUSCHANGE_INCREASE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_STATUSCHANGE_NOCHANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_STATUSCHANGE_START - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_MEDICATION_STATUSCHANGE_STOP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SEVERITY_MODERATE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SEVERITY_SEVERE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SEVERITY_SLIGHT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SEVERITY_UNMARKED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SUBJECT_DONOR_FAMILY_MEMBER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SUBJECT_DONOR_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SUBJECT_FAMILY_MEMBER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SUBJECT_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ATTR_SUBJECT_PATIENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
attrHeadings - Static variable in class org.apache.ctakes.assertion.cr.XMLReader
Attribute - Class in org.apache.ctakes.typesystem.type.refsem: The semantic encapsulation of a modifer.
Attribute() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute: Never called.
Attribute(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute: Internal - constructor used by generator
Attribute(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute
Attribute_Type - Class in org.apache.ctakes.typesystem.type.refsem: The semantic encapsulation of a modifer.
Attribute_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute_Type: initialize variables to correspond with Cas Type and Features
AttributeCalculator - Class in org.apache.ctakes.coreference.util
AttributeCalculator(JCas) - Constructor for class org.apache.ctakes.coreference.util.AttributeCalculator
attributeKey - Variable in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
attributeName - Variable in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
AttributeProductKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: Expects numeric values as input.
AttributeProductKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.AttributeProductKernel
AttributeRelation - Class in org.apache.ctakes.typesystem.type.relation: A real-world relationship between an Element and an Attribute.
AttributeRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation: Never called.
AttributeRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation: Internal - constructor used by generator
AttributeRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation
AttributeRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A real-world relationship between an Element and an Attribute.
AttributeRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type: initialize variables to correspond with Cas Type and Features
attributes - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
ATTRIBUTES_TO_IGNORE - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
attributeSelection - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
attributeType - Variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation.Options
attributeType - Variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
AttributeValue - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
AttributeValue() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue: Never called.
AttributeValue(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue: Internal - constructor used by generator
AttributeValue(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
AttributeValue(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
AttributeValue_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
AttributeValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type: initialize variables to correspond with Cas Type and Features
atui - Variable in class org.apache.ctakes.ytex.umls.model.MRSTY
aui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
aui - Variable in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord

B

B3Type - Enum in org.apache.ctakes.coreference.eval.helpers
B3Type() - Constructor for enum org.apache.ctakes.coreference.eval.helpers.B3Type
BackwardsTimeAnnotator - Class in org.apache.ctakes.temporal.ae
BackwardsTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
BAD_POS_TERMS - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
BagOfAnnotationsGenerator<T extends Annotation,K> - Class in org.apache.ctakes.clinicalpipeline.runtime
BagOfAnnotationsGenerator(String, String) - Constructor for class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
BagOfAnnotationsGenerator(String, String, String) - Constructor for class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
BagOfCUIsGenerator - Class in org.apache.ctakes.clinicalpipeline.runtime
BagOfCUIsGenerator(String, String) - Constructor for class org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator
BagOfWordsData - Class in org.apache.ctakes.ytex.kernel: Data structure populated by AbstractBagOfWordsExporter that has all the instance attributes needed for exporting to various formats.
BagOfWordsData() - Constructor for class org.apache.ctakes.ytex.kernel.BagOfWordsData
BagOfWordsDecorator - Interface in org.apache.ctakes.ytex.kernel: Classes that delegate to the BagOfWordsExporter can pass this decorator in to add additional attributes
BagOfWordsExporter - Interface in org.apache.ctakes.ytex.kernel
bagOfWordsExporter - Variable in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
BASE_DIRECTORY - Static variable in class org.apache.ctakes.assertion.util.AssertionConst: CHANGE THESE
BaseClassifierEvaluationParser - Class in org.apache.ctakes.ytex.kernel: miscellaneous methods used for parsing various output types
BaseClassifierEvaluationParser() - Constructor for class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
BaseClassifierEvaluationParser.InstanceClassInfo - Class in org.apache.ctakes.ytex.kernel
BaseClassifierEvaluationParser.InstanceClassInfo() - Constructor for class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
BaseClassifierEvaluationParser.InstanceClassInfo(long, boolean, String) - Constructor for class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
BaseDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup: Deprecated.
Use AbstractBaseDictionary
BaseDictionaryImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl: Deprecated.
baseline - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
baseline - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventRelations
baseline - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
baseline - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
baseline - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
baseline - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
Baseline1DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotated degree_of relation in sentences containing a single entity mention of a valid degree_of type and a single modifier.
Baseline1DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator
Baseline1EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate location_of relation between two entities in sentences containing exactly two entities (where the entities are of the correct types).
Baseline1EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
Baseline2DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotated degree_of relation between two entities in sentences with multiple modifiers (arg2) and a single legitimate degree_of arg1 (i.e.
Baseline2DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
Baseline2EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate location_of relation between two entities in sentences with multiple anatomical sites and a single legitimate location_of arg2.
Baseline2EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
Baseline3DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: This baseline links each modifier with the closest entity of a type that's suitable for degree_of, as long as there is no intervening modifier.
Baseline3DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
Baseline3EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: This baseline links each anatomical site with the closest entity of a type that's suitable for location_of, as long as there is no intervening anatomical site.
Baseline3EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
Baseline4DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate degree_of relation between two entities whenever they are enclosed within the same noun phrse.
Baseline4DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline4DegreeOfRelationExtractorAnnotator
Baseline4EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate location_of relation between two entities whenever they are enclosed within the same noun phrse.
Baseline4EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
BaseLookupConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: Provides some base functionality for subclasses.
BaseLookupConsumerImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl
BaseLookupConsumerImpl.LookupHitKey - Class in org.apache.ctakes.dictionary.lookup.ae: Using a String as a HashMap Key can be slow as the hashCode is computed per character with each call - ditto for equals
BaseLookupConsumerImpl.LookupHitKey(LookupHit) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey
BaseMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup: Deprecated.
please use AbstractBaseMetaDataHit
BaseMetaDataHitImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl: Deprecated.
BaseSimilarityMetric - Class in org.apache.ctakes.ytex.kernel.metric
BaseSimilarityMetric(ConceptSimilarityService) - Constructor for class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric
BaseSparseDataFormatter - Class in org.apache.ctakes.ytex.kernel
BaseSparseDataFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter
BaseToken - Interface in org.apache.ctakes.core.fsm.token
BaseToken - Class in org.apache.ctakes.typesystem.type.syntax: A supertype for tokens subsuming word, punctuation, symbol, newline, contraction, or number.
BaseToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.BaseToken: Never called.
BaseToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.BaseToken: Internal - constructor used by generator
BaseToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.BaseToken
BaseToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.BaseToken
BaseToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: A supertype for tokens subsuming word, punctuation, symbol, newline, contraction, or number.
BaseToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type: initialize variables to correspond with Cas Type and Features
BaseTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
BaseTokenAdapter(Annotation) - Constructor for class org.apache.ctakes.core.fsm.adapters.BaseTokenAdapter
BaseTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter
BaseTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.BaseTokenAdapter
BaseTokenImpl - Class in org.apache.ctakes.core.fsm.output
BaseTokenImpl(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.BaseTokenImpl
BaseTokenImpl - Class in org.apache.ctakes.drugner.fsm.output.elements
BaseTokenImpl(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl
basicNumber(Markable) - Method in class org.apache.ctakes.coreference.util.AttributeCalculator
batchProcessComplete() - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
batchProcessComplete() - Method in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
batchProcessComplete() - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the batchProcessing is completed.
batchSize - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
beanFactory - Static variable in class org.apache.ctakes.ytex.uima.ApplicationContextHolder
beforeSet - Static variable in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
begin - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
begin - Variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact.Span
begin - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
begin - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation.Span: The offset of the first character in the text span.
begin - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator.SideEffect
begin - Variable in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
begin - Variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
BEGIN_A - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
BEGIN_B - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
BEGIN_LARGEST - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
BEGIN_SMALLEST - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
beginTreeMap - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
begOff - Variable in class org.apache.ctakes.drugner.elements.AssociatedCodeElement
begOff - Variable in class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
begOff - Variable in class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
begOff - Variable in class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
begOff - Variable in class org.apache.ctakes.drugner.elements.DosageElement
begOff - Variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
begOff - Variable in class org.apache.ctakes.drugner.elements.DurationElement
begOff - Variable in class org.apache.ctakes.drugner.elements.FormElement
begOff - Variable in class org.apache.ctakes.drugner.elements.FrequencyElement
begOff - Variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
begOff - Variable in class org.apache.ctakes.drugner.elements.RouteElement
begOff - Variable in class org.apache.ctakes.drugner.elements.StartDateElement
begOff - Variable in class org.apache.ctakes.drugner.elements.StrengthElement
begOff - Variable in class org.apache.ctakes.drugner.elements.StrengthUnitElement
begOff - Variable in class org.apache.ctakes.drugner.elements.TextMentionElement
BEST_PARAMETERS - Static variable in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
BEST_PARAMETERS - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
BF - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
bfs(Queue<TreebankNode>, TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.coreference.util.HobbsTreeNavigator
BinaryAlphaFeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Selects features via binary Krippendorff's Alpha-Reliability between the a extracted feature and the outcome values they are paired with in classification instances.
BinaryAlphaFeatureSelection(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
BinaryAlphaFeatureSelection(String, double) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
BinaryAlphaFeatureSelection(String, double, String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
BinaryAlphaFeatureSelection.AlphaScorer<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Helper class for aggregating and computing mutual Odds Ratio statistics
BinaryAlphaFeatureSelection.AlphaScorer(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
binaryLookup(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Determines whether the input text is contained by the Dictionary.
BinaryTextRelation - Class in org.apache.ctakes.typesystem.type.relation: A super-type for relationships between two spans of text.
BinaryTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: Never called.
BinaryTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: Internal - constructor used by generator
BinaryTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation
BinaryTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A super-type for relationships between two spans of text.
BinaryTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type: initialize variables to correspond with Cas Type and Features
bins - Static variable in class org.apache.ctakes.temporal.duration.Utils
bInsertAnnotationContainmentLinks - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
BO - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
BodyLaterality - Class in org.apache.ctakes.typesystem.type.refsem: The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.).
BodyLaterality() - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodyLaterality: Never called.
BodyLaterality(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodyLaterality: Internal - constructor used by generator
BodyLaterality(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodyLaterality
BodyLaterality_Type - Class in org.apache.ctakes.typesystem.type.refsem: The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.).
BodyLaterality_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type: initialize variables to correspond with Cas Type and Features
BodyLateralityModifier - Class in org.apache.ctakes.typesystem.type.textsem: The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.).
BodyLateralityModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier: Never called.
BodyLateralityModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier: Internal - constructor used by generator
BodyLateralityModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier
BodyLateralityModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier
BodyLateralityModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.).
BodyLateralityModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type: initialize variables to correspond with Cas Type and Features
BodySide - Class in org.apache.ctakes.typesystem.type.refsem: Value set: unmarked (default), left, right, bilateral Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
BodySide() - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodySide: Never called.
BodySide(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodySide: Internal - constructor used by generator
BodySide(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodySide
BodySide_Type - Class in org.apache.ctakes.typesystem.type.refsem: Value set: unmarked (default), left, right, bilateral Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
BodySide_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.BodySide_Type: initialize variables to correspond with Cas Type and Features
BodySideModifier - Class in org.apache.ctakes.typesystem.type.textsem: Value set: unmarked (default), left, right, bilateral Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
BodySideModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodySideModifier: Never called.
BodySideModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodySideModifier: Internal - constructor used by generator
BodySideModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodySideModifier
BodySideModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodySideModifier
BodySideModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Value set: unmarked (default), left, right, bilateral Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
BodySideModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type: initialize variables to correspond with Cas Type and Features
BooleanLabeledFS - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
BooleanLabeledFS() - Constructor for class org.apache.ctakes.coreference.type.BooleanLabeledFS: Never called.
BooleanLabeledFS(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.BooleanLabeledFS: Internal - constructor used by generator
BooleanLabeledFS(JCas) - Constructor for class org.apache.ctakes.coreference.type.BooleanLabeledFS
BooleanLabeledFS_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
BooleanLabeledFS_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type: initialize variables to correspond with Cas Type and Features
BooleanLabeledTree - Class in org.apache.ctakes.constituency.parser.uima.type: Updated by JCasGen Wed Sep 30 11:05:41 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-constituency-parser/target/jcasgen/typesystem.xml
BooleanLabeledTree() - Constructor for class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: Never called.
BooleanLabeledTree(int, TOP_Type) - Constructor for class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: Internal - constructor used by generator
BooleanLabeledTree(JCas) - Constructor for class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree
BooleanLabeledTree(JCas, int, int) - Constructor for class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree
BooleanLabeledTree_Type - Class in org.apache.ctakes.constituency.parser.uima.type: Updated by JCasGen Wed Sep 30 11:05:41 EDT 2015
BooleanLabeledTree_Type(JCas, Type) - Constructor for class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type: initialize variables to correspond with Cas Type and Features
booleanSlots - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The boolean-valued annotation attributes
BooleanUtil - Class in org.apache.ctakes.ytex.uima.model
BooleanUtil() - Constructor for class org.apache.ctakes.ytex.uima.model.BooleanUtil
BOUNDARY_ANN_TYPE - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Annotation type that defines the boundary within which the dictionary hits should be present.
breakAtApostrophe(String, int) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB: Assumes apostrophe is not first character....
BrownClusterFeatureFunction - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
BrownClusterFeatureFunction() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.BrownClusterFeatureFunction
bStoreCAS - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
bStoreDocText - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
BSV_FILE_PATH - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
BSV_FILE_PATH - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
BsvConceptFactory - Class in org.apache.ctakes.dictionary.lookup2.concept: Author: SPF Affiliation: CHIP-NLP Date: 9/9/2014
BsvConceptFactory(String, UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
BsvConceptFactory(String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
BsvConceptFactory(String, File) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
BsvConceptFactory.CuiTuiTerm - Class in org.apache.ctakes.dictionary.lookup2.concept
BsvConceptFactory.CuiTuiTerm(String, String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
BsvRareWordDictionary - Class in org.apache.ctakes.dictionary.lookup2.dictionary: A RareWordDictionary created from a bar-separated value (BSV) file.
BsvRareWordDictionary(String, UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
BsvRareWordDictionary(String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
BsvRareWordDictionary(String, File) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
build(Reader, String, String, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory: Reads from a character stream.
build(Reader, String, String, FieldConstraint, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory: Reads from a character stream.
build(Reader, String, String[], boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory: Reads from a character stream.
build(Reader, String, String[], FieldConstraint, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory: Reads from a character stream.
buildAlignedTree(JCas, Parse, Sentence) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
buildDeleteAction(String[]) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator: Builds a DeleteAction implementation.
buildList(JCas, TOP[]) - Static method in class org.apache.ctakes.core.util.ListFactory: Builds a FSList from an array of JCas objects.
buildModifyAction(String[]) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator: Builds a ModifyAction implementation.
buildPattern(String[]) - Static method in class org.apache.ctakes.core.ae.CDASegmentAnnotator: Build a regex pattern from a list of section names.
BuildPear - Class in org.apache.ctakes.utils.build: Build a PEAR file for this project
Looks for BuildPear.properties file for classpath and datapath values to use for PEAR.
Expects the properties file to be in the same directory as this class file.
BuildPear() - Constructor for class org.apache.ctakes.utils.build.BuildPear
buildPermutations(int, List<Integer>, Collection<List<Integer>>, List<Integer>, int) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil: Recursively builds permutations of numbers specified by the base num list.
BuildPipelinePears - Class in org.apache.ctakes.utils.build: This class is used to edu.mayo.bmi.utils.build the PEAR files for the pipeline.
BuildPipelinePears() - Constructor for class org.apache.ctakes.utils.build.BuildPipelinePears
buildProcEntryList() - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
buildSentenceBoundaryMap() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
buildSentenceToTokenNumberMap() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
buildSimpleClonePET(TreebankNode, TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
buildTokenBoundaryMap() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
busyThreads - Variable in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
busyThreads - Variable in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
BY_RELATION_OFFSETS - Static variable in class org.apache.ctakes.temporal.eval.PrintRelations: Orders relations to match their order in the text (as defined by the spans of their arguments)
BY_TYPE_AND_OFFSETS - Static variable in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures

C

c1 - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
c2 - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
Cache - Class in org.apache.ctakes.utils.wiki
Cache() - Constructor for class org.apache.ctakes.utils.wiki.Cache
cache - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
cache - Variable in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
cachedDocID - Variable in class org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor
cachedDocID - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor
cacheHit - Static variable in class org.apache.ctakes.utils.wiki.ApproximateMath
CacheKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: consolidate caching in this class.
CacheKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
cacheKeyGenerator - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
CacheKeyGenerator - Interface in org.apache.ctakes.ytex.kernel.evaluator
cacheKeyGenerator - Variable in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
cacheManager - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
cacheManager - Variable in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
cacheManager - Variable in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
cacheManager - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
cacheMiss - Static variable in class org.apache.ctakes.utils.wiki.ApproximateMath
cacheName - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
cacheName - Variable in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
cacheNorm - Variable in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
cal - Static variable in class org.apache.ctakes.core.util.DateParser
calcAlias() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcAliasAnatomy() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcAliasDisorder() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcAliasDrug() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcAliasFinding() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcAliasProcedure() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcAnaphoricity(JCas, Markable) - Method in class org.apache.ctakes.coreference.util.SvmVectorCreator
calcBothDefinitesC() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcBothDefinitesI() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcBothDefinitesNA() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcBothPronouns() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcBothPronounsC() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcBothPronounsI() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcBothPronounsNA() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcCatNgrams(Integer, Markable) - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcClosestComp() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcDefinite1() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcDefinite2() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcDemonstrative2() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcDepPath() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcEndMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcEntityEndMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcEntityExactMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcEntityStartMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcEntityWikiSim() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcExactMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcFullPath() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcIndefinite() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcIRStats(String, Integer, ClassifierEvaluation, Integer) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
calcIsAnatomicalSite() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcIsDisorder() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcIsDrug() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcIsFinding() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcIsProcedure() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcmDefinite() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmDemonstrative() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcMergedJointDistribution(Map<String, ImputedFeatureEvaluatorImpl.JointDistribution>, Map<String, Integer>, ConcRel, Map<String, ImputedFeatureEvaluatorImpl.JointDistribution>, Map<String, Set<Long>>, String, double, List<String>) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
calcMidMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcmIndefinite() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmIsAnatomicalSite() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmIsDisorder() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmIsDrug() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmIsFinding() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmIsProcedure() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmNPHead() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmNumber() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmNumPlu() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmNumSing() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmNumUnk() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcModifier() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcmProStr() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmSimilarStr() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcmWnClass() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
calcNegatedBoth() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcNonNegatedBoth() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcNPHead() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcNPSubj(TreebankNode) - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPSubj1() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPSubj2() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPSubjBoth() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderPP(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderPP1() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderPP2() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderS(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderS1() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderS2() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderVP(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderVP1() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNPunderVP2() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcNumberMatchC() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcNumberMatchI() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcNumberMatchNA() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcPathLength() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcPermStrDist() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcPronoun() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcPronoun1() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcPronoun2() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcProStr() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcSameSection() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator: Determine whether the markables are located within the same section
calcSentenceDistance() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcSimSum() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcSoonStr() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcSoonStrNonpro() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcStartMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcStringMatch() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcTokenDistance() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calculateBeginAndEndOfConcept(ApiConcept) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
calculateBeginAndEndOfConcept(int, int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
calculateBeginAndEndOfConcept(ApiConcept) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
calculateBeginAndEndOfConcept(int, int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes: delegate to converter to determine offset.
calculateDistance(<any>, <any>) - Method in class org.apache.ctakes.temporal.utils.SMOTEplus
calculateFoldEntropy(Map<String, Set<Long>>) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
calcWikiSim() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
calcWnClass() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcWnClassC() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcWnClassI() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcWnClassNA() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcWordOverlap() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcWordsStr() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
calcWordsSubstr() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
call() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.SliceEvaluator
CANONICAL_VARIANT_ATTR - Variable in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl
CANONICAL_VARIANT_ATTR - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
CANONICAL_VARIANT_ATTR - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
CAPS_ALL - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
CAPS_ALL - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
CAPS_FIRST_ONLY - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
CAPS_FIRST_ONLY - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
CAPS_MIXED - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
CAPS_MIXED - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
CAPS_NONE - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
CAPS_NONE - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
CAPS_UNKNOWN - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
CAPS_UNKNOWN - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
CAPSULE - Static variable in class org.apache.ctakes.drugner.elements.FormElement
cas - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
cas - Variable in class org.apache.ctakes.ytex.uima.model.Document: the document CAS - serialised in XMI format and compressed.
CasConsumer - Class in org.apache.ctakes.core.cc: CasConsumer that writes a JCas (the current view) to an xml file
CasConsumer() - Constructor for class org.apache.ctakes.core.cc.CasConsumer
CASConsumerTestDriver - Class in org.apache.ctakes.core.cc
CASConsumerTestDriver() - Constructor for class org.apache.ctakes.core.cc.CASConsumerTestDriver
casDescriptor - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: cas loaded from strDescriptorFile
caseSensitive - Variable in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
caseSensitive - Variable in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
casFeat_abnormalInterpretation - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeat_abnormalInterpretation - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeat_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_anaphor - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
casFeat_anaphor - Variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
casFeat_anaphoric_prob - Variable in class org.apache.ctakes.coreference.type.Markable_Type
casFeat_antecedent - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
casFeat_antecedentList - Variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
casFeat_arg1 - Variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
casFeat_arg1 - Variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
casFeat_arg1 - Variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
casFeat_arg2 - Variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
casFeat_arg2 - Variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
casFeat_arg2 - Variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
casFeat_argument - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeat_argument - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
casFeat_aspect - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_assertionType - Variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
casFeat_associatedConcept - Variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
casFeat_associatedSignSymptom - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_associatedSignSymptom - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_attribute - Variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
casFeat_attributeName - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
casFeat_attributeStringValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
casFeat_authorSpecialty - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_birthDate - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_canonicalForm - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeat_capitalization - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeat_category - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_category - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_category - Variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
casFeat_changeStatus - Variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
casFeat_changeStatusBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_changeStatusEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_children - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_chunkType - Variable in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
casFeat_classification - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeat_classification - Variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
casFeat_code - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeat_codingScheme - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeat_conceptText - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeat_conceptType - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeat_conditional - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_conditional - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_conditional - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_confidence - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_confidence - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_confidence - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_confidence - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_content - Variable in class org.apache.ctakes.coreference.type.Markable_Type
casFeat_contextualAspect - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_contextualModality - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_course - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_course - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_course - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_course - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_cpostag - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_cuePhrase - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeat_cuePhraseAssertionFamily - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeat_cuePhraseCategory - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeat_cuePhraseFirstWord - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeat_cui - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
casFeat_date - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
casFeat_date - Variable in class org.apache.ctakes.ytex.uima.types.Date_Type
casFeat_dateValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
casFeat_day - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
casFeat_deathDate - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_degree - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_deltaFlag - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeat_deltaFlag - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeat_demographics - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeat_deprel - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_disambiguated - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeat_discoveryTechnique - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_discoveryTechnique - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_discoveryTechnique - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_docTimeRel - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_documentID - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
casFeat_documentID - Variable in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
casFeat_documentStandard - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_dosage - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_dosageBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_dosageEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_drug - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
casFeat_drugChangeStatus - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_duration - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_duration - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_duration - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_duration - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_duration - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_duration - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_duration - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_durationBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_durationEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_endDate - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_endDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_endDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_endTime - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_endTime - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_endTime - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_endTime - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_endTime - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_endTime - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_entity - Variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
casFeat_event - Variable in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
casFeat_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_externalId - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeat_feats - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_feature - Variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
casFeat_features - Variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
casFeat_firstName - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_firstNameSoundex - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_FocusText - Variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
casFeat_form - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_form - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_formBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_formEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_frameSet - Variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
casFeat_frequency - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_frequencyBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_frequencyEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_frequencyUnit - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_fuBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_fuEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_gender - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_generic - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_generic - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_head - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_headIndex - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_historyOf - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_historyOf - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_id - Variable in class org.apache.ctakes.coreference.type.Markable_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
casFeat_id - Variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
casFeat_index - Variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
casFeat_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
casFeat_intakeMethod - Variable in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
casFeat_items - Variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
casFeat_key - Variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
casFeat_key - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
casFeat_keyValuePairs - Variable in class org.apache.ctakes.ytex.uima.types.DocKey_Type
casFeat_label - Variable in class org.apache.ctakes.assertion.zoner.types.Heading_Type
casFeat_label - Variable in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
casFeat_label - Variable in class org.apache.ctakes.assertion.zoner.types.Zone_Type
casFeat_label - Variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
casFeat_label - Variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
casFeat_label - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
casFeat_label - Variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
casFeat_label - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
casFeat_labValue - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeat_labValue - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeat_lastName - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_lastNameSoundex - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_leaf - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_lemma - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_lemmaEntries - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeat_medicationAllergy - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationDosage - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationDosage - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationDosage - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationDuration - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationDuration - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationDuration - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationForm - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationForm - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationForm - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationFrequency - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationFrequency - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationFrequency - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationRoute - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationRoute - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationRoute - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationStatusChange - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationStatusChange - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationStatusChange - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_medicationStrength - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_medicationStrength - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_medicationStrength - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_members - Variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
casFeat_mentions - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_method - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_method - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_middleName - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeat_month - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
casFeat_nodeTags - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_nodeType - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_nodeValue - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_nominalValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
casFeat_normalizedForm - Variable in class org.apache.ctakes.typesystem.type.refsem.Time_Type
casFeat_normalizedForm - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeat_normalizedForm - Variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
casFeat_noteSubTypeCode - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_noteTypeCode - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_number - Variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
casFeat_number - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
casFeat_number - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
casFeat_numericValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
casFeat_numPosition - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeat_numType - Variable in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
casFeat_oid - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeat_ontologyConcept - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_ontologyConceptArr - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_ordinalInterpretation - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeat_ordinalInterpretation - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeat_originalEntityExternalId - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeat_originalText - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_oui - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeat_p1 - Variable in class org.apache.ctakes.coreference.type.Pair_Type
casFeat_p2 - Variable in class org.apache.ctakes.coreference.type.Pair_Type
casFeat_pairs - Variable in class org.apache.ctakes.typesystem.type.util.Pairs_Type
casFeat_parent - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeat_parentSectionId - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeat_participatesIn - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeat_partOfSpeech - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeat_patientID - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeat_pdeprel - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_period - Variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
casFeat_permanence - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_phead - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_polarity - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_polarity - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeat_polarity - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_polarity - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_postag - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeat_posTag - Variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
casFeat_predicate - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
casFeat_preferredText - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
casFeat_preferredText - Variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
casFeat_procedureDevice - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_procedureDevice - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_properties - Variable in class org.apache.ctakes.typesystem.type.refsem.Event_Type
casFeat_providerID - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeat_pseSen - Variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
casFeat_reason - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_recordID - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeat_recordID - Variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
casFeat_recordTextBegin - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeat_recordTextEnd - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeat_referenceRangeNarrative - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeat_referenceRangeNarrative - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeat_relation - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
casFeat_relations - Variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_role - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeat_route - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_routeBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_routeEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_Scope - Variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
casFeat_score - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeat_segmentID - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_segmentId - Variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
casFeat_sentence - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
casFeat_sentenceID - Variable in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
casFeat_sentenceID - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_sentenceNumber - Variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
casFeat_severity - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_severity - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_severity - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_sideEffect - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
casFeat_sourceApplication - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_sourceData - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeat_sourceEncounterId - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_sourceInstanceId - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_sourceInstitution - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_sourceOriginalDate - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_sourceRevisionDate - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_sourceRevisionNbr - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeat_startDate - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_startDate - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeat_startDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeat_startDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeat_startTime - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeat_startTime - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeat_startTime - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeat_startTime - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeat_startTime - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeat_startTime - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeat_status - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_status - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeat_strength - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_strengthBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_strengthEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_strengthUnit - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_suBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_subject - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_subject - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_subSectionBodyBegin - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeat_subSectionBodyEnd - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeat_subSectionHeaderBegin - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeat_subSectionHeaderEnd - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeat_suEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeat_suggestion - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeat_terminals - Variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
casFeat_time - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
casFeat_timeClass - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
casFeat_tokenIndex - Variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
casFeat_tokenNumber - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeat_tree - Variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
casFeat_treebankParse - Variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
casFeat_tui - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
casFeat_typeID - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_uncertainty - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeat_uncertainty - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeat_uncertainty - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeat_unit - Variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
casFeat_unit - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
casFeat_unit - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.Course_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
casFeat_value - Variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
casFeat_valueLong - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
casFeat_valueString - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
casFeat_year - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
casFeatCode_abnormalInterpretation - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeatCode_abnormalInterpretation - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeatCode_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_alleviatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_anaphor - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
casFeatCode_anaphor - Variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
casFeatCode_anaphoric_prob - Variable in class org.apache.ctakes.coreference.type.Markable_Type
casFeatCode_antecedent - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
casFeatCode_antecedentList - Variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
casFeatCode_arg1 - Variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
casFeatCode_arg1 - Variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
casFeatCode_arg1 - Variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
casFeatCode_arg2 - Variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
casFeatCode_arg2 - Variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
casFeatCode_arg2 - Variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
casFeatCode_argument - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeatCode_argument - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
casFeatCode_aspect - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_assertionType - Variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
casFeatCode_associatedConcept - Variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
casFeatCode_associatedSignSymptom - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_associatedSignSymptom - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_attribute - Variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
casFeatCode_attributeName - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
casFeatCode_attributeStringValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
casFeatCode_authorSpecialty - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_birthDate - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_bodyLaterality - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_bodyLocation - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_bodySide - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_canonicalForm - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeatCode_capitalization - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeatCode_category - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_category - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_category - Variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
casFeatCode_changeStatus - Variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
casFeatCode_changeStatusBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_changeStatusEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_children - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_chunkType - Variable in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
casFeatCode_classification - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeatCode_classification - Variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
casFeatCode_code - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeatCode_codingScheme - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeatCode_conceptText - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeatCode_conceptType - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeatCode_conditional - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_conditional - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_conditional - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_confidence - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_confidence - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_confidence - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_confidence - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_content - Variable in class org.apache.ctakes.coreference.type.Markable_Type
casFeatCode_contextualAspect - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_contextualModality - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_course - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_course - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_course - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_course - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_cpostag - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_cuePhrase - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeatCode_cuePhraseAssertionFamily - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeatCode_cuePhraseCategory - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeatCode_cuePhraseFirstWord - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeatCode_cui - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
casFeatCode_date - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
casFeatCode_date - Variable in class org.apache.ctakes.ytex.uima.types.Date_Type
casFeatCode_dateValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
casFeatCode_day - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
casFeatCode_deathDate - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_degree - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_deltaFlag - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeatCode_deltaFlag - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeatCode_demographics - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeatCode_deprel - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_disambiguated - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeatCode_discoveryTechnique - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_discoveryTechnique - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_discoveryTechnique - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_docTimeRel - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_documentID - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
casFeatCode_documentID - Variable in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
casFeatCode_documentStandard - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_dosage - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_dosageBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_dosageEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_drug - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
casFeatCode_drugChangeStatus - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_duration - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_duration - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_duration - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_duration - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_duration - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_duration - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_duration - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_durationBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_durationEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_endDate - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_endDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_endDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_endTime - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_endTime - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_endTime - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_endTime - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_endTime - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_endTime - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_entity - Variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
casFeatCode_event - Variable in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
casFeatCode_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_exacerbatingFactor - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_externalId - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeatCode_feats - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_feature - Variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
casFeatCode_features - Variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
casFeatCode_firstName - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_firstNameSoundex - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_FocusText - Variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
casFeatCode_form - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_form - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_formBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_formEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_frameSet - Variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
casFeatCode_frequency - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_frequencyBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_frequencyEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_frequencyUnit - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_fuBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_fuEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_gender - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_generic - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_generic - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_head - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_headIndex - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_historyOf - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_historyOf - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_id - Variable in class org.apache.ctakes.coreference.type.Markable_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
casFeatCode_id - Variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
casFeatCode_index - Variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
casFeatCode_indicated - Variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
casFeatCode_intakeMethod - Variable in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
casFeatCode_items - Variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
casFeatCode_key - Variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
casFeatCode_key - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
casFeatCode_keyValuePairs - Variable in class org.apache.ctakes.ytex.uima.types.DocKey_Type
casFeatCode_label - Variable in class org.apache.ctakes.assertion.zoner.types.Heading_Type
casFeatCode_label - Variable in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
casFeatCode_label - Variable in class org.apache.ctakes.assertion.zoner.types.Zone_Type
casFeatCode_label - Variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
casFeatCode_label - Variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
casFeatCode_label - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
casFeatCode_label - Variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
casFeatCode_label - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
casFeatCode_labValue - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeatCode_labValue - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeatCode_lastName - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_lastNameSoundex - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_leaf - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_lemma - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_lemmaEntries - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeatCode_medicationAllergy - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationDosage - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationDosage - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationDosage - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationDuration - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationDuration - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationDuration - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationForm - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationForm - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationForm - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationFrequency - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationFrequency - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationFrequency - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationRoute - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationRoute - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationRoute - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationStatusChange - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationStatusChange - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationStatusChange - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_medicationStrength - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_medicationStrength - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_medicationStrength - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_members - Variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
casFeatCode_mentions - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_method - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_method - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_middleName - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
casFeatCode_month - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
casFeatCode_nodeTags - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_nodeType - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_nodeValue - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_nominalValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
casFeatCode_normalizedForm - Variable in class org.apache.ctakes.typesystem.type.refsem.Time_Type
casFeatCode_normalizedForm - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeatCode_normalizedForm - Variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
casFeatCode_noteSubTypeCode - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_noteTypeCode - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_number - Variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
casFeatCode_number - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
casFeatCode_number - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
casFeatCode_numericValue - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
casFeatCode_numPosition - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeatCode_numType - Variable in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
casFeatCode_oid - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeatCode_ontologyConcept - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_ontologyConceptArr - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_ordinalInterpretation - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeatCode_ordinalInterpretation - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeatCode_originalEntityExternalId - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
casFeatCode_originalText - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_oui - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeatCode_p1 - Variable in class org.apache.ctakes.coreference.type.Pair_Type
casFeatCode_p2 - Variable in class org.apache.ctakes.coreference.type.Pair_Type
casFeatCode_pairs - Variable in class org.apache.ctakes.typesystem.type.util.Pairs_Type
casFeatCode_parent - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
casFeatCode_parentSectionId - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeatCode_participatesIn - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeatCode_partOfSpeech - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeatCode_patientID - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeatCode_pdeprel - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_period - Variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
casFeatCode_permanence - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_phead - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_polarity - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_polarity - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
casFeatCode_polarity - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_polarity - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_postag - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
casFeatCode_posTag - Variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
casFeatCode_predicate - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
casFeatCode_preferredText - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
casFeatCode_preferredText - Variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
casFeatCode_procedureDevice - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_procedureDevice - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_properties - Variable in class org.apache.ctakes.typesystem.type.refsem.Event_Type
casFeatCode_providerID - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeatCode_pseSen - Variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
casFeatCode_reason - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_recordID - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeatCode_recordID - Variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
casFeatCode_recordTextBegin - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeatCode_recordTextEnd - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
casFeatCode_referenceRangeNarrative - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
casFeatCode_referenceRangeNarrative - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
casFeatCode_relation - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
casFeatCode_relations - Variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_relativeTemporalContext - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_role - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
casFeatCode_route - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_routeBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_routeEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_Scope - Variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
casFeatCode_score - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
casFeatCode_segmentID - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_segmentId - Variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
casFeatCode_sentence - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
casFeatCode_sentenceID - Variable in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
casFeatCode_sentenceID - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_sentenceNumber - Variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
casFeatCode_severity - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_severity - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_severity - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_sideEffect - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
casFeatCode_sourceApplication - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_sourceData - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
casFeatCode_sourceEncounterId - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_sourceInstanceId - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_sourceInstitution - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_sourceOriginalDate - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_sourceRevisionDate - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_sourceRevisionNbr - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
casFeatCode_startDate - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_startDate - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
casFeatCode_startDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
casFeatCode_startDate - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
casFeatCode_startTime - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
casFeatCode_startTime - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
casFeatCode_startTime - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
casFeatCode_startTime - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
casFeatCode_startTime - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
casFeatCode_startTime - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
casFeatCode_status - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_status - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeatCode_strength - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_strengthBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_strengthEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_strengthUnit - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_suBegin - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_subject - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_subject - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_subSectionBodyBegin - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeatCode_subSectionBodyEnd - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeatCode_subSectionHeaderBegin - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeatCode_subSectionHeaderEnd - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
casFeatCode_suEnd - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
casFeatCode_suggestion - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
casFeatCode_terminals - Variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
casFeatCode_time - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
casFeatCode_timeClass - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
casFeatCode_tokenIndex - Variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
casFeatCode_tokenNumber - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
casFeatCode_tree - Variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
casFeatCode_treebankParse - Variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
casFeatCode_tui - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
casFeatCode_typeID - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_uncertainty - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
casFeatCode_uncertainty - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
casFeatCode_uncertainty - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
casFeatCode_unit - Variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
casFeatCode_unit - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
casFeatCode_unit - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.Course_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
casFeatCode_value - Variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
casFeatCode_valueLong - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
casFeatCode_valueString - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
casFeatCode_year - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
CasIndexer<T extends Annotation> - Class in org.apache.ctakes.assertion.medfacts
CasIndexer(JCas, Type) - Constructor for class org.apache.ctakes.assertion.medfacts.CasIndexer
CasIndexer() - Constructor for class org.apache.ctakes.assertion.medfacts.CasIndexer
cat - Variable in class org.apache.ctakes.utils.tree.SimpleTree
CategoricalDistribution - Class in org.apache.ctakes.relationextractor.data: Class for generating samples from a three dimensional Categorical distribution.
CategoricalDistribution(double, double, double) - Constructor for class org.apache.ctakes.relationextractor.data.CategoricalDistribution
category - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
category - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.CuePhrase
category - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
CausesBringsAbout - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
CausesBringsAbout() - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout: Never called.
CausesBringsAbout(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout: Internal - constructor used by generator
CausesBringsAbout(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout
CausesBringsAbout_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
CausesBringsAbout_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout_Type: initialize variables to correspond with Cas Type and Features
CausesBringsAboutRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies causes/brings_about relation.
CausesBringsAboutRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
CausesBringsAboutTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
CausesBringsAboutTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation: Never called.
CausesBringsAboutTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation: Internal - constructor used by generator
CausesBringsAboutTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
CausesBringsAboutTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
CausesBringsAboutTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation_Type: initialize variables to correspond with Cas Type and Features
causeVerb - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
causeWord1 - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
causeWord2 - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
CB - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
CDA_PROCESSING - Static variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: Specifies whether the cas should be handled as CDA (via 'plaintext' sofa view) or default (flat file)
CdaCasInitializer - Class in org.apache.ctakes.preprocessor.ae: Bootstraps the CAS by: Transforms document's original CDA text into plain text, inserting section (segment) markers into text . Transformation also inserts hyphens into words that should be hyphenated Stores the resulting text in a new View (which has its own Sofa) Detects sections and adds Segment (aka section) annotations Extracts document level data and stores in CAS as Property annotations.
CdaCasInitializer() - Constructor for class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
CDASegmentAnnotator - Class in org.apache.ctakes.core.ae: Creates segment annotations based on the ccda_sections.txt file Which is based on HL7/CCDA/LONIC standard headings Additional custom heading names can be added to the file.
CDASegmentAnnotator() - Constructor for class org.apache.ctakes.core.ae.CDASegmentAnnotator
CEAFType - Enum in org.apache.ctakes.coreference.eval.helpers
CEAFType() - Constructor for enum org.apache.ctakes.coreference.eval.helpers.CEAFType
CERT_ATTR - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.NamedEntityNegationKernel
cg - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.ConceptInstanceMapExtractor
cg - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
cgen - Variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: The feature context generator.
changeCurrentWorkingDirectory(String) - Method in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
changeNumThreads(int) - Method in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
changeStatus - Variable in class org.apache.ctakes.drugner.DrugMention: aka change.
CharacterOffsetToLineTokenConverterCtakesImpl - Class in org.apache.ctakes.assertion.medfacts.i2b2.api
CharacterOffsetToLineTokenConverterCtakesImpl() - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
CharacterOffsetToLineTokenConverterCtakesImpl(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
characters(char[], int, int) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
characters(char[], int, int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
CharacterToken - Interface in org.apache.ctakes.core.fsm.token
CharacterTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
CharacterTokenAdapter(BaseToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.CharacterTokenAdapter
CharacterTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter
CharacterTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.CharacterTokenAdapter
checkCycle(ConcRel, ConcRel) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
checkFileRead(String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
checkFileRead(String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil
checkFileRead(String) - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults
checkForAnatomicalSiteBetween(JCas, EntityMention, EntityMention) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
checkForAttrValue(IdentifiedAnnotation, String, String) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
checkFormat2(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
checkForModifierBetween(JCas, Modifier, EntityMention) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
CheckKnowtatorAnnotations - Class in org.apache.ctakes.temporal.utils: Checks Knowtator XML for possible annotation errors
CheckKnowtatorAnnotations() - Constructor for class org.apache.ctakes.temporal.utils.CheckKnowtatorAnnotations
CheckKnowtatorAnnotations.Options - Interface in org.apache.ctakes.temporal.utils
checkMedications - Variable in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
checkNegation(JCas, Sentence, Annotation) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator: check the negation status of the specfied term in the specified sentence
checkNegation2(JCas, Sentence, IdentifiedAnnotation, boolean) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
checkPossibilities - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
CheckSpecialWordRelationExtractor - Class in org.apache.ctakes.temporal.ae.feature
CheckSpecialWordRelationExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor
checkTermByConceptId(String) - Method in interface org.apache.ctakes.ytex.web.search.ConceptSearchService: if the conceptId is a valid conceptId, get the corresponding term
checkTermByConceptId(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
Chi2FeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.assertion.attributes.features.selection: Selects features via Chi-squared statistics between the features extracted from its sub-extractor and the outcome values they are paired with in classification instances.
Chi2FeatureSelection(String) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
Chi2FeatureSelection(String, double) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
Chi2FeatureSelection(String, double, boolean) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection: Constructor that can let use control the yate's correction
Chi2FeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Selects features via Chi-squared statistics between the features extracted from its sub-extractor and the outcome values they are paired with in classification instances.
Chi2FeatureSelection(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
Chi2FeatureSelection(String, double) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
Chi2FeatureSelection(String, double, boolean) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection: Constructor that can let use control the yate's correction
Chi2FeatureSelection.Chi2Scorer<OUTCOME_T> - Class in org.apache.ctakes.assertion.attributes.features.selection: Helper class for aggregating and computing mutual Chi2 statistics
Chi2FeatureSelection.Chi2Scorer(boolean) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
Chi2FeatureSelection.Chi2Scorer<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Helper class for aggregating and computing mutual Chi2 statistics
Chi2FeatureSelection.Chi2Scorer(boolean) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
chi2Function - Variable in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
chi2Function - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
chi2Threshold - Variable in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
chi2Threshold - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection: the percentage of total features that would be returned.
childAnnoBaseId - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
childAnnotationId - Variable in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
children - Variable in class org.apache.ctakes.utils.tree.SimpleTree
children - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel: children of this concept
children - Variable in class org.apache.ctakes.ytex.kernel.tree.Node
childrenArray - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel
childUimaTypeId - Variable in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
Chunk - Class in org.apache.ctakes.typesystem.type.syntax: Chunks are syntactic groupings of tokens, and are the results of a shallow parser (chunker).
Chunk() - Constructor for class org.apache.ctakes.typesystem.type.syntax.Chunk: Never called.
Chunk(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Chunk: Internal - constructor used by generator
Chunk(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Chunk
Chunk(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Chunk
Chunk_Type - Class in org.apache.ctakes.typesystem.type.syntax: Chunks are syntactic groupings of tokens, and are the results of a shallow parser (chunker).
Chunk_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Chunk_Type: initialize variables to correspond with Cas Type and Features
ChunkAdjuster - Class in org.apache.ctakes.chunker.ae.adjuster: UIMA annotator that uses a pattern and a rule about that pattern to adjust certain annotations.
ChunkAdjuster() - Constructor for class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster
ChunkAnnotation - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-drug-ner/target/jcasgen/typesystem.xml
ChunkAnnotation() - Constructor for class org.apache.ctakes.drugner.type.ChunkAnnotation: Never called.
ChunkAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.ChunkAnnotation: Internal - constructor used by generator
ChunkAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.ChunkAnnotation
ChunkAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.ChunkAnnotation
ChunkAnnotation_Type - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015
ChunkAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.ChunkAnnotation_Type: initialize variables to correspond with Cas Type and Features
ChunkCreator - Interface in org.apache.ctakes.chunker.ae: Implementations of this interface are responsible for creating chunk annotations.
chunkedBatchUpdate(String, List<T>, DocumentMapperServiceImpl.ChunkPreparedStatementSetter<T>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: for the list l, perform l.size()/batchSize batch updates.
Chunker - Class in org.apache.ctakes.chunker.ae: This class provides a UIMA wrapper for the OpenNLP opennlp.tools.chunker.Chunker class.
Chunker() - Constructor for class org.apache.ctakes.chunker.ae.Chunker
chunker - Variable in class org.apache.ctakes.chunker.ae.Chunker
CHUNKER_CREATOR_CLASS_PARAM - Static variable in class org.apache.ctakes.chunker.ae.Chunker: "ChunkCreatorClass" is a required, single, string parameter that specifies the chunker creator class to instantiate.
CHUNKER_MODEL_FILE_PARAM - Static variable in class org.apache.ctakes.chunker.ae.Chunker: "ChunkerModel" is a required, single, string parameter that contains the file name of the chunker model.
chunkerCreator - Variable in class org.apache.ctakes.chunker.ae.Chunker
chunkerCreatorClassName - Variable in class org.apache.ctakes.chunker.ae.Chunker
chunkerModelPath - Variable in class org.apache.ctakes.chunker.ae.Chunker
chunking - Variable in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
ChunkingExtractor - Class in org.apache.ctakes.temporal.ae.feature
ChunkingExtractor(String, <any>, JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Constructor for class org.apache.ctakes.temporal.ae.feature.ChunkingExtractor
chunksTypesInPattern - Variable in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster
CLASS - Static variable in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
CLASS - Static variable in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
CLASS_CURR_SMOKER - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_CURR_SMOKER_INT - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_KNOWN - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
CLASS_NON_SMOKER - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_PAST_SMOKER - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_PAST_SMOKER_INT - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_SMOKER - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_SMOKER_INT - Static variable in interface org.apache.ctakes.smokingstatus.Const
CLASS_UNKNOWN - Static variable in interface org.apache.ctakes.smokingstatus.Const
classAttributeName - Variable in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
classAuto - Variable in class org.apache.ctakes.ytex.uima.model.DocumentClass
classConditionalCounts - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
classConditionalCounts - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
classCounts - Variable in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
classCounts - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
classCounts - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
classCounts - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
classCounts - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
classCounts - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
classes - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: class labels
classFeatureQuery - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
classGold - Variable in class org.apache.ctakes.ytex.uima.model.DocumentClass
classIds - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
ClassifiableEntries - Class in org.apache.ctakes.smokingstatus.ae
ClassifiableEntries() - Constructor for class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
ClassifiableEntry - Class in org.apache.ctakes.smokingstatus.util
ClassifiableEntry() - Constructor for class org.apache.ctakes.smokingstatus.util.ClassifiableEntry
classifier - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
classifierAnnotatorClass - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
ClassifierEvaluation - Class in org.apache.ctakes.ytex.kernel.model
ClassifierEvaluation() - Constructor for class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
classifierEvaluation - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
classifierEvaluation - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
classifierEvaluation - Variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl.ClassifierEvaluationInstanceImporter
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
ClassifierEvaluationDao - Interface in org.apache.ctakes.ytex.kernel.dao
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
classifierEvaluationDao - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
ClassifierEvaluationDaoImpl - Class in org.apache.ctakes.ytex.kernel.dao
ClassifierEvaluationDaoImpl() - Constructor for class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
classifierEvaluationId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
ClassifierEvaluationImporter - Class in org.apache.ctakes.ytex.kernel: parse classifier evaluation results.
ClassifierEvaluationImporter() - Constructor for class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
ClassifierEvaluationIRStat - Class in org.apache.ctakes.ytex.kernel.model: summary IR statistics.
ClassifierEvaluationIRStat() - Constructor for class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
ClassifierEvaluationIRStat(ClassifierEvaluation, String, String, Integer, int, int, int, int) - Constructor for class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
classifierEvaluationIRStatId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
ClassifierEvaluationParser - Interface in org.apache.ctakes.ytex.kernel
ClassifierEvaluationParser.ParseOption - Enum in org.apache.ctakes.ytex.kernel: Property keys for various parse options
ClassifierEvaluationParser.ParseOption(String, String) - Constructor for enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption
ClassifierEvaluationResult - Class in org.apache.ctakes.ytex.kernel
ClassifierEvaluationResult() - Constructor for class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
ClassifierEvaluationResults - Class in org.apache.ctakes.ytex.kernel
ClassifierEvaluationResults() - Constructor for class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
ClassifierEvalUtil - Class in org.apache.ctakes.ytex.kernel
ClassifierEvalUtil(String) - Constructor for class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
ClassifierInstanceEvaluation - Class in org.apache.ctakes.ytex.kernel.model
ClassifierInstanceEvaluation() - Constructor for class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
classifierInstanceEvaluationId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
classifierInstanceEvaluations - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
classifierInstanceProbabilities - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Predict an outcome given a set of features.
classify(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.baselines.F1BaselineEventTimeRelationAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventEventRelationAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.baselines.TimidBaselineEventTimeRelationAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.baselines.TreeHeightBaseline
classifyBothDirections - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
classifyBothDirections - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
classifyWithLogic(HashMap<String, Boolean>) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
classifyWithLogic(HashMap<String, Boolean>) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
classifyWithLogic(HashMap<String, Boolean>) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
classOfT - Variable in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
clear() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
clear() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
clear() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
clear() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
clear() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
clear() - Method in class org.apache.ctakes.jdl.common.PropertiesFile: Clears this hashtable.
clearCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: clearCollection the collection mapped with key
clearCollection(K) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: clearCollection the collection mapped with key
clearCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: clearCollection the collection mapped with key
clearCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: clearCollection the collection mapped with key
clearCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: clearCollection the collection mapped with key
clearCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: clearCollection the collection mapped with key
ClearDependencyUtility - Class in org.apache.ctakes.dependency.parser.util
ClearDependencyUtility() - Constructor for class org.apache.ctakes.dependency.parser.util.ClearDependencyUtility
clearFold() - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: clear all data structures set up during initializeFold
clearFold() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter: clean up fold specific state
clearFold() - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter: clean up fold specific state
clearFold() - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
clearLabel() - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter
clearLabel() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter
clearLabel() - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
ClearNLPDependencyParserAE - Class in org.apache.ctakes.dependency.parser.ae: This class provides a UIMA wrapper for the CLEAR dependency parser.
ClearNLPDependencyParserAE() - Constructor for class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
ClearNLPPOSTaggerAE - Class in org.apache.ctakes.postagger: This class provides a UIMA wrapper for the CLEAR POSTagger.
ClearNLPPOSTaggerAE() - Constructor for class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
ClearNLPSemanticRoleLabelerAE - Class in org.apache.ctakes.dependency.parser.ae: This class provides a UIMA wrapper for the ClearNLP Semantic Role Labeler, which is available here.
ClearNLPSemanticRoleLabelerAE() - Constructor for class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
ClearTKDocTimeRelAnnotator - Class in org.apache.ctakes.temporal.ae: for every cTAKES EventMention annotation, create a ClearTK Event Annotation
ClearTKDocTimeRelAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator
ClearTKDocumentCreationTimeAnnotator - Class in org.apache.ctakes.temporal.ae: for every cTAKES JCas, create a ClearTK Document Creation Time Annotation, fake span, no attribute.
ClearTKDocumentCreationTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ClearTKDocumentCreationTimeAnnotator
ClearTKLinkToTHYMELinkAnnotator - Class in org.apache.ctakes.temporal.ae
ClearTKLinkToTHYMELinkAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ClearTKLinkToTHYMELinkAnnotator
ClinicalNotePreProcessor - Class in org.apache.ctakes.preprocessor: Given an HL7 document, the text contained inside a section is extracted.
ClinicalNotePreProcessor(InputStream, boolean) - Constructor for class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor: Constructor
ClinicalPipelineFactory - Class in org.apache.ctakes.clinicalpipeline
ClinicalPipelineFactory() - Constructor for class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations - Class in org.apache.ctakes.clinicalpipeline
ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations() - Constructor for class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations
ClinicalPipelineFactory.RemoveEnclosedLookupWindows - Class in org.apache.ctakes.clinicalpipeline
ClinicalPipelineFactory.RemoveEnclosedLookupWindows() - Constructor for class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows
ClinicalPipelineWithUmls - Class in org.apache.ctakes.clinicalpipeline: Run the plaintext clinical pipeline, using the dictionary of terms from UMLS.
ClinicalPipelineWithUmls() - Constructor for class org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls
clinicNumber - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
clone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Recursive, deep copy of this object, including attributes and references.
clone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
clone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile
close() - Method in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
close() - Method in class org.apache.ctakes.assertion.cr.NegExCorpusReader
close() - Method in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
close() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
close() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
close() - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader
close() - Method in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
close() - Method in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
close() - Method in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
close() - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
close() - Method in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
close() - Method in class org.apache.ctakes.utils.wiki.WikiIndex
close() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
closeConnection() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection: Releases this Connection object's database.
closeGoldRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
closeGoldRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
closeRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
closeRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
closestVerbExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
closestVerbExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
closestVerbExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
ClosestVerbExtractor - Class in org.apache.ctakes.temporal.ae.feature
ClosestVerbExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.ClosestVerbExtractor
closestVerbExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
closestVerbExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
clsIndex - Variable in class org.apache.ctakes.coreference.util.AbstractClassifier
cmdCacheFileLocation - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
cmdCacheFileLocation - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
cmdCacheFreqCutoff - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
cmdCacheFreqCutoff - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
CmdLineCpeRunner - Class in org.apache.ctakes.core.cpe: Author: SPF Affiliation: CHIP-NLP Date: 1/17/13
CmdLineCpeRunner() - Constructor for class org.apache.ctakes.core.cpe.CmdLineCpeRunner
CmdLineCpeRunner.MyStatusCallbackListener - Class in org.apache.ctakes.core.cpe: Callback Listener.
CmdLineCpeRunner.MyStatusCallbackListener() - Constructor for class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
CN - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
Code - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
code - Variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
code - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
CODE_MF_PRP_KEY - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
CODE_MF_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
CODE_MF_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
CODE_MF_PRP_KEY - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl
CODE_MF_PRP_KEY - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl
CODE_MF_PRP_KEY - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.UnknownSmokerNamedEntityLookupConsumerImpl
CodeToken - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
CODING_SCHEME_PRP_KEY - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
CODING_SCHEME_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
CODING_SCHEME_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
CODING_SCHEME_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
CODING_SCHEME_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
CODING_SCHEME_PRP_KEY - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl
CODING_SCHEME_PRP_KEY - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl
CODING_SCHEME_PRP_KEY - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.UnknownSmokerNamedEntityLookupConsumerImpl
codingScheme - Variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
coef - Variable in class org.apache.ctakes.utils.kernel.PolyKernel
cogved - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
coin - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
coin - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
collectCounts(String) - Static method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
collectFiles(File, List<File>) - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
CollectionCreator<V,T extends java.util.Collection<V>> - Interface in org.apache.ctakes.dictionary.lookup2.util.collection
CollectionCreatorFactory - Class in org.apache.ctakes.dictionary.lookup2.util.collection
CollectionCreatorFactory() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.CollectionCreatorFactory
CollectionFilter - Interface in org.apache.ctakes.dictionary.lookup.filter: Filters a Collection of MetaDataHit objects.
CollectionMap<K,V,T extends java.util.Collection<V>> - Interface in org.apache.ctakes.dictionary.lookup2.util.collection: Author: SPF Affiliation: CHIP-NLP Date: 6/24/14
collectionProcessComplete(ProcessTrace) - Method in class org.apache.ctakes.constituency.parser.uima.co.ParserTreeWriterConsumer
collectionProcessComplete(ProcessTrace) - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter: closes the PreparedStatements
collectionProcessComplete(ProcessTrace) - Method in class org.apache.ctakes.core.cc.TokenFreqCasConsumer: This method sorts the frequency counts and prints out the resulting frequencies in descending order to the frequency file in 'word|count' format.
collectionProcessComplete() - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
collectionProcessComplete() - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator: Close db connections in UmlsToSnomedDbConsumerImpl
collectionProcessComplete() - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
collectionProcessComplete() - Method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
collectionProcessComplete(ProcessTrace) - Method in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
collectionProcessComplete(ProcessTrace) - Method in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
collectionProcessComplete(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
collectionProcessComplete(ProcessTrace) - Method in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
collectionProcessComplete() - Method in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
collectionProcessComplete() - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the collection processing is completed.
CollectionTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
CollectionTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation: Never called.
CollectionTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation: Internal - constructor used by generator
CollectionTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation
CollectionTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
CollectionTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type: initialize variables to correspond with Cas Type and Features
ColumnMappingInfo - Class in org.apache.ctakes.ytex.uima.mapper
ColumnMappingInfo() - Constructor for class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
columnMappingInfos - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
columnName - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
CombineCondition - Class in org.apache.ctakes.core.fsm.condition
CombineCondition(Condition, Condition) - Constructor for class org.apache.ctakes.core.fsm.condition.CombineCondition
combineScoreMethod - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
combineScoreMethod - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
comboOperator - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
COMMA - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
CommandLine - Class in org.apache.ctakes.temporal.eval
CommandLine() - Constructor for class org.apache.ctakes.temporal.eval.CommandLine
CommandLine.IntegerRanges - Class in org.apache.ctakes.temporal.eval
CommandLine.IntegerRanges(String) - Constructor for class org.apache.ctakes.temporal.eval.CommandLine.IntegerRanges
CommandLineParserUtil - Class in org.apache.ctakes.constituency.parser.util
CommandLineParserUtil() - Constructor for class org.apache.ctakes.constituency.parser.util.CommandLineParserUtil
COMMENT_STRING - Static variable in class org.apache.ctakes.core.resource.LinesFromFileStringsResourceImpl
commitConnection() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection: Makes all changes made since the previous commit/rollback permanent and releases any database locks currently held by this Connection object.
common - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasDiff
commonNode - Variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
compare(Annotation, Annotation) - Method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier.AnnotLocationComparator
compare(Annotation, Annotation) - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer.AnnotationLengthComparator
compare(Annotation, Annotation) - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer.AnnotationPositionComparator
compare(Token, Token) - Method in class org.apache.ctakes.core.nlp.tokenizer.OffsetComparator
compare(Span, Span) - Method in class org.apache.ctakes.coreference.eval.helpers.SpanOffsetComparator
compare(Annotation, Annotation) - Method in class org.apache.ctakes.coreference.util.AnnotOffsetComparator
compare(MetaDataHit, MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator: Implementation
compare(LookupToken, LookupToken) - Method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator
compare(File, File) - Method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.FileSizeComparator
compare(Annotation, Annotation) - Method in enum org.apache.ctakes.temporal.utils.AnnotationIdCollection.ArgComparator
Compare - Class in org.apache.ctakes.utils.xcas_comparison: This class illustrates the basic usage of this tool.
Compare() - Constructor for class org.apache.ctakes.utils.xcas_comparison.Compare
compare(FeatureRank, FeatureRank) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank.FeatureRankAsc
compare(FeatureRank, FeatureRank) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank.FeatureRankDesc
CompareFeatureStructures - Class in org.apache.ctakes.temporal.data.analysis
CompareFeatureStructures() - Constructor for class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
CompareFeatureStructures.FeatureStructureEqualizer - Class in org.apache.ctakes.temporal.data.analysis
CompareFeatureStructures.FeatureStructureEqualizer() - Constructor for class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures.FeatureStructureEqualizer
CompareFeatureStructures.Options - Interface in org.apache.ctakes.temporal.data.analysis
compareTo(AssertionEvaluation.HashableAnnotation) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
compareTo(RelationExtractorEvaluation.HashableArguments) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
compareTo(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Determines the order of this and the specified XcasAnnotation.
compareTo(ConceptPair) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair: compare concept 1, then concept 2
compareTo(NegexAnnotator.NegexToken) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
compareToPattern(List<Chunk>, int) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: Compares the chunks at index i to the 1st element on the pattern, i+1 to the 2nd element, etc and returns true if the chunks starting at i fit the pattern
compile(String) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
compile(String, int) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
compilePatternCheck(String, String) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change
completed - Variable in class org.apache.ctakes.assertion.eval.XMIReader
completed - Variable in class org.apache.ctakes.core.cr.TextReader
completed - Variable in class org.apache.ctakes.core.cr.XMIReader
completed - Variable in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
completed - Variable in class org.apache.ctakes.relationextractor.eval.XMIReader
completeJointDistroForFold(Map<String, Map<String, Set<Long>>>, Map<String, Set<Long>>, Set<String>, Set<String>, String) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: finalize the joint distribution tables wrt a fold.
ComplicatesDisrupts - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ComplicatesDisrupts() - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts: Never called.
ComplicatesDisrupts(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts: Internal - constructor used by generator
ComplicatesDisrupts(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts
ComplicatesDisrupts_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ComplicatesDisrupts_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts_Type: initialize variables to correspond with Cas Type and Features
ComplicatesDisruptsTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ComplicatesDisruptsTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation: Never called.
ComplicatesDisruptsTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation: Internal - constructor used by generator
ComplicatesDisruptsTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation
ComplicatesDisruptsTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ComplicatesDisruptsTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation_Type: initialize variables to correspond with Cas Type and Features
components - Static variable in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
compress(StringBuffer) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
compress(StringBuffer) - Static method in class org.apache.ctakes.preprocessor.Utility: remove leading and trailing whitespace from each line
computeDotProduct(HashMap<String, Double>, HashMap<String, Double>) - Method in class org.apache.ctakes.utils.wiki.WikiIndex
computeEuclideanNorm(HashMap<String, Double>) - Method in class org.apache.ctakes.utils.wiki.WikiIndex
computeIC(IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo, int) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
computeSubsumerCount(ConcRel, Map<String, IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo>, Map<String, Set<String>>, short[], BufferedWriter) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl: add/update icInfoMap entry for concept with the concept's subsumer count
conAnal - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.NegationDependencyFeatureExtractor
Concept - Class in org.apache.ctakes.assertion.medfacts.types: Updated by JCasGen Wed Sep 30 11:06:05 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-assertion/target/jcasgen/typesystem.xml
Concept() - Constructor for class org.apache.ctakes.assertion.medfacts.types.Concept: Never called.
Concept(int, TOP_Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Concept: Internal - constructor used by generator
Concept(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Concept
Concept(JCas, int, int) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Concept
Concept - Class in org.apache.ctakes.dictionary.lookup2.concept: Author: SPF Affiliation: CHIP-NLP Date: 11/20/13
Concept(String) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.Concept
Concept(String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.Concept
Concept(String, String, CollectionMap<ConceptCode, String, ? extends Collection<String>>) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.Concept
concept - Variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
concept1 - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
concept1 - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
concept1Path - Variable in class org.apache.ctakes.ytex.kernel.metric.LCSPath
concept2 - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
concept2 - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
concept2Path - Variable in class org.apache.ctakes.ytex.kernel.metric.LCSPath
CONCEPT_FACTORIES_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
CONCEPT_GRAPH_PATH - Static variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
Concept_Type - Class in org.apache.ctakes.assertion.medfacts.types: Updated by JCasGen Wed Sep 30 11:06:05 EDT 2015
Concept_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Concept_Type: initialize variables to correspond with Cas Type and Features
ConceptCode - Enum in org.apache.ctakes.dictionary.lookup2.concept: Author: SPF Affiliation: CHIP-NLP Date: 11/20/13
ConceptCode() - Constructor for enum org.apache.ctakes.dictionary.lookup2.concept.ConceptCode
ConceptConverterAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts
ConceptConverterAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
conceptDao - Variable in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
ConceptDao - Interface in org.apache.ctakes.ytex.kernel.dao: create/retrieve concept graphs.
conceptDao - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
conceptDao - Variable in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
conceptDao - Variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
conceptDao - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
ConceptDaoImpl - Class in org.apache.ctakes.ytex.kernel.dao
ConceptDaoImpl() - Constructor for class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
ConceptFactory - Interface in org.apache.ctakes.dictionary.lookup2.concept: Term Attribute Repository used to lookup term attributes by the cui of the term Author: SPF Affiliation: CHIP-NLP Date: 11/20/13
conceptFilter - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
ConceptFirstWord - Class in org.apache.ctakes.ytex.web.search: Mapped to V_UMLS_FWORD_LOOKUP This table does not have a primary key, so we can't map it with hibernate.
ConceptFirstWord() - Constructor for class org.apache.ctakes.ytex.web.search.ConceptFirstWord
ConceptGraph - Class in org.apache.ctakes.ytex.kernel.model: A directed graph that spans a subset of the UMLS connecting concepts with IS-A links.
ConceptGraph() - Constructor for class org.apache.ctakes.ytex.kernel.model.ConceptGraph
conceptGraph - Variable in class org.apache.ctakes.ytex.ws.SimServiceInfo
conceptGraphName - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
conceptGraphName - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
conceptGraphName - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
conceptId - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
conceptId - Variable in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
conceptIdToTermQuery - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
ConceptInfo - Class in org.apache.ctakes.ytex.kernel.metric: we run into out of memory errors when preloading the intrinsic ic for large concept graphs.
ConceptInfo() - Constructor for class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
ConceptInfo(String, int, double, double) - Constructor for class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
conceptInstanceMap - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.ConceptInstanceMapExtractor
conceptList - Variable in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
ConceptLookup - Class in org.apache.ctakes.assertion.medfacts
ConceptLookup() - Constructor for class org.apache.ctakes.assertion.medfacts.ConceptLookup
ConceptLookupBean - Class in org.apache.ctakes.ytex.web.search: JSF Backing Bean for semanticSearch.jspx.
ConceptLookupBean() - Constructor for class org.apache.ctakes.ytex.web.search.ConceptLookupBean
conceptMap - Variable in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
ConceptPair - Class in org.apache.ctakes.ytex.kernel.metric: pair of concepts.
ConceptPair(String, String) - Constructor for class org.apache.ctakes.ytex.kernel.metric.ConceptPair
ConceptPair() - Constructor for class org.apache.ctakes.ytex.kernel.metric.ConceptPair
conceptPair - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
conceptPair - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
ConceptPairSimilarity - Class in org.apache.ctakes.ytex.kernel.metric
ConceptPairSimilarity() - Constructor for class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
conceptPairText - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
conceptPattern - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
conceptProperty - Variable in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
conceptSearchService - Variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
ConceptSearchService - Interface in org.apache.ctakes.ytex.web.search: Dao to get Concepts corresponding to the given text
conceptSearchService - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
ConceptSearchServiceImpl - Class in org.apache.ctakes.ytex.web.search
ConceptSearchServiceImpl() - Constructor for class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
ConceptSearchServiceImpl.ConceptFirstWordRowMapper - Class in org.apache.ctakes.ytex.web.search
ConceptSearchServiceImpl.ConceptFirstWordRowMapper() - Constructor for class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl.ConceptFirstWordRowMapper
conceptSetName - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
conceptSetName - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
ConceptSimilarityRestService - Interface in org.apache.ctakes.ytex.ws
conceptSimilarityService - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
conceptSimilarityService - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
ConceptSimilarityService - Interface in org.apache.ctakes.ytex.kernel.metric
conceptSimilarityService - Variable in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
conceptSimilarityService - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
ConceptSimilarityService.SimilarityMetricEnum - Enum in org.apache.ctakes.ytex.kernel.metric
ConceptSimilarityService.SimilarityMetricEnum(boolean, boolean) - Constructor for enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum
ConceptSimilarityServiceImpl - Class in org.apache.ctakes.ytex.kernel.metric: compute concept similarity
ConceptSimilarityServiceImpl() - Constructor for class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
ConceptSimilarityWebService - Interface in org.apache.ctakes.ytex.ws
ConceptSimilarityWebServiceImpl - Class in org.apache.ctakes.ytex.ws
ConceptSimilarityWebServiceImpl() - Constructor for class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
ConcRel - Class in org.apache.ctakes.ytex.kernel.model
ConcRel(String, int) - Constructor for class org.apache.ctakes.ytex.kernel.model.ConcRel
conditional - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
ConditionalCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
ConditionalCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
ConditionalModifier - Class in org.apache.ctakes.typesystem.type.textsem: The Conditional modifier refers to mentions which could exist under certain circumstances.
ConditionalModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier: Never called.
ConditionalModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier: Internal - constructor used by generator
ConditionalModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier
ConditionalModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier
ConditionalModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: The Conditional modifier refers to mentions which could exist under certain circumstances.
ConditionalModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type: initialize variables to correspond with Cas Type and Features
CONF_ATTR - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.NamedEntityNegationKernel
confidence - Variable in class org.apache.ctakes.drugner.DrugMention
confidence - Variable in class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
ConfidenceScoreElement - Class in org.apache.ctakes.drugner.elements
ConfidenceScoreElement() - Constructor for class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
ConfidenceScoreElement(double, int, int) - Constructor for class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
ConfidenceScoreToken - Class in org.apache.ctakes.drugner.fsm.output.elements
ConfidenceScoreToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.ConfidenceScoreToken
configInit() - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: Sets configuration parameters with values from the descriptor.
configInit() - Method in class org.apache.ctakes.core.ae.TokenizerAnnotator: Reads configuration parameters.
configInit() - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator: Reads configuration parameters.
configInit(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator: Reads configuration parameters.
configInit() - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator: Sets configuration parameters with values from the descriptor.
configInit() - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Sets configuration parameters with values from the descriptor.
configInit() - Method in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster: Sets configuration parameters with values from the descriptor.
configInit() - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: Reads configuration parameters.
configurationParameters - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
CONFIRMED_STATUS - Static variable in class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
confusionMatrix - Variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
confusions() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact: Returns the ConfusionMatrix tabulating reference outcomes matched to predicted outcomes.
CONJP - Class in org.apache.ctakes.typesystem.type.syntax: A phrase-level conjunction Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.CONJP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
CONJP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.CONJP: Never called.
CONJP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.CONJP: Internal - constructor used by generator
CONJP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.CONJP
CONJP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.CONJP
CONJP_Type - Class in org.apache.ctakes.typesystem.type.syntax: A phrase-level conjunction Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.CONJP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
CONJP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.CONJP_Type: initialize variables to correspond with Cas Type and Features
ConjunctionRelationFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
ConjunctionRelationFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor
ConllDependencyNode - Class in org.apache.ctakes.typesystem.type.syntax: A dependency parser node in the CONLL-X format, namely, where each node is a token with 10 fields.
ConllDependencyNode() - Constructor for class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: Never called.
ConllDependencyNode(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: Internal - constructor used by generator
ConllDependencyNode(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode
ConllDependencyNode(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode
ConllDependencyNode_Type - Class in org.apache.ctakes.typesystem.type.syntax: A dependency parser node in the CONLL-X format, namely, where each node is a token with 10 fields.
ConllDependencyNode_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type: initialize variables to correspond with Cas Type and Features
conLocs - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
connection - Variable in class org.apache.ctakes.jdl.data.base.JdlConnection
CONNECTIONS - Variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
CONS_SKIP_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator: specifies the number of consecutive non-comma tokens that can be skipped
ConsecutiveSentencesEventEventRelationAnnotator - Class in org.apache.ctakes.temporal.ae
ConsecutiveSentencesEventEventRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
ConsecutiveSentencesEventTimeRelationAnnotator - Class in org.apache.ctakes.temporal.ae
ConsecutiveSentencesEventTimeRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
Const - Interface in org.apache.ctakes.smokingstatus: Constants used by the SmokingStatus project.
CONST - Class in org.apache.ctakes.typesystem.type.constants: Contains a set of constants for feature values.
CONST() - Constructor for class org.apache.ctakes.typesystem.type.constants.CONST
Const - Class in org.apache.ctakes.utils.xcas_comparison
Const() - Constructor for class org.apache.ctakes.utils.xcas_comparison.Const
Constants - Class in org.apache.ctakes.relationextractor.data: Various global settings.
Constants() - Constructor for class org.apache.ctakes.relationextractor.data.Constants
ConstituencyBasedTimeAnnotator - Class in org.apache.ctakes.temporal.ae
ConstituencyBasedTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
ConstituencyParser - Class in org.apache.ctakes.constituency.parser.ae
ConstituencyParser() - Constructor for class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
ConstraintConstructor - Class in org.apache.ctakes.assertion.medfacts.i2b2.api
ConstraintConstructor() - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
ConstraintConstructor(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
ConstraintConstructorFindContainedBy - Class in org.apache.ctakes.assertion.medfacts.i2b2.api
ConstraintConstructorFindContainedBy() - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedBy
ConstraintConstructorFindContainedBy(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedBy
ConstraintConstructorFindContainedWithin - Class in org.apache.ctakes.assertion.medfacts.i2b2.api
ConstraintConstructorFindContainedWithin() - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedWithin
ConstraintConstructorFindContainedWithin(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedWithin
constrainToWindow(Annotation, Iterator<LookupToken>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator: Gets a list of LookupToken objects within the specified window annotation.
constrainToWindow(int, int, Iterator<Annotation>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets a list of LookupAnnotation objects within the specified window.
constrainToWindow(JCas, int, Annotation) - Method in class org.apache.ctakes.necontexts.ContextAnnotator: Gets a list of annotations within the specified window annotation.
constrainToWindow(int, int, Iterator<Annotation>) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets a list of LookupAnnotation objects within the specified window.
construct2DTokenArray(JCas) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
constructConstraintByBeginEnd(int, int, ConstraintFactory, FeaturePath, FeaturePath) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
constructConstraintByBeginEnd(int, int, ConstraintFactory, FeaturePath, FeaturePath) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedBy
constructConstraintByBeginEnd(int, int, ConstraintFactory, FeaturePath, FeaturePath) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedWithin
constructContainedByConstraint(int, int, ConstraintFactory, FeaturePath, FeaturePath) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedBy
constructContainedByConstraint(int, int, ConstraintFactory, FeaturePath, FeaturePath) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructorFindContainedWithin
constructRel(List<ConcRel>) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel: reconstruct the relationships to other ConcRel objects
consumeHit(JCas, Annotation, int, ContextHit) - Method in interface org.apache.ctakes.necontexts.ContextHitConsumer: Implementation determines how context data is stored to the CAS.
consumeHit(JCas, Annotation, int, ContextHit) - Method in class org.apache.ctakes.necontexts.ContextHitConsumerAdapter
consumeHit(JCas, Annotation, int, ContextHit) - Method in class org.apache.ctakes.necontexts.NamedEntityContextHitConsumer
consumeHit(JCas, Annotation, int, ContextHit) - Method in class org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
consumeHit(JCas, Annotation, int, ContextHit) - Method in class org.apache.ctakes.necontexts.status.StatusContextHitConsumer
consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.dictionary.lookup.ae.DebugConsumerImpl
consumeHits(JCas, Iterator<LookupHit>) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupConsumer: Consumes the hits produced by the LookupAnnotator.
consumeHits(JCas, Iterator<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl: Consumes the hits produced by the LookupAnnotator.
consumeHits(JCas, Iterator<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl: Consumes the hits produced by the LookupAnnotator.
consumeHits(JCas, Iterator<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl: Consumes the hits produced by the LookupAnnotator.
consumeHits(JCas, RareWordDictionary, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
consumeHits(JCas, RareWordDictionary, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in class org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer: Refine a collection of dictionary terms to only contain the most specific variations: "colon cancer" instead of "cancer", performed by span inclusion /complete containment, not overlap.
consumeHits(JCas, RareWordDictionary, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in interface org.apache.ctakes.dictionary.lookup2.consumer.TermConsumer
consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl
consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl
consumeHits(JCas, Iterator) - Method in class org.apache.ctakes.smokingstatus.lookup.ae.UnknownSmokerNamedEntityLookupConsumerImpl
ConsumeNamedEntityRecordModel - Class in org.apache.ctakes.drugner.cc: UIMA annotator that preps the CAS for extraction into DB2.
ConsumeNamedEntityRecordModel() - Constructor for class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
CONSUMER_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: XML key specifying the section that defines the single TermConsumer that should be used to consume discovered terms.
consumeTypeIdHits(JCas, String, int, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in class org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
consumeTypeIdHits(JCas, String, int, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in class org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer: Only uses the largest spans for the type
consumeTypeIdHits(JCas, String, int, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in class org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer
consumeTypeIdHits(JCas, String, int, CollectionMap<TextSpan, Long, ? extends Collection<Long>>, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Method in interface org.apache.ctakes.dictionary.lookup2.consumer.TermConsumer
containedTokens(int, int) - Method in class org.apache.ctakes.coreference.util.AttributeCalculator
containEvent(Annotation, Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.ae.feature.EventPositionFeatureExtractor
containEvent(Annotation, Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor
contains(SimpleTree, SimpleTree) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
contains(SimpleTree, SimpleTree, boolean) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
contains(String) - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl: Deprecated.
contains(String) - Method in interface org.apache.ctakes.dictionary.lookup.Dictionary: Determines whether the Dictionary contains the specified input text.
contains(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl
contains(MetaDataHit) - Method in interface org.apache.ctakes.dictionary.lookup.filter.PostLookupFilter
contains(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl
contains(String) - Method in interface org.apache.ctakes.dictionary.lookup.filter.PreLookupFilter
contains(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
contains(String) - Method in class org.apache.ctakes.dictionary.lookup.filter.StringPreLookupFilterImpl
contains(String) - Method in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl: Determines whether the Dictionary contains the specified input text.
contains(String) - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl: Determines whether the Dictionary contains the specified input text.
contains(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl: Determines whether the Dictionary contains the specified input text.
contains(int, int, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Returns 1 if 1 contains 2 Returns 2 if 2 contains 1 Returns 0 otherwise
contains(TlinkType) - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
contains(Object) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
containsAll(Collection<?>) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
containsAny(Chunk, LinkedList<Annotation>) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
containsDepFrag(SimpleTree, SimpleTree, boolean) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
containsDepFragIgnoreCase(SimpleTree, SimpleTree) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
containsIgnoreCase(SimpleTree, SimpleTree) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
containsKey(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
containsKey(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
containsKey(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
containsKey(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
containsKey(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
containsKey(String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings
containsLetter(String, int, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
ContainsSetTextValueCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Finds numeric values w/in tokens containing mixed text (integers contained in a string).
ContainsSetTextValueCondition(Set, boolean) - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.ContainsSetTextValueCondition: Constructor
containsValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: check the collection map for a key and value combination
containsValue(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
containsValue(K, V) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: check the collection map for a key and value combination
containsValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: check the collection map for a key and value combination
containsValue(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
containsValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: check the collection map for a key and value combination
containsValue(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
containsValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: check the collection map for a key and value combination
containsValue(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
containsValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: check the collection map for a key and value combination
containsValue(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
content - Variable in class org.apache.ctakes.core.util.DocumentSection
contentWords(int, int) - Method in class org.apache.ctakes.coreference.util.AttributeCalculator
contentWords(Markable) - Method in class org.apache.ctakes.coreference.util.AttributeCalculator
context - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
context - Variable in class org.apache.ctakes.jdl.data.loader.XmlLoader
context - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
context - Variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
context - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
context - Variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
CONTEXT_ANALYZER_CLASS_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "ContextAnalyzerClass" is a required, single, string parameter that specifies the context analyzer class that determines if a "hit" is found within a processed scope.
CONTEXT_ANNOTATION_CLASS_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "ContextAnnotationClass" is a required, single, string parameter that specifies the annotation type of the context annotations (often "tokens") that make up the context relative to a focus annotation within a scope that is being examined.
CONTEXT_HIT_CONSUMER_CLASS_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "ContextHitConsumerClass" is a required, single, string parameter that specifies the context hit consumer class that will process context hits that are found.
ContextAnalyzer - Interface in org.apache.ctakes.necontexts: A context analyzer analyzes a set of annotations that make up a context and produces context hits which are consumed by context hit consumers.
contextAnalyzer - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
ContextAnalyzerAdapter - Class in org.apache.ctakes.necontexts
ContextAnalyzerAdapter() - Constructor for class org.apache.ctakes.necontexts.ContextAnalyzerAdapter
ContextAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Contextual information of an entity.
ContextAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: Never called.
ContextAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: Internal - constructor used by generator
ContextAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation
ContextAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation
ContextAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Contextual information of an entity.
ContextAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type: initialize variables to correspond with Cas Type and Features
ContextAnnotator - Class in org.apache.ctakes.necontexts: The context annotator iterates through focus annotations and analyzes the surrounding context of each.
ContextAnnotator() - Constructor for class org.apache.ctakes.necontexts.ContextAnnotator
contextConsumer - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
ContextDependentTokenizerAnnotator - Class in org.apache.ctakes.contexttokenizer.ae: Finds tokens based on context.
ContextDependentTokenizerAnnotator() - Constructor for class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
contextExtractor - Variable in class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
contextExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
contextExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
contextExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
contextExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
contextExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
contextFeatureExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
contextFeatureExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
contextFeatureExtractors - Variable in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
contextFeatureExtractors - Variable in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
contextFeatureExtractors - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
ContextHit - Class in org.apache.ctakes.necontexts: Object represents a hit relating to a focus annotation.
ContextHit(int, int) - Constructor for class org.apache.ctakes.necontexts.ContextHit
ContextHitConsumer - Interface in org.apache.ctakes.necontexts: A context hit consumer is called by the context annotator when a context hit is returned by its context analyzer.
ContextHitConsumerAdapter - Class in org.apache.ctakes.necontexts
ContextHitConsumerAdapter() - Constructor for class org.apache.ctakes.necontexts.ContextHitConsumerAdapter
contextSize - Variable in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
contextType - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
CONTEXTUAL_MODALITY - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
ContextualModalityAnnotator - Class in org.apache.ctakes.temporal.ae
ContextualModalityAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
ContextWordWindowExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
ContextWordWindowExtractor(String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
contingencyTable - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
ContractionResult - Class in org.apache.ctakes.core.nlp.tokenizer
ContractionResult() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
ContractionsPTB - Class in org.apache.ctakes.core.nlp.tokenizer
ContractionsPTB() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
contractionsStartingWithApostrophe - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
contractionsStartingWithApostrophe - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
ContractionToken - Interface in org.apache.ctakes.core.fsm.token
ContractionToken - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a contraction rather than a punctuation, symbol, newline, word, or number.
ContractionToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.ContractionToken: Never called.
ContractionToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ContractionToken: Internal - constructor used by generator
ContractionToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ContractionToken
ContractionToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ContractionToken
ContractionToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a contraction rather than a punctuation, symbol, newline, word, or number.
ContractionToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ContractionToken_Type: initialize variables to correspond with Cas Type and Features
ContractionTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
ContractionTokenAdapter(ContractionToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.ContractionTokenAdapter
contractionTokenLen - Variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
Contraindicates - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
Contraindicates() - Constructor for class org.apache.ctakes.typesystem.type.relation.Contraindicates: Never called.
Contraindicates(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Contraindicates: Internal - constructor used by generator
Contraindicates(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Contraindicates
Contraindicates_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
Contraindicates_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Contraindicates_Type: initialize variables to correspond with Cas Type and Features
ContraindicatesTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ContraindicatesTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation: Never called.
ContraindicatesTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation: Internal - constructor used by generator
ContraindicatesTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation
ContraindicatesTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ContraindicatesTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation_Type: initialize variables to correspond with Cas Type and Features
convert(List<? extends <any>>, FeatureFunction) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ExtractorListFeatureFunctionConverter
convert(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
convert(Token, JCas, int) - Static method in class org.apache.ctakes.core.ae.TokenConverter: Converts from Java Tokenizer object into a JCas object.
convert(BaseToken) - Static method in class org.apache.ctakes.core.ae.TokenConverter: Convert from a JCas object into Java Tokenizer object.
convert(FSIterator) - Static method in class org.apache.ctakes.coreference.util.FSIteratorToList
convert(JCas, DEPTree, Sentence, List<BaseToken>) - Static method in class org.apache.ctakes.dependency.parser.util.ClearDependencyUtility
convert(org.cleartk.util.treebank.TopTreebankNode, JCas) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
convert(org.cleartk.util.treebank.TreebankNode, JCas, TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
convert(Class, Object) - Method in class org.apache.ctakes.ytex.uima.mapper.ISO8601Converter
convert2DTokenArrayToText(ArrayList<ArrayList<String>>) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
ConvertAndCompare - Class in org.apache.ctakes.utils.xcas_comparison
ConvertAndCompare() - Constructor for class org.apache.ctakes.utils.xcas_comparison.ConvertAndCompare
convertCharacterOffsetToLineToken(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
convertCharacterOffsetToLineToken(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes: delegate to converter to determine offset.
converter - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
convertFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
convertFromTextToNum(String) - Method in class org.apache.ctakes.drugner.DrugMention
Converti2b2AnnotationsToCTAKES - Class in org.apache.ctakes.assertion.medfacts
Converti2b2AnnotationsToCTAKES() - Constructor for class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
convertTime(String) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor: Given a drm string that may or may not contain the time, this method will return a string.
convertToChangeStatus(String) - Method in class org.apache.ctakes.drugner.DrugMention
convertToDebugOutput(String, T) - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
convertToDistribution(String) - Static method in class org.apache.ctakes.temporal.duration.Utils: Take a time unit and return a probability distribution in which p(this time unit) = 1 and all others are zero.
convertToInt(String) - Static method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
convertTokens(List<Token>) - Static method in class org.apache.ctakes.core.fsm.token.adapter.TokenConverter
convertToString(Clob) - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader: Loads the clob data into a String object.
ConvertXMIAssertionsToi2b2Format - Class in org.apache.ctakes.assertion.medfacts
ConvertXMIAssertionsToi2b2Format() - Constructor for class org.apache.ctakes.assertion.medfacts.ConvertXMIAssertionsToi2b2Format
ConvolutionKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: Apply the delegate kernel to the children of the given nodes.
ConvolutionKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
conWords - Variable in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
CoordinateFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
CoordinateFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.CoordinateFeaturesExtractor
copyAnnotation(Annotation, JCas) - Static method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
CopyAnnotator - Class in org.apache.ctakes.core.ae: Utility annotator that copy's data from an existing JCas object into a new JCas object.
CopyAnnotator() - Constructor for class org.apache.ctakes.core.ae.CopyAnnotator
CopyDrugAnnotator - Class in org.apache.ctakes.drugner.ae: Utility annotator that copy's data from an existing JCas object into a new JCas object.
CopyDrugAnnotator() - Constructor for class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
COREF_THRESHOLD - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
CorefConsts - Class in org.apache.ctakes.coreference.util
CorefConsts() - Constructor for class org.apache.ctakes.coreference.util.CorefConsts
CoreferenceRelation - Class in org.apache.ctakes.typesystem.type.relation: A coreference pair, with antecedent as arg1 and anaphor as arg2 Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
CoreferenceRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation: Never called.
CoreferenceRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation: Internal - constructor used by generator
CoreferenceRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation
CoreferenceRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A coreference pair, with antecedent as arg1 and anaphor as arg2 Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
CoreferenceRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation_Type: initialize variables to correspond with Cas Type and Features
corpus - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
corpusIC - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
corpusIC - Variable in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum
corpusICMap - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
CorpusKernelEvaluator - Interface in org.apache.ctakes.ytex.kernel.evaluator
CorpusKernelEvaluatorImpl - Class in org.apache.ctakes.ytex.kernel.evaluator
CorpusKernelEvaluatorImpl() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
CorpusKernelEvaluatorImpl.InstanceIDRowMapper - Class in org.apache.ctakes.ytex.kernel.evaluator
CorpusKernelEvaluatorImpl.InstanceIDRowMapper() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.InstanceIDRowMapper
CorpusKernelEvaluatorImpl.SliceEvaluator - Class in org.apache.ctakes.ytex.kernel.evaluator
CorpusKernelEvaluatorImpl.SliceEvaluator(Map<Long, Node>, int, int, boolean) - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.SliceEvaluator
corpusLcs - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
corpusLcsIC - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
corpusLcsTerm - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
corpusName - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
corpusName - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
corpusName - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
corpusName - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
corpusName - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
corpusName - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
corpusName - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter
correctArgOrder(Collection<BinaryTextRelation>, Collection<BinaryTextRelation>) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
correctOutcomes - Variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
cosine(double[], double[]) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
cosine(Map<T, Double>, Map<T, Double>) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl: cosine of two vectors
cost - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
countAnnotationsInSpan(JCas, int, int, int, int[]) - Static method in class org.apache.ctakes.core.util.FSUtil: Does not use FSUtil.getAnnotationsInSpan(JCas, int, int, int, int[]) so we don't create a collection unnecessarily.
countAnnotationsInSpan(JCas, int, int, int) - Static method in class org.apache.ctakes.core.util.FSUtil: returns the number of annotations of specified type in the
countCorrectOutcomes() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countCorrectOutcomes(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countDepFrags(SimpleTree, SimpleTree) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
countDistanceBetweenArguments(JCas, JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
countEntities(JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
countEntityMentionPairs(JCas, JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
countEntityMentionPairTypes(JCas, JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
CounterMap<K> - Class in org.apache.ctakes.utils.struct
CounterMap() - Constructor for class org.apache.ctakes.utils.struct.CounterMap
CounterTreeMap<K> - Class in org.apache.ctakes.utils.struct
CounterTreeMap() - Constructor for class org.apache.ctakes.utils.struct.CounterTreeMap
countFalseNegatives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countFalsePositives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countFrags(SimpleTree, SimpleTree) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
countInterval(Collection<? extends Annotation>, int, int) - Static method in class org.apache.ctakes.coreference.util.AnnotationCounter
countPoint(Collection<? extends Annotation>, int, int) - Static method in class org.apache.ctakes.coreference.util.AnnotationCounter
countPredictedOutcomes() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countPredictedOutcomes(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countReferenceOutcomes() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countReferenceOutcomes(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countRelationTypes(JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
countSentences(JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
countTokens(JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
countTrueNegatives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countTruePositives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
countUniqueCodes(Collection<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
Course - Class in org.apache.ctakes.typesystem.type.refsem: An indication of progress or decline of a condition.
Course() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Course: Never called.
Course(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Course: Internal - constructor used by generator
Course(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Course
Course_Type - Class in org.apache.ctakes.typesystem.type.refsem: An indication of progress or decline of a condition.
Course_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Course_Type: initialize variables to correspond with Cas Type and Features
CourseModifier - Class in org.apache.ctakes.typesystem.type.textsem: An indication of progress or decline of a condition.
CourseModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.CourseModifier: Never called.
CourseModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.CourseModifier: Internal - constructor used by generator
CourseModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.CourseModifier
CourseModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.CourseModifier
CourseModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: An indication of progress or decline of a condition.
CourseModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type: initialize variables to correspond with Cas Type and Features
coveredText - Variable in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor
coveredText - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor
coveredText - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor
coveredText - Variable in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor
coveredText - Variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
coveredTextColumn - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
coveredTextMaxLen - Variable in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
CoveredTextToValuesExtractor - Class in org.apache.ctakes.temporal.ae.feature
CoveredTextToValuesExtractor(String, Map<String, double[]>) - Constructor for class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor
CoveredTextToValuesExtractor.StringToDoublesProcessor - Class in org.apache.ctakes.temporal.ae.feature
CoveredTextToValuesExtractor.StringToDoublesProcessor() - Constructor for class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor.StringToDoublesProcessor
coveringClass - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
coveringMap - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor
CR - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
CR - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
CR - Static variable in class org.apache.ctakes.core.sentence.SentenceSpan
CR - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
CREAM - Static variable in class org.apache.ctakes.drugner.elements.FormElement
createAnaphoricityVector(Markable, JCas) - Method in class org.apache.ctakes.coreference.util.SvmVectorCreator
createAnnotations(JCas) - Method in class org.apache.ctakes.constituency.parser.MaxentParserWrapper
createAnnotations(JCas) - Method in interface org.apache.ctakes.constituency.parser.ParserWrapper
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
createAnnotatorDescription() - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
createAnnotatorDescription() - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
createAnnotatorDescription() - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
createAnnotatorDescription() - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
createAnnotatorDescription() - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
createAnnotatorDescription() - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
createAnnotatorDescription(String[], int) - Static method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster
createAnnotatorDescription() - Static method in class org.apache.ctakes.chunker.ae.Chunker
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.chunker.ae.Chunker
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
createAnnotatorDescription() - Static method in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
createAnnotatorDescription() - Static method in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
createAnnotatorDescription() - Static method in class org.apache.ctakes.core.ae.SentenceDetector
createAnnotatorDescription() - Static method in class org.apache.ctakes.core.ae.SimpleSegmentAnnotator
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.core.ae.SimpleSegmentAnnotator
createAnnotatorDescription() - Static method in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
createAnnotatorDescription() - Static method in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
createAnnotatorDescription() - Static method in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
createAnnotatorDescription(boolean, boolean) - Static method in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
createAnnotatorDescription() - Static method in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
createAnnotatorDescription() - Static method in class org.apache.ctakes.lvg.ae.LvgAnnotator
createAnnotatorDescription() - Static method in class org.apache.ctakes.postagger.POSTagger
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.postagger.POSTagger
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.baselines.F1BaselineEventTimeRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventEventRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.baselines.TimidBaselineEventTimeRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.baselines.TreeHeightBaseline
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
createAnnotatorDescription() - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.NEPredicateEventAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.NEPredicateEventAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.TimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.TimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createAnnotatorDescription(String) - Static method in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
createAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createArgument(JCas, DEPArc, BaseToken) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
CreateAssertionDescriptor - Class in org.apache.ctakes.assertion.medfacts.cleartk
CreateAssertionDescriptor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
CreateAssertionLuceneIndexFromDelimitedFile - Class in org.apache.ctakes.dictionary.assertion: Driver for populating a Lucene Index with assertion cue phrases, so that the tokenization of the dictionary entries matches the tokenization that will be done to clinical text during pipeline processing.
CreateAssertionLuceneIndexFromDelimitedFile(TokenizerPTB) - Constructor for class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile: Constructor
createBlob(IdentifiedAnnotation) - Static method in class org.apache.ctakes.core.cc.JdbcWriterTemplate
createChunk(JCas, int, int, String) - Method in interface org.apache.ctakes.chunker.ae.ChunkCreator
createChunk(JCas, int, int, String) - Method in class org.apache.ctakes.chunker.ae.DefaultChunkCreator
createChunk(JCas, int, int, String) - Method in class org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator
createCollection() - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionCreator
createCollection(int) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionCreator
createConcept(Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
createConcept(Long) - Method in interface org.apache.ctakes.dictionary.lookup2.concept.ConceptFactory
createConcept(Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
createConcept(Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.MemConceptFactory
createConcept(Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory
createConceptCol(JCas, String, String, Collection<String>) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl: For each SNOMED code, create a corresponding JCas UmlsConcept object and store in a Collection.
createConceptGraph(String, String, String, boolean, Set<String>) - Method in interface org.apache.ctakes.ytex.kernel.dao.ConceptDao: create the concept graph with specified name using specified query.
createConceptGraph(String, String, String, boolean, Set<String>) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
createConcepts(Collection<Long>) - Method in class org.apache.ctakes.dictionary.lookup2.concept.AbstractConceptFactory: Only creates non-empty concepts; Cuis for which additional info does not exist don't create concepts
createConcepts(Collection<Long>) - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
createConcepts(Collection<Long>) - Method in interface org.apache.ctakes.dictionary.lookup2.concept.ConceptFactory
createConcepts(Collection<Long>) - Method in class org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory
createContextAnnot(JCas, Annotation, int, ContextHit) - Method in class org.apache.ctakes.necontexts.NamedEntityContextHitConsumer
createCorefPairs(LinkedList<Annotation>, int, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
createCuiTuiTerm(String...) - Static method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
createCuiTuiTerm(String...) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
createCustomDictionaryLookupDescription(String) - Static method in class org.apache.ctakes.dictionary.lookup2.ae.DictionaryLookupFactory
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
createDataWriterDescription(Class<?>, File, float, float, float) - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
createDataWriterDescription(Class<? extends <any>>, File, double) - Static method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
createDataWriterDescription(Class<?>, File, float, float) - Static method in class org.apache.ctakes.temporal.ae.TimeAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
createDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
createDemPairs(LinkedList<Annotation>, int, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
createDirectories() - Method in class org.apache.ctakes.relationextractor.data.Splitter
createDirIfNotExist(String) - Static method in class org.apache.ctakes.utils.build.BuildPear
createDiscoveredPath(String, File, String) - Static method in class org.apache.ctakes.core.resource.FileLocator: Logs a debug message before returning the absolute path of a file derived from some relative path
createDocID(File) - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
createDocument(JCas, String, boolean, boolean) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
createEngineDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
createEngineDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createEngineDescription(String) - Static method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
createEngineDescription(File) - Static method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createEnsembleDescription(String, String) - Static method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
createEnsembleDescription(File, String) - Static method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createEnsembleDescription(String, String) - Static method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
createEnsembleDescription(File, String) - Static method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createEnsembleDescription(String, String) - Static method in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
createEnsembleDescription(File, String) - Static method in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator: Deprecated.
use String path instead of File. ClearTK will automatically Resolve the String to an InputStream. This will allow resources to be read within from a jar as well as File.
createEnsembleDescription(File, String) - Static method in class org.apache.ctakes.temporal.ae.TimeAnnotator
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
createFeatureSelection(double) - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
createFeatureSelection(double) - Static method in class org.apache.ctakes.temporal.ae.TimeAnnotator
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.temporal.ae.TimeAnnotator
createFilteredIterator(int, int, Type) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
createFolds(Map<String, List<Long>>, int, int, Random) - Static method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl: iterate through the labels, split instances into folds
createFolds(int, int, Random, SortedMap<Long, String>) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl: inver the map of instance id to class, call createFolds
createI2b2Concepts(Iterable<UmlsConcept>) - Static method in class org.apache.ctakes.core.cc.JdbcWriterTemplate: I2b2 only cares about Cui & preferred text.
createInstanceIdToIndexMap(SortedSet<Long>) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
createListCreator() - Static method in class org.apache.ctakes.dictionary.lookup2.util.collection.CollectionCreatorFactory
createLookupHitMap(Iterator<LookupHit>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl
createNewMention(JCas, IdentifiedAnnotation, HashSet<JudgeAttributeInstances.Selector>) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
createOntologyConceptArr(JCas, Collection) - Method in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl: For each valid code, a corresponding JCas OntologyConcept object is created and stored in a FSArray.
createOntologyConceptArr(JCas, Collection<String>) - Method in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl: For each valid code, a corresponding JCas OntologyConcept object is created and stored in a FSArray.
createOutdir(String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil
createPreciseTerms(CollectionMap<TextSpan, Long, ? extends Collection<Long>>) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer: Refine a collection of dictionary terms to only contain the most specific variations: "colon cancer" instead of "cancer", performed by span inclusion /complete containment, not overlap
createPredicate(JCas, String, BaseToken) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
createPronPairs(LinkedList<Annotation>, int, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
createRareWordTermMap(Iterable<RareWordTermMapCreator.CuiTerm>) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
createReciprocals() - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Create a UIMA relation type based on arguments and the relation label.
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Static method in class org.apache.ctakes.temporal.ae.TemporalRelationRuleAnnotator
createRelation(JCas, Annotation, Annotation, String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
createRelation(JCas, Annotation, Annotation, String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations
createRelation(JCas, Annotation, Annotation, String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations
createRowInsertSql(String, AbstractJdbcWriter.FieldInfo...) - Static method in class org.apache.ctakes.core.cc.AbstractJdbcWriter
createSelectCall(Connection, String) - Method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
createSelectCall(Connection, String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
createSemanticAnnotation(JCas, int) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
createSetCreator() - Static method in class org.apache.ctakes.dictionary.lookup2.util.collection.CollectionCreatorFactory
createTagDictionary(BufferedReader, boolean) - Static method in class org.apache.ctakes.postagger.TagDictionaryCreator: Create a tag dictionary from a POS corpus in OpenNLP format.
createTempDir() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: copied from AnnotationViewerDialog.
createTempDir() - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
createTestDescriptor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
createTlink(JCas, int, int, TlinkType) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
createToken(Class<? extends BaseToken>, String, JCas, int, int, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: if clas is null, determine token class for the caller if jcas is null,
createTokenCountMap(Iterable<RareWordTermMapCreator.CuiTerm>) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
createTrainDescriptor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
createUmlsConcept(JCas, String, String, String, String, String) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
createUmlsConcepts(JCas, String, int, Long, CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
createUmlsConcepts(JCas, String, String, Concept) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
createUmlsDictionaryLookupDescription() - Static method in class org.apache.ctakes.dictionary.lookup2.ae.DictionaryLookupFactory
CRFTimeAnnotator - Class in org.apache.ctakes.temporal.ae
CRFTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
CRLF - Static variable in class org.apache.ctakes.core.sentence.SentenceSpan
CRLF - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
crListToString(List<ConcRel>) - Static method in class org.apache.ctakes.ytex.kernel.model.ConcRel
CrossValidateAttributeModels - Class in org.apache.ctakes.assertion.train
CrossValidateAttributeModels() - Constructor for class org.apache.ctakes.assertion.train.CrossValidateAttributeModels
CrossValidateChi2GridSearch - Class in org.apache.ctakes.assertion.train
CrossValidateChi2GridSearch() - Constructor for class org.apache.ctakes.assertion.train.CrossValidateChi2GridSearch
CrossValidationFold - Class in org.apache.ctakes.ytex.kernel.model
CrossValidationFold() - Constructor for class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
CrossValidationFold(String, String, String, Integer, Integer, Set<CrossValidationFoldInstance>) - Constructor for class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
crossValidationFoldId - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
crossValidationFoldId - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
CrossValidationFoldInstance - Class in org.apache.ctakes.ytex.kernel.model
CrossValidationFoldInstance(long, boolean) - Constructor for class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
CrossValidationFoldInstance() - Constructor for class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
crossValidationFolds - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
CsvLoader - Class in org.apache.ctakes.jdl.data.loader: Loader of CSV file.
CsvLoader(CsvLoadType, File) - Constructor for class org.apache.ctakes.jdl.data.loader.CsvLoader
CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents
CTAKES_HOME - Static variable in class org.apache.ctakes.core.resource.FileLocator: $CTAKES_HOME is an environment variable that may be set to indicate the absolute directory path of the ctakes installation
CTAKES_HOME - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
CTAKES_RXNORM_CODING_SCHEME - Static variable in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
CTAKES_SNOMED_CODING_SCHEME - Static variable in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
CtakesFileNamer - Class in org.apache.ctakes.core.util: This is a very simple implementation of XWriterFileNamer that generates file names based on a prefix string and a incrementing counter.
CtakesFileNamer() - Constructor for class org.apache.ctakes.core.util.CtakesFileNamer
ctakesTokensToOpennlpTokens(Sentence, FSArray) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
ctkRels - Static variable in class org.apache.ctakes.temporal.ae.ClearTKLinkToTHYMELinkAnnotator
CTX_HIT_KEY_STATUS_TYPE - Static variable in class org.apache.ctakes.necontexts.status.StatusContextAnalyzer
CTX_KEY_WINDOW_ANNOTATIONS - Static variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Key value for context map.
CUE_PHRASE_CATEGORY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
CUE_PHRASE_CATEGORY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
CUE_PHRASE_FAMILY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
CUE_PHRASE_FAMILY_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
CUE_PHRASE_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
CUE_PHRASE_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
CUE_PHRASE_FIRST_WORD_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
CUE_PHRASE_FIRST_WORD_FIELD_NAME - Static variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
CuePhrase - Class in org.apache.ctakes.assertion.medfacts.cleartk
CuePhrase(String, String, String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.CuePhrase
cuePhraseInWindowExtractor - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
cueWords - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
CueWordTest - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
CueWordTest() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest
CueWordTest2 - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
CueWordTest2() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest2
cui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
cui - Variable in class org.apache.ctakes.ytex.umls.model.MRSTY
cui1 - Variable in class org.apache.ctakes.ytex.umls.model.MRREL
cui2 - Variable in class org.apache.ctakes.ytex.umls.model.MRREL
CUI_MAPPING_PRP_KEY - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
CUI_MF_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
cuiCode - Variable in class org.apache.ctakes.drugner.elements.AssociatedCodeElement
cuiCode - Variable in class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
cuiCode - Variable in class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
CuiCodeUtil - Class in org.apache.ctakes.dictionary.lookup2.util: Author: SPF Affiliation: CHIP-NLP Date: 9/5/2014
CuiCodeUtil() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil
cuiDictionary - Variable in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
cuiMainSuiMap - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
cuiPattern - Static variable in interface org.apache.ctakes.ytex.umls.dao.UMLSDao: pattern to match cuis and parse out their number
cuiText - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
cuiTuiMap - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
cuiTuiMap - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
cuiTuiQuery - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
current - Variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
currentContextLen - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
currentCUI - Variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
currentCUI - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
currentDomain - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction
currRowCount - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
cutoff - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
cvf - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
cvf - Variable in class org.apache.ctakes.ytex.umls.model.MRSTY
CWD_PROPERTY - Static variable in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
CytoscapeHelper - Interface in org.apache.ctakes.ytex.kernel
CytoscapeHelperImpl - Class in org.apache.ctakes.ytex.kernel
CytoscapeHelperImpl() - Constructor for class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl

D

DAILY - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
DASH - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
data - Variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests.TestPair
data - Variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests.TestPair
DATA_DIR - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
dataInsert(JdlConnection) - Method in class org.apache.ctakes.jdl.data.loader.CsvLoader
dataInsert(JdlConnection) - Method in class org.apache.ctakes.jdl.data.loader.Loader
dataInsert(JdlConnection) - Method in class org.apache.ctakes.jdl.data.loader.XmlLoader
dataSource - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
dataSource - Variable in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
dataSource - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
dataSource - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
dataSource - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
dataSource - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
dataSource - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
dataWriterClass - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
dataWriterClass - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
Date - Class in org.apache.ctakes.typesystem.type.refsem: A normalized form for dates, namely with day, month, and year.
Date() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Date: Never called.
Date(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Date: Internal - constructor used by generator
Date(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Date
Date - Class in org.apache.ctakes.ytex.uima.types: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
Date() - Constructor for class org.apache.ctakes.ytex.uima.types.Date: Never called.
Date(int, TOP_Type) - Constructor for class org.apache.ctakes.ytex.uima.types.Date: Internal - constructor used by generator
Date(JCas) - Constructor for class org.apache.ctakes.ytex.uima.types.Date
Date(JCas, int, int) - Constructor for class org.apache.ctakes.ytex.uima.types.Date
DATE_FORMAT - Static variable in class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
Date_Type - Class in org.apache.ctakes.typesystem.type.refsem: A normalized form for dates, namely with day, month, and year.
Date_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Date_Type: initialize variables to correspond with Cas Type and Features
Date_Type - Class in org.apache.ctakes.ytex.uima.types: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
Date_Type(JCas, Type) - Constructor for class org.apache.ctakes.ytex.uima.types.Date_Type: initialize variables to correspond with Cas Type and Features
DateAndMeasurementExtractor - Class in org.apache.ctakes.temporal.ae.feature
DateAndMeasurementExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.DateAndMeasurementExtractor
DateAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.DateAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
DateAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.DateAnnotation: Never called.
DateAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DateAnnotation: Internal - constructor used by generator
DateAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DateAnnotation
DateAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DateAnnotation
DateAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.DateAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
DateAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type: initialize variables to correspond with Cas Type and Features
DateAnnotator - Class in org.apache.ctakes.ytex.uima.annotators: The cTAKES date doesn't actually parse the date.
DateAnnotator() - Constructor for class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
DateAttributeValue - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
DateAttributeValue() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue: Never called.
DateAttributeValue(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue: Internal - constructor used by generator
DateAttributeValue(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue
DateAttributeValue(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue
DateAttributeValue_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
DateAttributeValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type: initialize variables to correspond with Cas Type and Features
dateExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
dateExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
dateExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
dateExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
dateFrom - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
DateFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect dates in the given input of tokens.
DateFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.DateFSM: Constructor
DateParser - Class in org.apache.ctakes.core.util
DateParser() - Constructor for class org.apache.ctakes.core.util.DateParser
dateTo - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
DateToken - Class in org.apache.ctakes.core.fsm.output
DateToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.DateToken
dateType - Variable in class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
DayNightWordCondition - Class in org.apache.ctakes.core.fsm.condition: Handles case of A.M.
DayNightWordCondition() - Constructor for class org.apache.ctakes.core.fsm.condition.DayNightWordCondition
DB_CONN_RESRC_KEY_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
DBAnnotationViewerDialog - Class in org.apache.ctakes.ytex.tools.docanalyzer: Dialog that loads analyzed documents stored in XMI or XCAS format and allows them to be viewed using the Java-based CAS viewer or a web browser, in either an HTML/Javascript format or in the inline XML format.
DBAnnotationViewerDialog(JFrame, String, PrefsMediator, File, String, TypeSystem, String[], String, boolean, boolean, boolean, CAS) - Constructor for class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Create an AnnotationViewer Dialog
DBAnnotationViewerDialog(JFrame, String, PrefsMediator, File, String, TypeSystem, String[], boolean, CAS) - Constructor for class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
DBAnnotationViewerDialog.InteractiveFilter - Class in org.apache.ctakes.ytex.tools.docanalyzer: Filter to not show the two interactive-mode directories in the file list
DBAnnotationViewerDialog.InteractiveFilter() - Constructor for class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog.InteractiveFilter
DBAnnotationViewerDialog.MyListCellRenderer - Class in org.apache.ctakes.ytex.tools.docanalyzer
DBAnnotationViewerDialog.MyListCellRenderer() - Constructor for class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog.MyListCellRenderer
DBAnnotationViewerMain - Class in org.apache.ctakes.ytex.tools: Main Annotation Viewer GUI.
DBAnnotationViewerMain() - Constructor for class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Constructor.
DBCollectionReader - Class in org.apache.ctakes.ytex.uima: Read documents from db.
DBCollectionReader() - Constructor for class org.apache.ctakes.ytex.uima.DBCollectionReader
DBConsumer - Class in org.apache.ctakes.ytex.uima.annotators: Store the document text, cas, and annotations in the database.
DBConsumer() - Constructor for class org.apache.ctakes.ytex.uima.annotators.DBConsumer
DBPing - Class in org.apache.ctakes.ytex.tools
DBPing() - Constructor for class org.apache.ctakes.ytex.tools.DBPing
dbSchema - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
dbType - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
DBUtil - Class in org.apache.ctakes.ytex.dao: Oracle differs from sql server & mysql in handling of empty string.
DBUtil() - Constructor for class org.apache.ctakes.ytex.dao.DBUtil
debug - Variable in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
debug - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
debugAnnotationsInCas(JCas, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
DebugConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: LookupConsumer implementation that outputs debug info to the log about each LookupHit.
DebugConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.DebugConsumerImpl
DecimalCondition - Class in org.apache.ctakes.core.fsm.condition
DecimalCondition() - Constructor for class org.apache.ctakes.core.fsm.condition.DecimalCondition
DecimalRangeCondition - Class in org.apache.ctakes.core.fsm.condition
DecimalRangeCondition(double, double) - Constructor for class org.apache.ctakes.core.fsm.condition.DecimalRangeCondition
DecimalStrengthAnnotation - Class in org.apache.ctakes.drugner.type: The decimal portion of dosages stength determination for the Drug NER profile.
DecimalStrengthAnnotation() - Constructor for class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation: Never called.
DecimalStrengthAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation: Internal - constructor used by generator
DecimalStrengthAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation
DecimalStrengthAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation
DecimalStrengthAnnotation_Type - Class in org.apache.ctakes.drugner.type: The decimal portion of dosages stength determination for the Drug NER profile.
DecimalStrengthAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation_Type: initialize variables to correspond with Cas Type and Features
DecimalStrengthFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect decimal fractions in the given input of tokens.
DecimalStrengthFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.DecimalStrengthFSM: Constructor
DecimalStrengthStatusCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a FractionToken.
DecimalStrengthStatusCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.DecimalStrengthStatusCondition
DecimalStrengthToken - Class in org.apache.ctakes.drugner.fsm.output.util
DecimalStrengthToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.DecimalStrengthToken
DecimalToken - Interface in org.apache.ctakes.core.fsm.token
DecimalTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
DecimalTokenAdapter(NumToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter
DecimalTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter
DecimalTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.DecimalTokenAdapter
DecimalValueCondition - Class in org.apache.ctakes.core.fsm.condition
DecimalValueCondition(double) - Constructor for class org.apache.ctakes.core.fsm.condition.DecimalValueCondition
decorateNominalInstanceWords(Map<Long, SortedMap<String, String>>, Map<String, SortedSet<String>>) - Method in interface org.apache.ctakes.ytex.kernel.BagOfWordsDecorator
decorateNominalInstanceWords(Map<Long, SortedMap<String, String>>, Map<String, SortedSet<String>>) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixArffDecorator: Deprecated.

do nothing
decorateNumericInstanceWords(Map<Long, SortedMap<String, Double>>, SortedSet<String>) - Method in interface org.apache.ctakes.ytex.kernel.BagOfWordsDecorator
decorateNumericInstanceWords(Map<Long, SortedMap<String, Double>>, SortedSet<String>) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixArffDecorator: Deprecated.
DECREASE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
DECREASE_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
DECREASEFROM - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
deepCopy(Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
deepCopy(Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
deepCopy() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo: copy values from other annoMappingInfo
deepCopy() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
DEFAULT_BOTH_DIRECTIONS - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
DEFAULT_CONTEXT_LEN - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances: The parameter name which to ignore
DEFAULT_DOWNSAMPLE - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
DEFAULT_DTD_FILE - Static variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
DEFAULT_EXCLUSION_TAGS - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
DEFAULT_HYPHEN_FILE - Static variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
DEFAULT_LAMBDA - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
DEFAULT_LOOKUP_WINDOW - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
DEFAULT_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
DEFAULT_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
DEFAULT_NAME - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.BrownClusterFeatureFunction
DEFAULT_PRED_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
DEFAULT_ROLE_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
DEFAULT_ROOT_ID - Static variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: the default concept id for the root.
DEFAULT_SECTION_FILE_NAME - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
DEFAULT_SRL_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
DEFAULT_SVM_C - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
DEFAULT_SVM_G - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
DEFAULT_TK - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
defaultAEPath - Static variable in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
defaultCasViewName - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
defaultCasViewName - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
DefaultChunkCreator - Class in org.apache.ctakes.chunker.ae: This chunker creator simply creates annotations of type edu.mayo.bmi.chunker.type.Chunk and sets the chunkType feature of the annotation to the passed in parameter chunkType.
DefaultChunkCreator() - Constructor for class org.apache.ctakes.chunker.ae.DefaultChunkCreator
DefaultCollectionMap<K,V,T extends java.util.Collection<V>> - Class in org.apache.ctakes.dictionary.lookup2.util.collection
DefaultCollectionMap(Map<K, T>, CollectionCreator<V, T>) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
defaultConceptGraphName - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
DefaultDictionarySpec - Class in org.apache.ctakes.dictionary.lookup2.util
DefaultDictionarySpec(Map<String, String>, Map<String, String>, Map<String, RareWordDictionary>, Map<String, ConceptFactory>, TermConsumer) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
defaultExclusionWords - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
defaultForbiddenConceptArr - Static variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: ignore forbidden concepts.
defaultForbiddenConcepts - Static variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
defaultIndexPath - Static variable in class org.apache.ctakes.utils.wiki.WikiIndex
DefaultJCasTermAnnotator - Class in org.apache.ctakes.dictionary.lookup2.ae: A direct string match using phrase permutations Author: SPF Affiliation: CHIP-NLP Date: 11/19/13
DefaultJCasTermAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator
defaultMaxHits - Static variable in class org.apache.ctakes.utils.wiki.WikiIndex
defaultParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
defaultSearchField - Static variable in class org.apache.ctakes.utils.wiki.WikiIndex
defaultSegmentId - Variable in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
DefaultTermConsumer - Class in org.apache.ctakes.dictionary.lookup2.consumer: Author: SPF Affiliation: CHIP-NLP Date: 1/9/14
DefaultTermConsumer(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
DefaultTextSpan - Class in org.apache.ctakes.dictionary.lookup2.textspan: A useful key for hash collections based upon start and end indices.
DefaultTextSpan(int, int) - Constructor for class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan: Given span indices should be ordered start < end, but it is not an absolute requirement.
defaultTreebankMap - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
defaultValue - Variable in enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption
degree - Variable in class org.apache.ctakes.utils.kernel.PolyKernel
degree - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
degree - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
DegreeOf - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between an attribute and an entity/event.
DegreeOf() - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOf: Never called.
DegreeOf(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOf: Internal - constructor used by generator
DegreeOf(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOf
DegreeOf_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between an attribute and an entity/event.
DegreeOf_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOf_Type: initialize variables to correspond with Cas Type and Features
DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies Degree_Of relations between EventMentions and Modifiers.
DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
DegreeOfTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
DegreeOfTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation: Never called.
DegreeOfTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation: Internal - constructor used by generator
DegreeOfTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
DegreeOfTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
DegreeOfTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation_Type: initialize variables to correspond with Cas Type and Features
delegateKernel - Variable in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
delegateKernel - Variable in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
delegateKernel - Variable in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
delegateKernel - Variable in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
delegateKernels - Variable in class org.apache.ctakes.ytex.kernel.evaluator.ProductKernel: use array instead of list.
delegateKernels - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SumKernel
deletableMentions - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
deleteAuiFirstWord() - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao
deleteAuiFirstWord() - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
deleteCrossValidationFoldByName(String, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
deleteCrossValidationFoldByName(String, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
deleteFeatureEval(ImputedFeatureEvaluatorImpl.Parameters, String, int) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: delete the feature evaluations before we insert them
deleteFeatureEvaluation(String, String, String, String, Integer, Double, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
deleteFeatureEvaluation(String, String, String, String, Integer, Double, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
deleteFeatureEvaluationByNameAndType(String, String, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
deleteFeatureEvaluationByNameAndType(String, String, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
Delim - Class in org.apache.ctakes.dependency.parser.util
Delim() - Constructor for class org.apache.ctakes.dependency.parser.util.Delim
DELIMITER - Variable in class org.apache.ctakes.core.resource.StringIntegerMapResourceImpl
DELIMITER - Variable in class org.apache.ctakes.core.resource.StringMapResourceImpl
delimiter - Static variable in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
DEM - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
dem_coref_feats - Static variable in class org.apache.ctakes.coreference.util.FeatureVector
demFeatSet - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
DemMarkable - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
DemMarkable() - Constructor for class org.apache.ctakes.coreference.type.DemMarkable: Never called.
DemMarkable(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.DemMarkable: Internal - constructor used by generator
DemMarkable(JCas) - Constructor for class org.apache.ctakes.coreference.type.DemMarkable
DemMarkable(JCas, int, int) - Constructor for class org.apache.ctakes.coreference.type.DemMarkable
DemMarkable_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
DemMarkable_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.DemMarkable_Type: initialize variables to correspond with Cas Type and Features
Demographics - Class in org.apache.ctakes.typesystem.type.structured: Demographic information about the patient in a clinical document.
Demographics() - Constructor for class org.apache.ctakes.typesystem.type.structured.Demographics: Never called.
Demographics(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.Demographics: Internal - constructor used by generator
Demographics(JCas) - Constructor for class org.apache.ctakes.typesystem.type.structured.Demographics
Demographics_Type - Class in org.apache.ctakes.typesystem.type.structured: Demographic information about the patient in a clinical document.
Demographics_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.Demographics_Type: initialize variables to correspond with Cas Type and Features
demOut - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
demTreeOut - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
DEP_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
DEPENDENCY_FILE_PARAM - Static variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader: "DependencyFile" is a required, single, string parameter that specifies the location of a data file that contains dependency data in it.
DependencyFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
DependencyFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.DependencyFeatureExtractor
DependencyFileCollectionReader - Class in org.apache.ctakes.dependency.parser.cr: This collection reader reads in dependency tree training/test data in a tab- delimited format.
DependencyFileCollectionReader() - Constructor for class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
DependencyNodeWriter - Class in org.apache.ctakes.dependency.parser: CasConsumer that writes a JCas (the current view) to an xml file
DependencyNodeWriter() - Constructor for class org.apache.ctakes.dependency.parser.DependencyNodeWriter
DependencyParseUtils - Class in org.apache.ctakes.relationextractor.ae.features
DependencyParseUtils() - Constructor for class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils
DependencyParseUtils - Class in org.apache.ctakes.temporal.ae.feature: This is a slightly modified version of the same class from relation extraction.
DependencyParseUtils() - Constructor for class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils
DependencyPath - Class in org.apache.ctakes.dependency.parser.util
DependencyPath() - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyPath
DependencyPathFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
DependencyPathFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.DependencyPathFeaturesExtractor
DependencyPathFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
DependencyPathFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor
DependencyPathRegexpFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
DependencyPathRegexpFeatureExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.DependencyPathRegexpFeatureExtractor
DependencyRegex - Class in org.apache.ctakes.dependency.parser.util
DependencyRegex(String, String) - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyRegex
DependencyRegex(DependencyPath, String) - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyRegex
DependencyRegex(String) - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyRegex
DependencyRegex(DEPNode[], int) - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyRegex
DependencyRegex(DEPNode[], int, String) - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyRegex
DependencySingleTreeExtractor - Class in org.apache.ctakes.temporal.ae.feature.treekernel: Given a focused annotation, get the whole sentence-level dependency tree that cover this annotation.
DependencySingleTreeExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.treekernel.DependencySingleTreeExtractor
DependencyTreeFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
DependencyTreeFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor
DependencyUtility - Class in org.apache.ctakes.dependency.parser.util
DependencyUtility() - Constructor for class org.apache.ctakes.dependency.parser.util.DependencyUtility
DependencyWordsFragmentExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
DependencyWordsFragmentExtractor(String, String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.DependencyWordsFragmentExtractor
DependingVerbsFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
DependingVerbsFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor
depFragmentMatch(SimpleTree, SimpleTree, boolean) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
depLca - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
depPath - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
depth - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
depth - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel
depthMax - Variable in class org.apache.ctakes.ytex.kernel.metric.RadaMetric
depthMax - Variable in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
depthMax() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
description() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Returns a String representation of this object, including its type, and all attributes and references.
description - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
description - Variable in class org.apache.ctakes.ytex.ws.SimServiceInfo
destClassName - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
destroy() - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
DeterminerRelationFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature: extract the nearby nearest time, date information for any event
DeterminerRelationFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.DeterminerRelationFeaturesExtractor
determineTokenType(String, int, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
DEV_REMAINDERS - Static variable in class org.apache.ctakes.temporal.eval.THYMEData
devDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
DEVLOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
devSize - Variable in class org.apache.ctakes.relationextractor.data.Splitter
df - Static variable in class org.apache.ctakes.core.util.DateParser
Diagnoses - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
Diagnoses() - Constructor for class org.apache.ctakes.typesystem.type.relation.Diagnoses: Never called.
Diagnoses(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Diagnoses: Internal - constructor used by generator
Diagnoses(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Diagnoses
Diagnoses_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
Diagnoses_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Diagnoses_Type: initialize variables to correspond with Cas Type and Features
DiagnosesTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
DiagnosesTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation: Never called.
DiagnosesTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation: Internal - constructor used by generator
DiagnosesTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation
DiagnosesTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
DiagnosesTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation_Type: initialize variables to correspond with Cas Type and Features
dialect - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
dialectClassName - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
DICTIONARIES_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: XML keys specifying the main sections that define dictionaries, concept factories, and the pairing of the two
Dictionary - Interface in org.apache.ctakes.dictionary.lookup
DICTIONARY_DESCRIPTOR_KEY - Static variable in interface org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator
DictionaryDescriptorParser - Class in org.apache.ctakes.dictionary.lookup2.dictionary: Parses the XML descriptor indicated by the externalResource for DictionaryDescriptorFile in the XML descriptor for the Rare Word Term Lookup Annotator DefaultJCasTermAnnotator
DictionaryDescriptorParser() - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: A Utility Class cannot be instantiated
DictionaryEngine - Class in org.apache.ctakes.dictionary.lookup: The engine adds additional functionality to executing a dictionary.
DictionaryEngine(Dictionary, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.DictionaryEngine
DictionaryException - Exception in org.apache.ctakes.dictionary.lookup
DictionaryException(Throwable) - Constructor for exception org.apache.ctakes.dictionary.lookup.DictionaryException
DictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae: UIMA annotator that identified entities based on lookup.
DictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
DictionaryLookupFactory - Class in org.apache.ctakes.dictionary.lookup2.ae
DictionaryLookupFactory() - Constructor for class org.apache.ctakes.dictionary.lookup2.ae.DictionaryLookupFactory
dictionaryPath - Variable in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
DictionarySpec - Interface in org.apache.ctakes.dictionary.lookup2.util: Simple Container class that holds a RareWordDictionary collection, a a ConceptFactory and a TermConsumer
differ(int, int) - Method in class org.apache.ctakes.coreference.util.ParentPtrTree
difference(Map<T, Double>, Map<T, Double>) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl: difference between 2 vectors
difference(double[], double[]) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
dimensionality - Variable in class org.apache.ctakes.utils.distsem.WordEmbeddings
dimensionality - Variable in class org.apache.ctakes.utils.distsem.WordVectorReader
dir - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
DirectLookupInitializerImpl - Class in org.apache.ctakes.dictionary.lookup.ae
DirectLookupInitializerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl
directoryOfDelimitedFiles - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
DirectPassThroughImpl - Class in org.apache.ctakes.dictionary.lookup.algorithms: Each individual LookupToken is referenced against a Dictionary.
DirectPassThroughImpl(DictionaryEngine, PhraseBuilder) - Constructor for class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl: Constructor
dirWithGoldViews - Static variable in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
DISABLED - Static variable in class org.apache.ctakes.jdl.data.loader.CsvLoader: copied from CSVStrategy
disabled - Variable in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
disambiguate(List<Set<String>>, int, Set<String>, int, ConceptSimilarityService.SimilarityMetricEnum, Map<String, Double>) - Method in interface org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguator
disambiguate(List<Set<String>>, int, Set<String>, int, ConceptSimilarityService.SimilarityMetricEnum, Map<String, Double>, boolean) - Method in interface org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguator: Disambiguate a named entity.
disambiguate(List<Set<String>>, int, Set<String>, int, ConceptSimilarityService.SimilarityMetricEnum, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
disambiguate(List<Set<String>>, int, Set<String>, int, ConceptSimilarityService.SimilarityMetricEnum, Map<String, Double>, boolean) - Method in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
disambiguate(JCas, List<IdentifiedAnnotation>) - Method in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
disassemble(Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
disassemble(Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
discardedFeatureNames - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
discardedFeatureNames - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
discontVerb - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
DISCUSSION_DEPPATH - Static variable in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
DISCUSSION_DEPPATH - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
DiseaseDisorder - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Disorders (except that Sign and Symptom types are separate).
DiseaseDisorder() - Constructor for class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: Never called.
DiseaseDisorder(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: Internal - constructor used by generator
DiseaseDisorder(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder
DiseaseDisorder_Type - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Disorders (except that Sign and Symptom types are separate).
DiseaseDisorder_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type: initialize variables to correspond with Cas Type and Features
DiseaseDisorderMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (DiseaseDisorder) Event.
DiseaseDisorderMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: Never called.
DiseaseDisorderMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: Internal - constructor used by generator
DiseaseDisorderMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
DiseaseDisorderMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
DiseaseDisorderMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (DiseaseDisorder) Event.
DiseaseDisorderMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type: initialize variables to correspond with Cas Type and Features
DisjoinCondition - Class in org.apache.ctakes.core.fsm.condition
DisjoinCondition(Condition, Condition) - Constructor for class org.apache.ctakes.core.fsm.condition.DisjoinCondition
DISO - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
DISO_TUIS - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
DISORDER_ANNOTATIONS - Static variable in class org.apache.ctakes.core.ae.FilterAnnotator
DISORDER_TUIS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
displayContext - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
displayEntities - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
displayError(String) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Displays an error message to the user.
displayError(Throwable) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Displays an error message to the user.
displayError(String) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Displays an error message to the user.
displayError(Throwable) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Displays an error message to the user.
distance(String, String) - Static method in class org.apache.ctakes.coreference.util.EditDistance
distance(String, String, boolean) - Static method in class org.apache.ctakes.coreference.util.EditDistance
DISTANCE - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
distance - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
DISTANCE_ANN_TYPE - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Annotation type that is used to count the distance.
distanceFromRoot(ConllDependencyNode) - Static method in class org.apache.ctakes.assertion.util.AssertionDepUtils
distanceFromRoot(ConllDependencyNode) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
distanceFromRoot(SimpleTree) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
DistanceMetrics - Class in org.apache.ctakes.utils.distsem
DistanceMetrics() - Constructor for class org.apache.ctakes.utils.distsem.DistanceMetrics
DN_ARC_A - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
DN_ARC_A - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
DN_ARC_A - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
DN_ARC_B - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
DN_ARC_B - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
DN_ARC_B - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
DOC_TIME_PATTERN - Static variable in class org.apache.ctakes.temporal.data.analysis.PrintFailedTimeNormalizations
DOC_TIME_REL - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
DOC_TIME_REL - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
docColType - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
docColTypeName - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
docCtr - Variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
docIdColNames - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
docIdDelimiter - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
DocKey - Class in org.apache.ctakes.ytex.uima.types: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
DocKey() - Constructor for class org.apache.ctakes.ytex.uima.types.DocKey: Never called.
DocKey(int, TOP_Type) - Constructor for class org.apache.ctakes.ytex.uima.types.DocKey: Internal - constructor used by generator
DocKey(JCas) - Constructor for class org.apache.ctakes.ytex.uima.types.DocKey
DocKey(JCas, int, int) - Constructor for class org.apache.ctakes.ytex.uima.types.DocKey
DocKey_Type - Class in org.apache.ctakes.ytex.uima.types: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
DocKey_Type(JCas, Type) - Constructor for class org.apache.ctakes.ytex.uima.types.DocKey_Type: initialize variables to correspond with Cas Type and Features
docLengthMap - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: for tf-idf, length of each instance
docLinkId - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
docName - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
docNum - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
docPredImport(String, String) - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults
docResultInstanceImporter - Variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl: this imports the classification results for a document
docRevision - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
docs - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
docTableCols - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
docText - Variable in class org.apache.ctakes.ytex.uima.model.Document: document plain text
docText - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
docText - Variable in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
docTextColName - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
DocTimeRelAnnotator - Class in org.apache.ctakes.temporal.ae
DocTimeRelAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
DocTimeRelFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
DocTimeRelFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.DocTimeRelFeatureExtractor
document - Variable in class org.apache.ctakes.jdl.data.xml.Validation
Document - Class in org.apache.ctakes.ytex.uima.model: Mapped to document table.
Document() - Constructor for class org.apache.ctakes.ytex.uima.model.Document
document - Variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
document - Variable in class org.apache.ctakes.ytex.uima.model.DocumentClass
DocumentAnnotation - Class in org.apache.ctakes.ytex.uima.model: Mapped to uima Annotation.
DocumentAnnotation() - Constructor for class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
DocumentAnnotation(UimaType, Document) - Constructor for class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
documentAnnotationID - Variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
documentAnnotations - Variable in class org.apache.ctakes.ytex.uima.model.Document
DocumentClass - Class in org.apache.ctakes.ytex.uima.model: Mapped to document_class.
DocumentClass() - Constructor for class org.apache.ctakes.ytex.uima.model.DocumentClass
documentClasses - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: Map of instance id to class label
documentClasses - Variable in class org.apache.ctakes.ytex.uima.model.Document
documentClassID - Variable in class org.apache.ctakes.ytex.uima.model.DocumentClass
DocumentClassification - Class in org.apache.ctakes.typesystem.type.structured: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
DocumentClassification() - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentClassification: Never called.
DocumentClassification(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentClassification: Internal - constructor used by generator
DocumentClassification(JCas) - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentClassification
DocumentClassification_Type - Class in org.apache.ctakes.typesystem.type.structured: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
DocumentClassification_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type: initialize variables to correspond with Cas Type and Features
DocumentDao - Interface in org.apache.ctakes.ytex.uima.dao: DAO interface for accessing Document objects.
DocumentDaoImpl - Class in org.apache.ctakes.ytex.uima.dao
DocumentDaoImpl() - Constructor for class org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl
documentDate - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
DocumentID - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
DocumentID() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID: Never called.
DocumentID(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID: Internal - constructor used by generator
DocumentID(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID
DocumentID(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID
DocumentID - Class in org.apache.ctakes.typesystem.type.structured: Equivalent to cTAKES: org.apache.ctakes.typesystem.type.DocumentID, but its supertype changed to uima.cas.TOP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
DocumentID() - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentID: Never called.
DocumentID(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentID: Internal - constructor used by generator
DocumentID(JCas) - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentID
documentID - Variable in class org.apache.ctakes.ytex.uima.model.Document: the document id
documentID - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
documentID - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
documentID - Variable in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
DocumentID_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
DocumentID_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type: initialize variables to correspond with Cas Type and Features
DocumentID_Type - Class in org.apache.ctakes.typesystem.type.structured: Equivalent to cTAKES: org.apache.ctakes.typesystem.type.DocumentID, but its supertype changed to uima.cas.TOP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
DocumentID_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.DocumentID_Type: initialize variables to correspond with Cas Type and Features
DocumentIDAnnotationUtil - Class in org.apache.ctakes.core.util
DocumentIDAnnotationUtil() - Constructor for class org.apache.ctakes.core.util.DocumentIDAnnotationUtil
documentIDField - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
documentIDField - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
DocumentIdPrinterAnalysisEngine - Class in org.apache.ctakes.core.ae
DocumentIdPrinterAnalysisEngine() - Constructor for class org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine
documentMapperService - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
DocumentMapperService - Interface in org.apache.ctakes.ytex.uima.mapper
DocumentMapperServiceImpl - Class in org.apache.ctakes.ytex.uima.mapper: Map document annotations to the database.
DocumentMapperServiceImpl() - Constructor for class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
DocumentMapperServiceImpl.AnnoFSAttribute - Class in org.apache.ctakes.ytex.uima.mapper: holder for FeatureStruct attributes
DocumentMapperServiceImpl.AnnoFSAttribute() - Constructor for class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
DocumentMapperServiceImpl.AnnoFSAttribute(int, FeatureStructure, Integer) - Constructor for class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
DocumentMapperServiceImpl.AnnoLink - Class in org.apache.ctakes.ytex.uima.mapper
DocumentMapperServiceImpl.AnnoLink(int, int, String) - Constructor for class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
DocumentMapperServiceImpl.ChunkPreparedStatementSetter<T> - Interface in org.apache.ctakes.ytex.uima.mapper
DocumentMetaData - Class in org.apache.ctakes.preprocessor
DocumentMetaData() - Constructor for class org.apache.ctakes.preprocessor.DocumentMetaData
DocumentResultInstanceImporter - Class in org.apache.ctakes.ytex.weka
DocumentResultInstanceImporter() - Constructor for class org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter
documentScore - Variable in class org.apache.ctakes.utils.wiki.SearchResult
DocumentSearchResult - Class in org.apache.ctakes.ytex.web.search: Encapsulates document search results
DocumentSearchResult(int, String, Date, String, String, String) - Constructor for class org.apache.ctakes.ytex.web.search.DocumentSearchResult
DocumentSearchResult() - Constructor for class org.apache.ctakes.ytex.web.search.DocumentSearchResult
DocumentSearchService - Interface in org.apache.ctakes.ytex.web.search: Service for searching documents.
documentSearchService - Variable in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
documentSearchService - Variable in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
documentSearchService - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
DocumentSearchServiceImpl - Class in org.apache.ctakes.ytex.web.search
DocumentSearchServiceImpl() - Constructor for class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
DocumentSearchServiceImpl.DocumentSearchResultMapper - Class in org.apache.ctakes.ytex.web.search
DocumentSearchServiceImpl.DocumentSearchResultMapper() - Constructor for class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl.DocumentSearchResultMapper
DocumentSection - Class in org.apache.ctakes.core.util: Class containing relevant information for a given document section
DocumentSection(int, int, String) - Constructor for class org.apache.ctakes.core.util.DocumentSection
documentTitle - Variable in class org.apache.ctakes.utils.wiki.SearchResult
documentTitle - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
documentTypeName - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
DocumentViewBean - Class in org.apache.ctakes.ytex.web.search: JSF bean for viewing a document retrieved via semanticSearch.jspx.
DocumentViewBean() - Constructor for class org.apache.ctakes.ytex.web.search.DocumentViewBean
doesSubsume(Annotation, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Checks if one annotation subsumes another
doEventEvent - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
doEventTime - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
dom - Variable in class org.apache.ctakes.jdl.data.xml.DomParser
DOMAIN_ADAPTATION_ALGORITHM - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction
domainIds - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction
dominates(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
DomParser - Class in org.apache.ctakes.jdl.data.xml: To parse DOM.
DomParser(String) - Constructor for class org.apache.ctakes.jdl.data.xml.DomParser
domSucceed() - Method in class org.apache.ctakes.jdl.data.xml.Validation
DomUtil - Class in org.apache.ctakes.jdl.data.xml: Utility to manage DOM.
DomUtil() - Constructor for class org.apache.ctakes.jdl.data.xml.DomUtil
DONOR_DEPPATH - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
DONOR_DEPTOK - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
DONOR_OR - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
DONOR_SRLARG - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
DONOR_TOKEN - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
dosage - Variable in class org.apache.ctakes.drugner.DrugMention: e.g.
DosageCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a DosageToken.
DosageCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.DosageCondition
DosageElement - Class in org.apache.ctakes.drugner.elements
DosageElement() - Constructor for class org.apache.ctakes.drugner.elements.DosageElement
DosageElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.DosageElement
DosagesAnnotation - Class in org.apache.ctakes.drugner.type: The dosage determination for the Drug NER profile.
DosagesAnnotation() - Constructor for class org.apache.ctakes.drugner.type.DosagesAnnotation: Never called.
DosagesAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.DosagesAnnotation: Internal - constructor used by generator
DosagesAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.DosagesAnnotation
DosagesAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.DosagesAnnotation
DosagesAnnotation_Type - Class in org.apache.ctakes.drugner.type: The dosage determination for the Drug NER profile.
DosagesAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.DosagesAnnotation_Type: initialize variables to correspond with Cas Type and Features
DosagesFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect dosages in the given input of tokens.
DosagesFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM: Constructor
DosageToken - Class in org.apache.ctakes.drugner.fsm.output.elements
DosageToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.DosageToken
doseage - Variable in class org.apache.ctakes.drugner.elements.DosageElement
DOT_LOGGER - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
DOT_LOGGER - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
dotPattern - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
dotProd(svm_node[], svm_node[]) - Static method in class org.apache.ctakes.utils.kernel.Kernel
doubleFormat - Static variable in class org.apache.ctakes.ytex.kernel.IRMetrics
driver - Variable in class org.apache.ctakes.jdl.data.base.JdlConnection
DRUG - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
drug - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.PotentialSideEffect
DRUG_TUIS - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
drugChange - Variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
DrugChangeStatusAnnotation - Class in org.apache.ctakes.drugner.type: The change status of dosages determination for the Drug NER profile.
DrugChangeStatusAnnotation() - Constructor for class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation: Never called.
DrugChangeStatusAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation: Internal - constructor used by generator
DrugChangeStatusAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation
DrugChangeStatusAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation
DrugChangeStatusAnnotation_Type - Class in org.apache.ctakes.drugner.type: The change status of dosages determination for the Drug NER profile.
DrugChangeStatusAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type: initialize variables to correspond with Cas Type and Features
DrugChangeStatusCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a DrugChangeStatusToken.
DrugChangeStatusCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.DrugChangeStatusCondition
DrugChangeStatusElement - Class in org.apache.ctakes.drugner.elements
DrugChangeStatusElement() - Constructor for class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
DrugChangeStatusElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
DrugChangeStatusFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect change status data in the given input of tokens.
DrugChangeStatusFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Constructor
DrugChangeStatusToken - Class in org.apache.ctakes.drugner.fsm.output.elements
DrugChangeStatusToken(int, int, String) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
drugHeaders - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
DrugLookupWindowAnnotation - Class in org.apache.ctakes.typesystem.type.textspan: Similar to LookupWindowAnnotation however, these annotations are restricted to the segments/sections specified in the parameter - sectionOverrideSet - in DrugCNP2LookupWindow Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-drug-ner/target/jcasgen/typesystem.xml
DrugLookupWindowAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation: Never called.
DrugLookupWindowAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation: Internal - constructor used by generator
DrugLookupWindowAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation
DrugLookupWindowAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation
DrugLookupWindowAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textspan: Similar to LookupWindowAnnotation however, these annotations are restricted to the segments/sections specified in the parameter - sectionOverrideSet - in DrugCNP2LookupWindow Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015
DrugLookupWindowAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation_Type: initialize variables to correspond with Cas Type and Features
DrugMention - Class in org.apache.ctakes.drugner: Contains information from a single document - is not the result of data mining.
DrugMention(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.DrugMention
DrugMentionAnnotation - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-drug-ner/target/jcasgen/typesystem.xml
DrugMentionAnnotation() - Constructor for class org.apache.ctakes.drugner.type.DrugMentionAnnotation: Never called.
DrugMentionAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.DrugMentionAnnotation: Internal - constructor used by generator
DrugMentionAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.DrugMentionAnnotation
DrugMentionAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.DrugMentionAnnotation
DrugMentionAnnotation_Type - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015
DrugMentionAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type: initialize variables to correspond with Cas Type and Features
DrugMentionAnnotator - Class in org.apache.ctakes.drugner.ae: Finds tokens based on context.
DrugMentionAnnotator() - Constructor for class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
drugMentionText - Variable in class org.apache.ctakes.drugner.DrugMention: The word(s) in the note that indicate the drug.
DrugModel - Interface in org.apache.ctakes.drugner
drugName - Variable in class org.apache.ctakes.drugner.elements.TextMentionElement
dtdfilepath - Variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
DTDloader - Class in org.apache.ctakes.preprocessor: Use to load DTD from classpath.
DTDloader(InputStream) - Constructor for class org.apache.ctakes.preprocessor.DTDloader
dumpCache() - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath
dumpDependencyGraph(Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
dumpDependencyRelations(JCas, Annotation) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils
dumpDependencyRelations(JCas, Annotation) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils
dumpSRLOutput(Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.SRLUtility
duration - Variable in class org.apache.ctakes.drugner.DrugMention: e.g.
duration - Variable in class org.apache.ctakes.drugner.elements.DurationElement
DurationAnnotation - Class in org.apache.ctakes.drugner.type: The duration determination for the Drug NER profile.
DurationAnnotation() - Constructor for class org.apache.ctakes.drugner.type.DurationAnnotation: Never called.
DurationAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.DurationAnnotation: Internal - constructor used by generator
DurationAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.DurationAnnotation
DurationAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.DurationAnnotation
DurationAnnotation_Type - Class in org.apache.ctakes.drugner.type: The duration determination for the Drug NER profile.
DurationAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.DurationAnnotation_Type: initialize variables to correspond with Cas Type and Features
DurationDistributionFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature.duration
DurationDistributionFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.duration.DurationDistributionFeatureExtractor
durationDistributionPath - Static variable in class org.apache.ctakes.temporal.duration.Utils
DurationElement - Class in org.apache.ctakes.drugner.elements
DurationElement() - Constructor for class org.apache.ctakes.drugner.elements.DurationElement
DurationElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.DurationElement
DurationEventEventFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature.duration
DurationEventEventFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.duration.DurationEventEventFeatureExtractor
DurationEventTimeFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature.duration: Calculate probability that CONTAINS relation can exist between two arguments.
DurationEventTimeFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.duration.DurationEventTimeFeatureExtractor
DurationExpectationFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature.duration
DurationExpectationFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.duration.DurationExpectationFeatureExtractor
DurationFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect duration data in the given input of tokens.
DurationFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM: Constructor
DurationTimeUnitFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature.duration: Assumes all relations whose argument have no duration data have been deleted.
DurationTimeUnitFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.duration.DurationTimeUnitFeatureExtractor
DurationToken - Class in org.apache.ctakes.drugner.fsm.output.elements
DurationToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.DurationToken
DYNAMIC_VALIDATION_FEATURE_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Dynamic validation feature id (http://apache.org/xml/features/validation/dynamic).

E

EditDistance - Class in org.apache.ctakes.coreference.util
EditDistance() - Constructor for class org.apache.ctakes.coreference.util.EditDistance
Element - Class in org.apache.ctakes.typesystem.type.refsem: A basic semantic unit that refers to something in the real world, including Entities, Events, Attributes, Dates.
Element() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Element: Never called.
Element(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Element: Internal - constructor used by generator
Element(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Element
Element_Type - Class in org.apache.ctakes.typesystem.type.refsem: A basic semantic unit that refers to something in the real world, including Entities, Events, Attributes, Dates.
Element_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Element_Type: initialize variables to correspond with Cas Type and Features
ElementRelation - Class in org.apache.ctakes.typesystem.type.relation: A super-type referring to real-world semantic relationships, e.g., TemporalRelations between two Events.
ElementRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.ElementRelation: Never called.
ElementRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ElementRelation: Internal - constructor used by generator
ElementRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ElementRelation
ElementRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A super-type referring to real-world semantic relationships, e.g., TemporalRelations between two Events.
ElementRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type: initialize variables to correspond with Cas Type and Features
elevateAdjectives(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
elevateListConcepts(JCas, TreebankNode) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
ELIXIR - Static variable in class org.apache.ctakes.drugner.elements.FormElement
ellipsis - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
EmbeddingFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
EmbeddingFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.EmbeddingFeatureExtractor
embeddingPath - Static variable in class org.apache.ctakes.relationextractor.data.analysis.Utils
embeddings - Variable in class org.apache.ctakes.utils.distsem.WordVectorReader
EMPTY_COLLECTION - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
EMPTY_CONCEPT_FACTORY - Static variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
EMPTY_DICTIONARY - Static variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
EMPTY_FEATURE_ARRAY - Static variable in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
EMPTY_ITERATOR - Static variable in class org.apache.ctakes.temporal.utils.TlinkTypeSet
EMPTY_OBJECT_ARRAY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
EmptyFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
EmptyFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EmptyFeaturesExtractor
emptyStringList - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
emptyTokenList - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
EMULSION - Static variable in class org.apache.ctakes.drugner.elements.FormElement
end - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
end - Variable in class org.apache.ctakes.assertion.cr.Span
end - Variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact.Span
end - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
end - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation.Span: The offset immediately after the last character in the text span.
end - Variable in class org.apache.ctakes.core.sentence.SentenceSpan
end - Variable in class org.apache.ctakes.preprocessor.IntegerRange
end - Variable in class org.apache.ctakes.relationextractor.knowtator.Span
end - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator.SideEffect
end - Variable in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
end - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
end - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
end - Variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
END_A - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
END_B - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
END_LARGEST - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
END_SMALLEST - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
endDate - Variable in class org.apache.ctakes.drugner.DrugMention
endDocument() - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
endElement(String, String, String) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
endElement(String, String, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
endLine - Variable in class org.apache.ctakes.core.util.DocumentSection
endMatch(String, String) - Static method in class org.apache.ctakes.coreference.util.TextMatch
endOff - Variable in class org.apache.ctakes.drugner.elements.AssociatedCodeElement
endOff - Variable in class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
endOff - Variable in class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
endOff - Variable in class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
endOff - Variable in class org.apache.ctakes.drugner.elements.DosageElement
endOff - Variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
endOff - Variable in class org.apache.ctakes.drugner.elements.DurationElement
endOff - Variable in class org.apache.ctakes.drugner.elements.FormElement
endOff - Variable in class org.apache.ctakes.drugner.elements.FrequencyElement
endOff - Variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
endOff - Variable in class org.apache.ctakes.drugner.elements.RouteElement
endOff - Variable in class org.apache.ctakes.drugner.elements.StartDateElement
endOff - Variable in class org.apache.ctakes.drugner.elements.StrengthElement
endOff - Variable in class org.apache.ctakes.drugner.elements.StrengthUnitElement
endOff - Variable in class org.apache.ctakes.drugner.elements.TextMentionElement
endOffset - Variable in class org.apache.ctakes.preprocessor.Annotation
EndOfSentenceScannerImpl - Class in org.apache.ctakes.core.sentence: End of Sentence scanner with more candidate end-of-sentence characters than the default.
EndOfSentenceScannerImpl() - Constructor for class org.apache.ctakes.core.sentence.EndOfSentenceScannerImpl
ENEMA - Static variable in class org.apache.ctakes.drugner.elements.FormElement
ENG_LEMMATIZER_DATA_FILE - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
enter(Object) - Method in class org.apache.ctakes.core.fsm.state.NamedState
enter(Object) - Method in class org.apache.ctakes.core.fsm.state.NonTerminalEndState
enter(Object) - Method in class org.apache.ctakes.drugner.fsm.states.util.IndentStartState
Entity - Class in org.apache.ctakes.typesystem.type.refsem: A real-world entity such as a body part.
Entity() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Entity: Never called.
Entity(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Entity: Internal - constructor used by generator
Entity(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Entity
Entity_Type - Class in org.apache.ctakes.typesystem.type.refsem: A real-world entity such as a body part.
Entity_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Entity_Type: initialize variables to correspond with Cas Type and Features
entityChunking - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
entityCount - Variable in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
entityCount - Variable in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl
entityCoveredText - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
entityFeatureExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
EntityMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to an Entity.
EntityMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.EntityMention: Never called.
EntityMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EntityMention: Internal - constructor used by generator
EntityMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EntityMention
EntityMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EntityMention
EntityMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to an Entity.
EntityMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type: initialize variables to correspond with Cas Type and Features
entityMentionCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
entityMentionPairCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
entityMentionPairTypes - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
entityProcessComplete(CAS, EntityProcessStatus) - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
entityProcessComplete(CAS, EntityProcessStatus) - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the processing of a Document is completed.
EntitySpanFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that indicate whether both arguments are contained within an NP.
EntitySpanFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.EntitySpanFeatureExtractor
entityTreeExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
entropy(double[]) - Static method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
entropy(Iterable<Double>) - Static method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: calculate entropy from a list/array of probabilities
entropyX - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: the entropy of X.
entropyXY - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: the entropy of X*Y.
entrySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
entrySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
entrySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
entrySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
entrySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
EnumSetMap<K extends java.lang.Enum<K>,V> - Class in org.apache.ctakes.dictionary.lookup2.util.collection
EnumSetMap(Class<K>) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
EnvironmentVariable - Class in org.apache.ctakes.utils.env
EnvironmentVariable() - Constructor for class org.apache.ctakes.utils.env.EnvironmentVariable
EO - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
EOL_LOGGER - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
EOL_LOGGER - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
EolToken - Interface in org.apache.ctakes.core.fsm.token
eosCandidates - Static variable in class org.apache.ctakes.core.sentence.EndOfSentenceScannerImpl
EQ_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
EQ_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
equalCoverage(Annotation, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.ClearDependencyUtility: Equality expressions to aid in converting between DepNodes and CAS objects
equalCoverage(Annotation, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Equality expressions to aid in converting between DepNodes and CAS objects
EqualityKernel - Class in org.apache.ctakes.ytex.kernel.evaluator
EqualityKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.EqualityKernel
equals(Object) - Method in class org.apache.ctakes.assertion.cr.RelationInfo
equals(Object) - Method in class org.apache.ctakes.assertion.cr.Span
equals(Object) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact.Span
equals(Object) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
equals(Object) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CuePhrase
equals(Object) - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
equals(Object) - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation
equals(Object) - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation.Span
equals(Object) - Method in class org.apache.ctakes.coreference.eval.helpers.Span
equals(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit: Two MetaDataHits are equal if their Meta field name/value pairs are equal.
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupHitKey
equals(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl: Deprecated.

Two MetaDataHits are equal if their Meta field name/value pairs are equal.
equals(MetaDataHit) - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit: Override default equals method.
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm: Override default equals method.
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
equals(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken: Two lookup tokens are equal iff the spans are equal.
equals(Object) - Method in class org.apache.ctakes.relationextractor.eval.ParameterSettings
equals(Object) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
equals(Object) - Method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
equals(Object) - Method in class org.apache.ctakes.relationextractor.knowtator.Span
equals(FeatureStructure, FeatureStructure) - Method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures.FeatureStructureEqualizer
equals(FeatureStructure, FeatureStructure, List<FeatureStructure>) - Method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures.FeatureStructureEqualizer
equals(Object) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Determines whether the specified object equals to this one.
equals(Object) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
equals(Object) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Checks whether the specified object has the same set of annotations.
equals(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
equals(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.OrderedPair
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.Pair
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.tree.Node
equals(Object) - Method in class org.apache.ctakes.ytex.kernel.tree.NodeKey
equals(Object) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
equals(Object) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
equals(Object) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
equals(Object) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
equals(Object) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
equals(Object) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
equals(Object) - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
equals(Object) - Method in class org.apache.ctakes.ytex.uima.model.UimaType
equals(Object) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
equals(Object) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
equals(Object) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
equivCls(int[]) - Method in class org.apache.ctakes.coreference.util.ParentPtrTree
error - Variable in class org.apache.ctakes.jdl.data.xml.Validation
error(String, String) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
errorFlag - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
es1 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
es2 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
escapeBegin - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
escapeCat(String) - Static method in class org.apache.ctakes.utils.tree.SimpleTree
escapeEnd - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
eval(Object, Object) - Method in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
eval(Object, Object) - Method in class org.apache.ctakes.utils.kernel.Kernel
eval(Object, Object) - Method in class org.apache.ctakes.utils.kernel.PolyKernel
eval(Object, Object) - Method in class org.apache.ctakes.utils.kernel.RBFKernel
evalInstance(Map<Long, Node>, KernelEvaluation, long, SortedSet<Long>) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
evalKernel(ApplicationContext, CommandLine) - Static method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
evalOnly - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
evalOutputDir - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
evalTest - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.SliceEvaluator
evaluate(SHARPXMI.EvaluationOptions, ParameterSettings, List<ParameterSettings>, <any>) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.AttributeProductKernel
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel: c1 and c2 must be Nodes.
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.EqualityKernel
evaluate(Object, Object) - Method in interface org.apache.ctakes.ytex.kernel.evaluator.Kernel
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NamedEntityNegationKernel
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel: override CacheKernel - don't bother caching evaluation if the concepts are not in the conceptFilter, or if they are identical.
evaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
evaluateAttributes(String, String, String, Instances, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl: evaluate attributes, store in db
evaluateAttributesFromFile(String, String, String, String) - Method in interface org.apache.ctakes.ytex.weka.WekaAttributeEvaluator: evaluate attributes in an arff file, save rank in db
evaluateAttributesFromFile(String, String, String, String) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
evaluateAttributesFromProps(String, String, String, Properties) - Method in interface org.apache.ctakes.ytex.weka.WekaAttributeEvaluator: create instances from properties file, evaluate, save in db
evaluateAttributesFromProps(String, String, String, Properties) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
evaluateCorpus(String) - Method in interface org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator
evaluateCorpus(ImputedFeatureEvaluatorImpl.Parameters) - Method in interface org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator
evaluateCorpus(ImputedFeatureEvaluatorImpl.Parameters) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
evaluateCorpus(String) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
evaluateCorpusFold(ImputedFeatureEvaluatorImpl.Parameters, Map<String, Set<Long>>, ConceptGraph, InstanceData, String, Map<String, Map<String, Set<Long>>>, int) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
evaluateCorpusInfoContent(String, String, String, String) - Method in interface org.apache.ctakes.ytex.kernel.InfoContentEvaluator: calculate information content for all concepts
evaluateCorpusInfoContent(String, String, String, String) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
evaluateCorpusLabel(ImputedFeatureEvaluatorImpl.Parameters, ConceptGraph, InstanceData, String) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: evaluate corpus on label
evaluateIntrinsicInfoContent(Properties) - Method in interface org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluator
evaluateIntrinsicInfoContent(String, String, ConceptGraph) - Method in interface org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluator
evaluateIntrinsicInfoContent(Properties) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
evaluateIntrinsicInfoContent(String, String, ConceptGraph) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
evaluateKernelOnCorpus() - Method in interface org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluator
evaluateKernelOnCorpus(Map<Long, Node>, int, int, boolean) - Method in interface org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluator
evaluateKernelOnCorpus(Map<Long, Node>, int, boolean) - Method in interface org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluator
evaluateKernelOnCorpus() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
evaluateKernelOnCorpus(Map<Long, Node>, int, boolean) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
evaluateKernelOnCorpus(Map<Long, Node>, int, int, boolean) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
evaluation - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureRank
Evaluation_ImplBase<STATISTICS_TYPE> - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File) - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
Evaluation_ImplBase.CopyFromGold - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.CopyFromGold() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyFromGold
Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations
Evaluation_ImplBase.EntityMentionRemover - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.EntityMentionRemover() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.EntityMentionRemover
Evaluation_ImplBase.EventMentionRemover - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.EventMentionRemover() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.EventMentionRemover
Evaluation_ImplBase.Options - Interface in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.RemoveEnclosedLookupWindows - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.RemoveEnclosedLookupWindows() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows
Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator
Evaluation_ImplBase.Subcorpus - Enum in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.Subcorpus() - Constructor for enum org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Subcorpus
Evaluation_ImplBase.TimexAnnotationCorrector - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.TimexAnnotationCorrector() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.TimexAnnotationCorrector
Evaluation_ImplBase.UriToDocumentTextAnnotatorCtakes - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.UriToDocumentTextAnnotatorCtakes() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.UriToDocumentTextAnnotatorCtakes
Evaluation_ImplBase.WriteAnaforaXML - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.WriteAnaforaXML() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML
Evaluation_ImplBase.WriteI2B2XML - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.WriteI2B2XML() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML
Evaluation_ImplBase.XMIReader - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.XMIReader() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader
Evaluation_ImplBase.XMIWriter - Class in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.XMIWriter() - Constructor for class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIWriter
Evaluation_ImplBase.XMLFormat - Enum in org.apache.ctakes.temporal.eval
Evaluation_ImplBase.XMLFormat() - Constructor for enum org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat
evaluationLogFile - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
evaluationLogFileOut - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
evaluationLogFilePath - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
EvaluationOfAnnotationSpans_ImplBase - Class in org.apache.ctakes.temporal.eval
EvaluationOfAnnotationSpans_ImplBase(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, Class<? extends Annotation>) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
EvaluationOfAnnotationSpans_ImplBase(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, Class<? extends Annotation>) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
EvaluationOfBothEEAndETRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, boolean, boolean, boolean, String, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
EvaluationOfBothEEAndETRelations.AddClosure - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.AddClosure() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddClosure
EvaluationOfBothEEAndETRelations.AddContain2Overlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.AddContain2Overlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddContain2Overlap
EvaluationOfBothEEAndETRelations.AddFlippedOverlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.AddFlippedOverlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddFlippedOverlap
EvaluationOfBothEEAndETRelations.AddTransitiveContainsRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.AddTransitiveContainsRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddTransitiveContainsRelations
EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations
EvaluationOfBothEEAndETRelations.RemoveNonTLINKRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.RemoveNonTLINKRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveNonTLINKRelations
EvaluationOfBothEEAndETRelations.RemoveNonUMLSEvents - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.RemoveNonUMLSEvents() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveNonUMLSEvents
EvaluationOfBothEEAndETRelations.RemoveRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfBothEEAndETRelations.RemoveRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveRelations
EvaluationOfBothEEAndETRelations.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfClearTKEventProperties - Class in org.apache.ctakes.temporal.eval
EvaluationOfClearTKEventProperties(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
EvaluationOfClearTKEventProperties.ClearEventProperties - Class in org.apache.ctakes.temporal.eval
EvaluationOfClearTKEventProperties.ClearEventProperties() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties.ClearEventProperties
EvaluationOfClearTKEventSpans - Class in org.apache.ctakes.temporal.eval
EvaluationOfClearTKEventSpans(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
EvaluationOfClearTKRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfClearTKRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
EvaluationOfClearTKRelations.EvalOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfClearTKTimeSpans - Class in org.apache.ctakes.temporal.eval
EvaluationOfClearTKTimeSpans(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
EvaluationOfEventEventRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, boolean, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventRelations
EvaluationOfEventEventThymeRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, boolean, boolean, boolean, String, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
EvaluationOfEventEventThymeRelations.AddClosure - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.AddClosure() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddClosure
EvaluationOfEventEventThymeRelations.AddContain2Overlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.AddContain2Overlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddContain2Overlap
EvaluationOfEventEventThymeRelations.AddEEPotentialRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.AddEEPotentialRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations
EvaluationOfEventEventThymeRelations.AddFlippedOverlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.AddFlippedOverlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddFlippedOverlap
EvaluationOfEventEventThymeRelations.AddTransitiveContainsRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.AddTransitiveContainsRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddTransitiveContainsRelations
EvaluationOfEventEventThymeRelations.CountCloseRelation - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.CountCloseRelation() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.CountCloseRelation
EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations
EvaluationOfEventEventThymeRelations.RemoveNonUMLSEvents - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.RemoveNonUMLSEvents() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveNonUMLSEvents
EvaluationOfEventEventThymeRelations.RemoveRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventEventThymeRelations.RemoveRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveRelations
EvaluationOfEventEventThymeRelations.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfEventProperties - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventProperties(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
EvaluationOfEventProperties.ClearEventProperties - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventProperties.ClearEventProperties() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.ClearEventProperties
EvaluationOfEventProperties.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfEventSpans - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventSpans(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, float, float, float) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
EvaluationOfEventSpans.Options - Interface in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, boolean, boolean, boolean, String, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
EvaluationOfEventTimeRelations.AddClosure - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.AddClosure() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddClosure
EvaluationOfEventTimeRelations.AddContain2Overlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.AddContain2Overlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddContain2Overlap
EvaluationOfEventTimeRelations.AddFlippedOverlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.AddFlippedOverlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddFlippedOverlap
EvaluationOfEventTimeRelations.AddPotentialRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.AddPotentialRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations
EvaluationOfEventTimeRelations.AddTransitiveContainsRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.AddTransitiveContainsRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddTransitiveContainsRelations
EvaluationOfEventTimeRelations.CountCloseRelation - Class in org.apache.ctakes.temporal.eval: public static class CountSentenceContainsTimes extends JCasAnnotator_ImplBase { public static final String PARAM_SENTENCE_VIEW = "SentenceView";
EvaluationOfEventTimeRelations.CountCloseRelation() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.CountCloseRelation
EvaluationOfEventTimeRelations.Overlap2Contains - Class in org.apache.ctakes.temporal.eval: For conflicting temporal relations on the same pair of arguments, if some of the relation types are "overlap", and "contains", remove "overlap" and keep "contains"
EvaluationOfEventTimeRelations.Overlap2Contains() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.Overlap2Contains
EvaluationOfEventTimeRelations.ParameterSettings - Class in org.apache.ctakes.temporal.eval: Holds a set of parameters for a relation extraction model
EvaluationOfEventTimeRelations.ParameterSettings(boolean, float, String, double, double, String, CompositeKernel.ComboOperator, double, double) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations
EvaluationOfEventTimeRelations.RemoveEventEventRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.RemoveEventEventRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveEventEventRelations
EvaluationOfEventTimeRelations.RemoveNonUMLSEtEvents - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.RemoveNonUMLSEtEvents() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveNonUMLSEtEvents
EvaluationOfEventTimeRelations.RemoveRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfEventTimeRelations.RemoveRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveRelations
EvaluationOfEventTimeRelations.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfI2B2TemporalRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfI2B2TemporalRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, boolean, boolean, boolean, String, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
EvaluationOfI2B2TemporalRelations.AddClosure - Class in org.apache.ctakes.temporal.eval
EvaluationOfI2B2TemporalRelations.AddClosure() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.AddClosure
EvaluationOfI2B2TemporalRelations.AddFlippedOverlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfI2B2TemporalRelations.AddFlippedOverlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.AddFlippedOverlap
EvaluationOfI2B2TemporalRelations.FindLongDisRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfI2B2TemporalRelations.FindLongDisRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.FindLongDisRelations
EvaluationOfI2B2TemporalRelations.RemoveNonTLINKRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfI2B2TemporalRelations.RemoveNonTLINKRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.RemoveNonTLINKRelations
EvaluationOfI2B2TemporalRelations.RemoveNullArgumentRelations - Class in org.apache.ctakes.temporal.eval: public static class RemoveEventEventRelations extends JCasAnnotator_ImplBase { public static final String PARAM_RELATION_VIEW = "RelationView";
EvaluationOfI2B2TemporalRelations.RemoveNullArgumentRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.RemoveNullArgumentRelations
EvaluationOfI2B2TemporalRelations.RemoveRelations - Class in org.apache.ctakes.temporal.eval: public static class RemoveCrossSentenceRelations extends JCasAnnotator_ImplBase { public static final String PARAM_SENTENCE_VIEW = "SentenceView";
EvaluationOfI2B2TemporalRelations.RemoveRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.RemoveRelations
EvaluationOfI2B2TemporalRelations.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfMetaTimeExpressionExtractor - Class in org.apache.ctakes.temporal.eval
EvaluationOfMetaTimeExpressionExtractor(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, List<Integer>, Class<? extends Annotation>) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
EvaluationOfMetaTimeExpressionExtractor.MetaOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfNEPredicateEventSpans - Class in org.apache.ctakes.temporal.eval
EvaluationOfNEPredicateEventSpans(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, Class<? extends Annotation>) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
EvaluationOfNEPredicateEventSpans(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
EvaluationOfSelfEventTimeRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, boolean, boolean, boolean, String, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
EvaluationOfSelfEventTimeRelations.AddClosure - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.AddClosure() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddClosure
EvaluationOfSelfEventTimeRelations.AddContain2Overlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.AddContain2Overlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddContain2Overlap
EvaluationOfSelfEventTimeRelations.AddFlippedOverlap - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.AddFlippedOverlap() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddFlippedOverlap
EvaluationOfSelfEventTimeRelations.OverwriteTemporalRelationToSystem - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.OverwriteTemporalRelationToSystem() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.OverwriteTemporalRelationToSystem
EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations
EvaluationOfSelfEventTimeRelations.RemoveEventEventRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.RemoveEventEventRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveEventEventRelations
EvaluationOfSelfEventTimeRelations.RemoveRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfSelfEventTimeRelations.RemoveRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveRelations
EvaluationOfSelfEventTimeRelations.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfTemporalRelations_ImplBase - Class in org.apache.ctakes.temporal.eval
EvaluationOfTemporalRelations_ImplBase(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, boolean, boolean, EvaluationOfEventTimeRelations.ParameterSettings) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations
EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes - Class in org.apache.ctakes.temporal.eval
EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes
EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations - Class in org.apache.ctakes.temporal.eval
EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations() - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations
EvaluationOfTemporalRelations_ImplBase.TempRelOptions - Interface in org.apache.ctakes.temporal.eval
EvaluationOfTimeSpans - Class in org.apache.ctakes.temporal.eval
EvaluationOfTimeSpans(File, File, File, Evaluation_ImplBase.XMLFormat, Evaluation_ImplBase.Subcorpus, File, File, float, float, Class<? extends JCasAnnotator_ImplBase>, boolean, String[]) - Constructor for class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
EvaluationOfTimeSpans.Options - Interface in org.apache.ctakes.temporal.eval
evaluationOutputDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
evaluationOutputDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
evaluationType - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
Event - Class in org.apache.ctakes.typesystem.type.refsem: A real-world event; similar to Entity, but may bear some temporal properties and relationships.
Event() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Event: Never called.
Event(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Event: Internal - constructor used by generator
Event(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Event
EVENT_ADMISSION - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
EVENT_DISCHARGE - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
EVENT_EVENT - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
EVENT_TIME - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
Event_Type - Class in org.apache.ctakes.typesystem.type.refsem: A real-world event; similar to Entity, but may bear some temporal properties and relationships.
Event_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Event_Type: initialize variables to correspond with Cas Type and Features
EventAdmissionTimeAnnotator - Class in org.apache.ctakes.temporal.ae
EventAdmissionTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
EventAndEntityViewer - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold entities and events (potential relation arguments).
EventAndEntityViewer() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer
EventAndEntityViewer.Options - Interface in org.apache.ctakes.relationextractor.data.analysis
EventAndEntityViewer.RelationContextPrinter - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold standard entities and events.
EventAndEntityViewer.RelationContextPrinter() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer.RelationContextPrinter
EventAndTimeExtractionPipeline - Class in org.apache.ctakes.temporal.pipelines: Given a trained event extraction model, run the event extractor on files in a directory.
EventAndTimeExtractionPipeline() - Constructor for class org.apache.ctakes.temporal.pipelines.EventAndTimeExtractionPipeline
EventAndTimeExtractionPipeline.ETOptions - Interface in org.apache.ctakes.temporal.pipelines
EventAnnotator - Class in org.apache.ctakes.temporal.ae
EventAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventAnnotator
EventArgumentPropertyExtractor - Class in org.apache.ctakes.temporal.ae.feature
EventArgumentPropertyExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor
eventChunking - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
EventContextAnalysisPipeline - Class in org.apache.ctakes.temporal.data.analysis: Print events and tokens with contexts to two separeate files.
EventContextAnalysisPipeline() - Constructor for class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline
EventContextAnalysisPipeline.EventAndTokenContextWriter - Class in org.apache.ctakes.temporal.data.analysis: Print all tokens with contexts and all events with contexts for further analysis.
EventContextAnalysisPipeline.EventAndTokenContextWriter() - Constructor for class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
EventContextAnalysisPipeline.Options - Interface in org.apache.ctakes.temporal.data.analysis
EventDischargeTimeAnnotator - Class in org.apache.ctakes.temporal.ae
EventDischargeTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
EventDurationDistribution - Class in org.apache.ctakes.temporal.duration: Extract durations of event mentions (e.g.
EventDurationDistribution() - Constructor for class org.apache.ctakes.temporal.duration.EventDurationDistribution
EventDurationDistribution.FileSizeComparator - Class in org.apache.ctakes.temporal.duration
EventDurationDistribution.FileSizeComparator() - Constructor for class org.apache.ctakes.temporal.duration.EventDurationDistribution.FileSizeComparator
EventDurationDistribution.Options - Class in org.apache.ctakes.temporal.duration
EventDurationDistribution.Options() - Constructor for class org.apache.ctakes.temporal.duration.EventDurationDistribution.Options
EventDurationDistribution.TemporalDurationExtractor - Class in org.apache.ctakes.temporal.duration
EventDurationDistribution.TemporalDurationExtractor() - Constructor for class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
EventEventDurationStatistics - Class in org.apache.ctakes.temporal.duration: Analyze duration information for the relation arguments of CONTAINS relation.
EventEventDurationStatistics() - Constructor for class org.apache.ctakes.temporal.duration.EventEventDurationStatistics
EventEventDurationStatistics.AnalyseRelationArgumentDuration - Class in org.apache.ctakes.temporal.duration: Look at event-event relations whose event arguments have duration data.
EventEventDurationStatistics.AnalyseRelationArgumentDuration() - Constructor for class org.apache.ctakes.temporal.duration.EventEventDurationStatistics.AnalyseRelationArgumentDuration
EventEventDurationStatistics.Options - Interface in org.apache.ctakes.temporal.duration
EventEventI2B2RelationAnnotator - Class in org.apache.ctakes.temporal.ae
EventEventI2B2RelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
EventEventRelationAnnotator - Class in org.apache.ctakes.temporal.ae
EventEventRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
EventExtractionPipeline - Class in org.apache.ctakes.temporal.pipelines: Given a trained event extraction model, run the event extractor on files in a directory.
EventExtractionPipeline() - Constructor for class org.apache.ctakes.temporal.pipelines.EventExtractionPipeline
EventExtractionPipeline.EventOptions - Interface in org.apache.ctakes.temporal.pipelines
EventMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to an Event.
EventMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.EventMention: Never called.
EventMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EventMention: Internal - constructor used by generator
EventMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EventMention
EventMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EventMention
EventMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to an Event.
EventMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.EventMention_Type: initialize variables to correspond with Cas Type and Features
eventOutputFile - Variable in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
eventOutputFile - Variable in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.EventWriter
eventOutputFile - Variable in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
eventPositionExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
eventPositionExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
EventPositionFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature: Event postion feature extractor: 1.
EventPositionFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EventPositionFeatureExtractor
EventPositionRelationFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature: extract the nearby nearest time, date information for any event
EventPositionRelationFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor
EventPrinterPipeline - Class in org.apache.ctakes.temporal.data.analysis: Print events of given UMLS semantic type.
EventPrinterPipeline() - Constructor for class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline
EventPrinterPipeline.EventWriter - Class in org.apache.ctakes.temporal.data.analysis: Print events with a given UMLS semantic type.
EventPrinterPipeline.EventWriter() - Constructor for class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.EventWriter
EventPrinterPipeline.Options - Interface in org.apache.ctakes.temporal.data.analysis
EventPrintingPipeline - Class in org.apache.ctakes.temporal.pipelines: Print event annotations and their context.
EventPrintingPipeline() - Constructor for class org.apache.ctakes.temporal.pipelines.EventPrintingPipeline
EventPrintingPipeline.Options - Interface in org.apache.ctakes.temporal.pipelines
EventPrintingPipeline.PrintEventAnnotations - Class in org.apache.ctakes.temporal.pipelines
EventPrintingPipeline.PrintEventAnnotations() - Constructor for class org.apache.ctakes.temporal.pipelines.EventPrintingPipeline.PrintEventAnnotations
EventProperties - Class in org.apache.ctakes.typesystem.type.refsem: A set of mostly temporal properties that are unique to Events.
EventProperties() - Constructor for class org.apache.ctakes.typesystem.type.refsem.EventProperties: Never called.
EventProperties(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.EventProperties: Internal - constructor used by generator
EventProperties(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.EventProperties
EventProperties_Type - Class in org.apache.ctakes.typesystem.type.refsem: A set of mostly temporal properties that are unique to Events.
EventProperties_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type: initialize variables to correspond with Cas Type and Features
EventPropertyExtractor - Class in org.apache.ctakes.temporal.ae.feature
EventPropertyExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EventPropertyExtractor
eventSectionTimeRelationLookup - Variable in class org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor
EventTimeDurationStatistics - Class in org.apache.ctakes.temporal.duration: Analyze duration information for the relation arguments of CONTAINS relation.
EventTimeDurationStatistics() - Constructor for class org.apache.ctakes.temporal.duration.EventTimeDurationStatistics
EventTimeDurationStatistics.AnalyseRelationArgumentDuration - Class in org.apache.ctakes.temporal.duration: Look at those event-time relations whose event argument has duration data and whose time argument can be normalized using Bethard timex normalizer.
EventTimeDurationStatistics.AnalyseRelationArgumentDuration() - Constructor for class org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.AnalyseRelationArgumentDuration
EventTimeDurationStatistics.Options - Interface in org.apache.ctakes.temporal.duration
EventTimeFlatTreeFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature.treekernel
EventTimeFlatTreeFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor
EventTimeI2B2RelationAnnotator - Class in org.apache.ctakes.temporal.ae
EventTimeI2B2RelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
EventTimeRelationAnnotator - Class in org.apache.ctakes.temporal.ae
EventTimeRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
EventTimeRelationFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature: Given a pair of arguments, if any one of them is an event, get the related event-sectiontime as features
EventTimeRelationFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor
EventTimeRelationsFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
EventTimeRelationsFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.EventTimeRelationsFeaturesExtractor
EventTimeSelfRelationAnnotator - Class in org.apache.ctakes.temporal.ae
EventTimeSelfRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
eventTimeUnitCount - Variable in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
EventToClearTKEventAnnotator - Class in org.apache.ctakes.temporal.ae: for every cTAKES EventMention annotation, create a ClearTK Event Annotation
EventToClearTKEventAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.EventToClearTKEventAnnotator
EVERYOTHERDAY - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
ExampleAggregatePipeline - Class in org.apache.ctakes.examples.pipelines: Example of a running a pipeline programatically w/o uima xml descriptor xml files Adds the default Tokenization pipeline and adding the Example HelloWorld Annotator
ExampleAggregatePipeline() - Constructor for class org.apache.ctakes.examples.pipelines.ExampleAggregatePipeline
ExampleHelloWorldAnnotator - Class in org.apache.ctakes.examples.ae
ExampleHelloWorldAnnotator() - Constructor for class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
EXC_TAGS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
EXC_TAGS_PRP_KEY - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
EXCLUDE_RELA - Static variable in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
exclusionSet - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
exclusionSet - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
exclusionSet - Variable in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
execute() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionSampleFeatureGenerator
execute() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
execute() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest
execute() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest2
execute(List<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.DateFSM: Executes the finite state machines.
execute(List<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.FractionFSM: Executes the finite state machines.
execute(List) - Method in interface org.apache.ctakes.core.fsm.machine.FSM
execute(List<? extends BaseToken>, Set<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.MeasurementFSM: Executes the finite state machines.
execute(List<?>) - Method in class org.apache.ctakes.core.fsm.machine.NegationFSM: Executes the finite state machines.
execute(List<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.PersonTitleFSM: Executes the finite state machines.
execute(List<? extends BaseToken>, Set<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.RangeFSM: Executes the finite state machines.
execute(List<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM: Executes the finite state machines.
execute(List<TextToken>) - Method in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM: Executes the finite state machines.
execute(List<? extends BaseToken>) - Method in class org.apache.ctakes.core.fsm.machine.TimeFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DecimalStrengthFSM: Executes the finite state machines.
execute(List, Set, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FormFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FormFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM: Executes the finite state machines.
execute(List, Set, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Executes the finite state machines.
execute(List, Set, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM: Executes the finite state machines.
execute(List, Set, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.util.HyphenatedDrugFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM: Executes the finite state machines.
execute(List) - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM: Executes the finite state machines.
execute(List, Set) - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM: Executes the finite state machines.
execute() - Method in class org.apache.ctakes.jdl.AppJdl: Execute the loader of the data into the database.
execute(List<?>) - Method in class org.apache.ctakes.smokingstatus.machine.NegationFSM: Executes the finite state machines.
executeBatch(PreparedStatement) - Static method in class org.apache.ctakes.jdl.data.loader.Loader
executeFSMs(JCas, List<? extends BaseToken>) - Method in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
executeFSMs(JCas, List, List, List) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: The namedE consists of a list of the Named Entities (NE) found in the prior method.
exists(File) - Static method in class org.apache.ctakes.preprocessor.test.TestDriver
exit() - Method in class org.apache.ctakes.core.fsm.state.NamedState
exit() - Method in class org.apache.ctakes.core.fsm.state.NonTerminalEndState
exit() - Method in class org.apache.ctakes.drugner.fsm.states.util.IndentStartState
expandToNP(JCas, LinkedList<Annotation>) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
expandToNP(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
expandToNP(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline
expectedDuration(Map<String, Float>) - Static method in class org.apache.ctakes.temporal.duration.Utils: Compute expected duration in seconds.
experiencer - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
experiment - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
experiment - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
experiment - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
exportAttributeNames(SparseData, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter
exportAttributeNames(BufferedWriter, SparseData) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: assign indices to each attribute.
exportAttributeNames(BufferedWriter, SparseData) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter: add instance_id as first in the map of numeric attribute
exportBagOfWords(String) - Method in interface org.apache.ctakes.ytex.kernel.BagOfWordsExporter
ExportBagOfWords - Class in org.apache.ctakes.ytex.weka: Export bag of words using the queries specified in the given property/xml file.
ExportBagOfWords() - Constructor for class org.apache.ctakes.ytex.weka.ExportBagOfWords
exportBagOfWords(String, String, String, String, BufferedWriter) - Method in interface org.apache.ctakes.ytex.weka.WekaBagOfWordsExporter
exportBagOfWords(String, BagOfWordsDecorator) - Method in interface org.apache.ctakes.ytex.weka.WekaBagOfWordsExporter
exportBagOfWords(String, String, String, String, BufferedWriter) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
exportBagOfWords(String, String, String, String, BufferedWriter, BagOfWordsDecorator) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
exportBagOfWords(String) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
exportBagOfWords(String, BagOfWordsDecorator) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
ExportCAS - Class in org.apache.ctakes.ytex.tools: read specified document id's cas, send to stdout
ExportCAS() - Constructor for class org.apache.ctakes.ytex.tools.ExportCAS
exportClassIds(String, Map<String, Integer>, String) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil: export the class id to class name map.
exportClassIds(String, Map<String, Integer>, String) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl: export the class id to class name map.
exportData(String, String) - Method in interface org.apache.ctakes.ytex.kernel.SparseDataExporter
exportData(Properties, SparseDataFormatter, BagOfWordsDecorator) - Method in interface org.apache.ctakes.ytex.kernel.SparseDataExporter
exportData(InstanceData, SparseDataFormatter, Properties, BagOfWordsDecorator) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
exportData(Properties, SparseDataFormatter, BagOfWordsDecorator) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
exportData(String, String) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
exportData(SparseData, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory.SVMLinDataFormatter
exportData(SparseData, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
exportData(SparseData, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory.SGTFormatter
exportDataForInstances(SparseData, SortedMap<Long, String>, <any>, BufferedWriter, BufferedWriter) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter
exportDataForLabel(String, String, SparseData, SortedMap<Long, String>, <any>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter: Export data file and id file
exportEdges(ConceptGraph, BufferedWriter) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: export the fold train/test set.
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter: export the given train/test set
exportFold(double[][], Map<Boolean, SortedMap<Long, String>>, boolean, Map<Long, Integer>, String, Map<String, Integer>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl: export the train or test gram matrix.
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter: export the given train/test set
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter
exportFold(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
exportGramMatrices(String, String, double, String, String, String, String, InstanceData, Map<String, <any>>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl: Load the gram matrix based on scope.
exportGramMatrices(String, String, double, String, String, String, String, InstanceData) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
exportGramMatrix(Properties) - Method in interface org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporter
exportGramMatrix(Properties) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
exportGramMatrix(Properties) - Method in interface org.apache.ctakes.ytex.R.RGramMatrixExporter
exportGramMatrix(String, String, double, String, String, String, InstanceData, String, int, int) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
exportGramMatrix(Properties) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
ExportGramMatrix - Class in org.apache.ctakes.ytex.weka
ExportGramMatrix() - Constructor for class org.apache.ctakes.ytex.weka.ExportGramMatrix
exportGramMatrix(String) - Method in interface org.apache.ctakes.ytex.weka.GramMatrixExporter
exportGramMatrix(String) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
exportGramMatrix(BufferedWriter, KernelEvaluation, GramMatrixExporterImpl.GramMatrixType, Map<Long, String>, Map<Long, Integer>) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
exportLabel(String, SortedMap<Long, Integer>) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter: Write the 'label' file.
exportNetwork(String, Properties) - Method in interface org.apache.ctakes.ytex.kernel.CytoscapeHelper
exportNetwork(ConceptGraph, String, String, String, int, BufferedWriter, BufferedWriter) - Method in interface org.apache.ctakes.ytex.kernel.CytoscapeHelper
exportNetwork(ConceptGraph, String, String, String, int, BufferedWriter, BufferedWriter) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
exportNetwork(String, Properties) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
exportNodes(List<String>, BufferedWriter, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
exportNodes(Set<String>, BufferedWriter, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
exportOneAgainstAllCodes(String, Integer, Integer, SortedMap<Long, Integer>, Map<Integer, String>) - Method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory.SVMLinDataFormatter: recode the classes.
exportProperties - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: export properties - properties file that controls what to do for this export
exportSparseMatrix(String, SparseData) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: export sparse matrix data for use in matlab/R.
exportSparseMatrix(SparseData, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
exportSparseRow(SparseData, long, BufferedWriter, int) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter
exportSubtree(String, Properties) - Method in interface org.apache.ctakes.ytex.kernel.CytoscapeHelper
exportSubtree(String, Properties) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
exportTransductiveData(String, String, SparseData, SortedMap<Long, String>, Set<Long>, <any>) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter: Export data file and id file
exportType - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
exportWekaGramMatrix(double[][], BufferedWriter) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
extendChunk(Chunk, int) - Static method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: Update the end value for the chunk to have the new value
extendedSearch(String, String, Date, Date, Integer, Boolean) - Method in interface org.apache.ctakes.ytex.web.search.DocumentSearchService: Extended search
extendedSearch(String, String, Date, Date, Integer, Boolean) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl: Extended search
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.attributes.features.GenericFeaturesExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.attributes.features.HistoryFeaturesExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor
extract(JCas, Annotation) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
extract(JCas, Annotation) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
extract(JCas, Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveLeftFragmentExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveRightFragmentExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionAboveLeftTreeExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionDependencyTreeExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.DependencyPathRegexpFeatureExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.DependencyWordsFragmentExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.NegationDependencyFeatureExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SRLFeatureExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SurroundingExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
extract(JCas, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.UncertaintyFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.ArgumentOrderFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.DependencyPathFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.EmbeddingFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.EntitySpanFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.FlatTreeFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PETFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PrepositionFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PunctuationFeatureExtractor
extract(JCas, T1, T2) - Method in interface org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor: Extract features for the pair of named entity mentions.
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.TreeFragmentFeatureExtractor
extract(JCas, IdentifiedAnnotation, IDictionary) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor
extract(int, int, int) - Method in class org.apache.ctakes.temporal.ae.feature.ChunkingExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.ClosestVerbExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.CoordinateFeaturesExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.DateAndMeasurementExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.DependencyFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.DeterminerRelationFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.DocTimeRelFeatureExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.duration.DurationDistributionFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.duration.DurationEventEventFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.duration.DurationEventTimeFeatureExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.duration.DurationExpectationFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.duration.DurationTimeUnitFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.EmptyFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.EventPositionFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.EventPropertyExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.EventTimeRelationsFeaturesExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.FramesetCategoryExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.ListFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseXExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.NearestFlagFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.NumberOfEventsInTheSameSentenceExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.NumberOfEventTimeBetweenCandidatesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.OverlappedHeadFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.ParseFeatureExtractor
extract(JCas, int, int) - Method in class org.apache.ctakes.temporal.ae.feature.ParseSpanFeatureExtractor
extract(BaseToken) - Method in class org.apache.ctakes.temporal.ae.feature.PredicateArgumentExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.SectionHeaderExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.SpecialAnnotationRelationExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.SyntacticParentFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.TemporalAttributeForMixEventTimeExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.TimeXExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.TimeXPropertyRelationFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.TokenPropertyFeaturesExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.treekernel.DependencySingleTreeExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.treekernel.SyntaticSingleTreeExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalFTExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPathExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.UmlsFeatureExtractor
extract(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.feature.UmlsSingleFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor
extractAboveLeftConceptTree(JCas, Annotation, SemanticClasses) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
extractAboveRightConceptTree(JCas, Annotation, SemanticClasses) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
extractAndSaveDocKey(JCas, Document) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
ExtractDurationsUsingContainsRelation - Class in org.apache.ctakes.temporal.duration: Use event-time CONTAINS relations to extract event duration distributions.
ExtractDurationsUsingContainsRelation() - Constructor for class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation
ExtractDurationsUsingContainsRelation.Options - Interface in org.apache.ctakes.temporal.duration
ExtractDurationsUsingContainsRelation.ProcessRelations - Class in org.apache.ctakes.temporal.duration: Go over even-time relations and collect all times with which each of the events occurs in CONTAINS relation.
ExtractDurationsUsingContainsRelation.ProcessRelations() - Constructor for class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
extractFeature(String, Object) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: apply jxpath to object
extractFeatures(JCas, EventMention) - Method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
extractFeatures(JCas, EventMention) - Method in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
extractFeatureTree(JCas, Annotation, SemanticClasses) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
extractFirstToken(String, Pattern) - Static method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
extractForNode(JCas, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor
extractInformation(T) - Method in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
extractInformation(IdentifiedAnnotation) - Method in class org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator
ExtractionPrepAnnotator - Class in org.apache.ctakes.clinicalpipeline.ae: UIMA annotator that prepares the CAS for output - performs some (final) updates to the CAS
ExtractionPrepAnnotator() - Constructor for class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator
extractList(FeatureStructure) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: covert a FSArray or FSList into a List
ExtractorListFeatureFunctionConverter - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
ExtractorListFeatureFunctionConverter() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ExtractorListFeatureFunctionConverter
extractPathEnclosedTree(TreebankNode, TreebankNode, JCas) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
extractPathTree(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
extractPhraseHeadByTreenode(JCas, List<TreebankNode>) - Method in class org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor
extractSRLInfo(JCas, List<BaseToken>, DEPTree) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE: Converts the output from the ClearNLP Semantic Role Labeler to the ClearTK Predicate and SemanticArgument Types.
extractUMLSFirstWord(String) - Static method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
extractUMLSFirstWord(String) - Static method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean

F

f(double) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
f(double, OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
f - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile
f1() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
f1(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
f1 - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasDiff
f1 - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
f1_uniq - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasDiff
F1BaselineEventTimeRelationAnnotator - Class in org.apache.ctakes.temporal.ae.baselines
F1BaselineEventTimeRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.baselines.F1BaselineEventTimeRelationAnnotator
f2 - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasDiff
f2_uniq - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasDiff
FALSE_STRING - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
FALSE_STRING - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
family - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.CuePhrase
FAMILY_DEPPATH - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
FAMILY_DEPTOK - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
FAMILY_HISTORY_STATUS - Static variable in class org.apache.ctakes.core.fsm.output.StatusIndicator
FAMILY_HISTORY_STATUS - Static variable in class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
FAMILY_OR - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
FAMILY_SRLARG - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
FAMILY_TOKEN - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
FastLookupToken - Class in org.apache.ctakes.dictionary.lookup2.util: Container class that holds a text span, actual text, and possible variant text for a lookup token.
FastLookupToken(Annotation) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
fastSplit(String, int) - Static method in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
fastSplit(String, char) - Static method in class org.apache.ctakes.dictionary.lookup2.util.LookupUtil: Splits a string using a character.
feaMap - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceClassifierAnnotator
FEAT_NAME - Static variable in class org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor
FEAT_NAME - Static variable in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
FEAT_NAME - Static variable in class org.apache.ctakes.temporal.ae.feature.treekernel.DependencySingleTreeExtractor
FEAT_NAME - Static variable in class org.apache.ctakes.temporal.ae.feature.treekernel.SyntaticSingleTreeExtractor
FEAT_NAME - Static variable in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalFTExtractor
featConfig - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
featConfig - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
featOkTst - Static variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
featOkTst - Static variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
featOkTst - Static variable in class org.apache.ctakes.assertion.zoner.types.Heading_Type
featOkTst - Static variable in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
featOkTst - Static variable in class org.apache.ctakes.assertion.zoner.types.Zone_Type
featOkTst - Static variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.DemMarkable_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.Markable_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.NEMarkable_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.Pair_Type
featOkTst - Static variable in class org.apache.ctakes.coreference.type.PronounMarkable_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.DosagesAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.DurationAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.FormAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.FrequencyAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.StrengthAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.sideeffect.type.PSESentence_Type
featOkTst - Static variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
featOkTst - Static variable in class org.apache.ctakes.sideeffect.type.SESentence_Type
featOkTst - Static variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
featOkTst - Static variable in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Attribute_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Course_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Entity_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Event_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.Time_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.Affects_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.Contraindicates_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOf_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.Diagnoses_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.Indicates_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOf_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreats_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOf_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.Prevents_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOf_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.relation.UMLSRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADJP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADVP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.CONJP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.ContractionToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.INTJ_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.LST_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.NewlineToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.NP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.O_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.PP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.PRT_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.SBAR_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.SymbolToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.UCP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.VP_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.Markable_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textspan.Paragraph_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.util.Pairs_Type
featOkTst - Static variable in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type
featOkTst - Static variable in class org.apache.ctakes.ytex.uima.types.Date_Type
featOkTst - Static variable in class org.apache.ctakes.ytex.uima.types.DocKey_Type
featOkTst - Static variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
featSet - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
feature - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
feature - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
feature - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
FEATURE_NAME - Static variable in class org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor
FEATURE_SELECTION_NAME - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
FEATURE_SELECTION_NAME - Static variable in class org.apache.ctakes.temporal.ae.EventAnnotator
FEATURE_SELECTION_NAME - Static variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
featureEval - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureRank
FeatureEvaluation - Class in org.apache.ctakes.ytex.kernel.model
FeatureEvaluation() - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
FeatureEvaluation(String, String, Integer, String) - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
featureEvaluationId - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
featureExtractors - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
featureExtractors - Variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
featureFunctionExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
FeatureIndex - Static variable in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
FeatureIndex - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
FeatureIndex - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
featureName - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
featureName - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
featureName - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureRank
FeatureParentChild - Class in org.apache.ctakes.ytex.kernel.model
FeatureParentChild() - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
featureParentChildId - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
FeatureRank - Class in org.apache.ctakes.ytex.kernel.model
FeatureRank() - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureRank
FeatureRank(String, double) - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureRank
FeatureRank(FeatureEvaluation, String, double) - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureRank
FeatureRank(FeatureEvaluation, String, double, int) - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureRank
FeatureRank.FeatureRankAsc - Class in org.apache.ctakes.ytex.kernel.model: Sort features by ascending evaluation score
FeatureRank.FeatureRankAsc() - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureRank.FeatureRankAsc
FeatureRank.FeatureRankDesc - Class in org.apache.ctakes.ytex.kernel.model: Sort features by descending evaluation score if two features have the same score, order them by name
FeatureRank.FeatureRankDesc() - Constructor for class org.apache.ctakes.ytex.kernel.model.FeatureRank.FeatureRankDesc
featureRankChild - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
featureRankId - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureRank
featureRankParent - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
features - Variable in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData
FeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.assertion.attributes.features.selection
FeatureSelection(String) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
featureSelection - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
featureSelection - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
FeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection
FeatureSelection(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
featureSelection - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
featureSelectionThreshold - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
featureSelectionThreshold - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
featureSelectionThreshold - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
featureSelectionThreshold - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
featureSelectionThreshold - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
featureSelectionThreshold - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
featureSelectionThreshold - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
featureSelectionURI - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
featureSelectionURI - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
featureSelectionURI - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
featureSetName - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
featureSetName - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter
featureValue - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
featureValue - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
FeatureVector - Class in org.apache.ctakes.coreference.util
FeatureVector() - Constructor for class org.apache.ctakes.coreference.util.FeatureVector
featValueClassCount - Variable in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
featValueClassCount - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
featValueClassCount - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
featValueClassCount - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
feda - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
FedaFeatureFunction - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
FedaFeatureFunction(List<String>) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction
ffDomainAdaptor - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
FIELD_DELIM - Static variable in interface org.apache.ctakes.ytex.sparsematrix.InstanceDataExporter
FieldConstraint - Interface in org.apache.ctakes.dictionary.lookup.strtable: Defines when a row should NOT be added to a StringTable object.
FieldConstraintImpl - Class in org.apache.ctakes.dictionary.lookup.strtable
FieldConstraintImpl(String, int, String, Class<?>) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
FILE_TO_DOMAIN_MAP - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
fileDomainMap - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
fileForIO - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
FileLocator - Class in org.apache.ctakes.core.resource: Utility class that attempts to locate files.
FileLocator() - Constructor for class org.apache.ctakes.core.resource.FileLocator
filePatt - Static variable in class org.apache.ctakes.temporal.eval.I2B2Data
FileResource - Interface in org.apache.ctakes.core.resource
FileResourceImpl - Class in org.apache.ctakes.core.resource
FileResourceImpl() - Constructor for class org.apache.ctakes.core.resource.FileResourceImpl
files - Variable in class org.apache.ctakes.assertion.eval.XMIReader
files - Variable in class org.apache.ctakes.core.cr.TextReader
files - Variable in class org.apache.ctakes.core.cr.XMIReader
files - Variable in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
files - Variable in class org.apache.ctakes.relationextractor.eval.XMIReader
FilesInDirectoryCasConsumer - Class in org.apache.ctakes.core.cc: For each CAS a local file with the document text is written to a directory specifed by a parameter.
FilesInDirectoryCasConsumer() - Constructor for class org.apache.ctakes.core.cc.FilesInDirectoryCasConsumer
FilesInDirectoryCollectionCyclicalReads - Class in org.apache.ctakes.core.cr
FilesInDirectoryCollectionCyclicalReads() - Constructor for class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
FilesInDirectoryCollectionReader - Class in org.apache.ctakes.core.cr
FilesInDirectoryCollectionReader() - Constructor for class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
filesIter - Variable in class org.apache.ctakes.assertion.eval.XMIReader
filesIter - Variable in class org.apache.ctakes.core.cr.TextReader
filesIter - Variable in class org.apache.ctakes.core.cr.XMIReader
filesIter - Variable in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
filesIter - Variable in class org.apache.ctakes.relationextractor.eval.XMIReader
fileToDomain - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
FileUtil - Class in org.apache.ctakes.jdl.common: Utility to get a file.
FileUtil() - Constructor for class org.apache.ctakes.jdl.common.FileUtil
FileUtil - Class in org.apache.ctakes.ytex.kernel: miscellaneous utility functions used for data import/export
FileUtil() - Constructor for class org.apache.ctakes.ytex.kernel.FileUtil
FileUtil.DirectoryFileFilter - Class in org.apache.ctakes.ytex.kernel: file filter to get directories
FileUtil.DirectoryFileFilter() - Constructor for class org.apache.ctakes.ytex.kernel.FileUtil.DirectoryFileFilter
FileUtil.PrefixFileFilter - Class in org.apache.ctakes.ytex.kernel: get files that start with specified prefix.
FileUtil.PrefixFileFilter(String) - Constructor for class org.apache.ctakes.ytex.kernel.FileUtil.PrefixFileFilter
FileUtil.SuffixFileFilter - Class in org.apache.ctakes.ytex.kernel: filter files by suffix
FileUtil.SuffixFileFilter(String) - Constructor for class org.apache.ctakes.ytex.kernel.FileUtil.SuffixFileFilter
fillGramMatrix(KernelEvaluation, SortedSet<Long>, double[][]) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil
fillGramMatrix(KernelEvaluation, SortedSet<Long>, double[][]) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
fillLabelToClassIndexMap(Map<String, SortedSet<String>>) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
fillLabelToClassIndexMap(Map<String, SortedSet<String>>) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter
fillLabelToClassToIndexMap(Map<String, SortedSet<String>>, Map<String, <any>>) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil
fillLabelToClassToIndexMap(Map<String, SortedSet<String>>, Map<String, <any>>) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl: assign numeric indices to string class names
fillSelectCall(PreparedStatement, Long) - Static method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
fillSelectCall(String) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
filter(Annotation) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NamedEntityTargetAnnoFilter
filter(Annotation) - Method in interface org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.TargetAnnoFilter
FilterAnnotator - Class in org.apache.ctakes.core.ae
FilterAnnotator() - Constructor for class org.apache.ctakes.core.ae.FilterAnnotator
FilterException - Exception in org.apache.ctakes.dictionary.lookup.filter
FilterException(Throwable) - Constructor for exception org.apache.ctakes.dictionary.lookup.filter.FilterException
filterHitDups(Collection<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator: Filters out duplicate LookupHit objects.
filterHitDups(Collection<LookupHit>) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator: Filters out duplicate LookupHit objects.
filterNonIncreasingLists(Collection<List<Integer>>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil: Filters the number lists such that only lists with increasing numbers are kept.
filterTokens(List<Token>) - Method in class org.apache.ctakes.core.ci.HyphenTextModifierImpl: Filters out unwanted tokens - newlines.
filterToNamedEntitiesOnly(HashMap<String, ArrayList<Span>>, HashMap<String, String>) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
filterToNamedEntitiesOnly(HashMap<String, ArrayList<Span>>, String, String) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
FINAL_CLASS_FILE - Static variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: Optional path and file name of the output file which holds the patient level classification summary
finalAssignment - Static variable in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
find(int) - Method in class org.apache.ctakes.coreference.util.ParentPtrTree
find(String) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
FIND - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
FIND_TUIS - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
findAnnotationHead(JCas, Annotation) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: Finds the head word within a given annotation span
findAnnotationHead(JCas, Annotation) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils: Finds the head word within a given annotation span
findCoveredTextInSpan(JCas, int, int, int, String[]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findDosageElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findDrugAttributesInRange(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: finds drug attributes using the given range, this method uses FSM
findDrugChangeStatusElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findDurationElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findElementRelativeToNE(int[][], int[][], int, int, int, int, int, MedicationMention) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findEndDateElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findFirstCharOfNextToken(String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
findFormElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findFrequencyElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findFrequencyUnitElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findFSMInRange(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
FINDING_TUIS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
findInPattern(JCas, int, int, int, int[][]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findMaxValue - Variable in class org.apache.ctakes.drugner.DrugMention
findNegationContext(List<ConllDependencyNode>, ConllDependencyNode) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer: Executes the regular expressions on paths.
findNextClosestRightParenRelativeToElement(int, int[][], Annotation, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findNextDrugEntityPost(int, int[][], MedicationMention, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findNextDrugEntityPre(int, int[][], MedicationMention, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findNextNonAlphaNum(String, int) - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
findNextParenRelativeToElement(int, int[][], Annotation, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findNextParenRelativeToNE(int, int[][], MedicationMention, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findNextParenRelativeToNE(int, int[][], MedicationMention, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findOffsetsInPattern(JCas, int, int, int, int[][], boolean) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
findP(TreebankNode, String, int) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
findPathMatches(DependencyPath) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
findPreviousOrCurrentSentence(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
findPunctSymbolInsideToken(List<Token>, Token, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Finds punctuation/symbols located inside a token.
findRouteElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findStartDateElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findStrengthElement(JCas, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
findTerms(Iterable<RareWordDictionary>, List<FastLookupToken>, List<Integer>, Map<RareWordDictionary, CollectionMap<TextSpan, Long, ? extends Collection<Long>>>) - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: Given a set of dictionaries, tokens, and lookup token indices, populate a terms map with discovered terms
findTerms(RareWordDictionary, List<FastLookupToken>, List<Integer>, CollectionMap<TextSpan, Long, ? extends Collection<Long>>) - Method in class org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator: Given a dictionary, tokens, and lookup token indices, populate a terms collection with discovered terms
findTerms(RareWordDictionary, List<FastLookupToken>, List<Integer>, CollectionMap<TextSpan, Long, ? extends Collection<Long>>) - Method in interface org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator: Given a dictionary, tokens, and lookup token indices, populate a terms collection with discovered terms
findTerms(RareWordDictionary, List<FastLookupToken>, List<Integer>, CollectionMap<TextSpan, Long, ? extends Collection<Long>>) - Method in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator: Given a dictionary, tokens, and lookup token indices, populate a terms collection with discovered terms
findTextualStringOffset(String) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Finds offset of string the represents end of numeric portion
findTokenByTag(String, String[], boolean, int, int, NegexAnnotator.NegexToken[]) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
findUniqueMentions(Object[]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: finds unique annotations by their begin offsets
FirstTokenPermLookupInitializerImpl - Class in org.apache.ctakes.dictionary.lookup.ae
FirstTokenPermLookupInitializerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
FirstTokenPermLookupInitializerImpl - Class in org.apache.ctakes.ytex.uima.lookup.ae
FirstTokenPermLookupInitializerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
FirstTokenPermutationImpl - Class in org.apache.ctakes.dictionary.lookup.algorithms: OVERVIEW: Each LookupToken is fed into a "first token" Dictionary.
FirstTokenPermutationImpl(DictionaryEngine, PhraseBuilder, String[], int) - Constructor for class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Constructor
FirstWord - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
flatParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
flatParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
flatParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
flatParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
flatParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
FlatTreeFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
FlatTreeFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.FlatTreeFeatureExtractor
FLOAT_TYPE - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
fn - Variable in class org.apache.ctakes.ytex.kernel.IRMetrics
fn - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
fnMatch - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
FOCUS_ANNOTATION_CLASS_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "FocusAnnotationClass" is a required, single, string parameter that specifies the annotation type of the focus annotations that are going to be examined by this annotator.
focusType - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
fold - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
fold - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
FoldGenerator - Interface in org.apache.ctakes.ytex.kernel
foldGenerator - Variable in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
FoldGeneratorImpl - Class in org.apache.ctakes.ytex.kernel: utility generates cv fold splits, stores in db.
FoldGeneratorImpl() - Constructor for class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
foldId - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
foldId - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
foldInstanceLabelMap - Variable in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter
forArg1(Annotation, String, KnowtatorAnnotation, Class<? extends BinaryTextRelation>, Class<? extends Annotation>) - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
forArg1(Annotation, String, KnowtatorAnnotation, Class<? extends BinaryTextRelation>, Class<? extends Annotation>) - Static method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
forArg2(Annotation, String, KnowtatorAnnotation, Class<? extends BinaryTextRelation>, Class<? extends Annotation>) - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
forArg2(Annotation, String, KnowtatorAnnotation, Class<? extends BinaryTextRelation>, Class<? extends Annotation>) - Static method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
form - Variable in class org.apache.ctakes.drugner.DrugMention: Span the drug form, if available.
form - Variable in class org.apache.ctakes.drugner.elements.FormElement
FormAnnotation - Class in org.apache.ctakes.drugner.type: The value represents the form portion of the drug mention.
FormAnnotation() - Constructor for class org.apache.ctakes.drugner.type.FormAnnotation: Never called.
FormAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.FormAnnotation: Internal - constructor used by generator
FormAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.FormAnnotation
FormAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.FormAnnotation
FormAnnotation_Type - Class in org.apache.ctakes.drugner.type: The value represents the form portion of the drug mention.
FormAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.FormAnnotation_Type: initialize variables to correspond with Cas Type and Features
format(Annotation) - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
format(Annotation) - Static method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
format(IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
formatDistribution(<any>) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
formatDistribution(String, <any>, String, boolean) - Static method in class org.apache.ctakes.temporal.duration.Utils: Convert duration distribution multiset to a format that's easy to parse automatically.
formatDouble(double) - Static method in class org.apache.ctakes.ytex.kernel.IRMetrics
formatError(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
formatFieldName(String) - Static method in class org.apache.ctakes.ytex.dao.DBUtil
formatMap - Variable in class org.apache.ctakes.jdl.data.loader.CsvLoader
formatPath(StringBuilder, String, Iterator<String>) - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
formatPaths(List<LCSPath>) - Static method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
formatRelation(BinaryTextRelation) - Static method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
formatRelation(BinaryTextRelation) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
formatTableName(String) - Static method in class org.apache.ctakes.ytex.dao.DBUtil
formattedTableName - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
formatUMLSFirstWord(ConceptFirstWord) - Static method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
formatUMLSFirstWord(ConceptFirstWord) - Static method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
formatWeightKey(String, String) - Static method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory
FormCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a FormToken.
FormCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.FormCondition
FormElement - Class in org.apache.ctakes.drugner.elements
FormElement() - Constructor for class org.apache.ctakes.drugner.elements.FormElement
FormElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.FormElement
FormFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect form tokens in the given input of tokens.
FormFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.FormFSM: Constructor
FormToken - Class in org.apache.ctakes.drugner.fsm.output.elements
FormToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.FormToken
fp - Variable in class org.apache.ctakes.ytex.kernel.IRMetrics
fp - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
FractionAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.FractionAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
FractionAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation: Never called.
FractionAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation: Internal - constructor used by generator
FractionAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
FractionAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
FractionAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.FractionAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
FractionAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type: initialize variables to correspond with Cas Type and Features
FractionCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a FractionToken.
FractionCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.FractionCondition
FractionFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect fractions in the given input of tokens.
FractionFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.FractionFSM: Constructor
FractionStrengthAnnotation - Class in org.apache.ctakes.drugner.type: The fraction portion of dosages strength determination for the Drug NER profile.
FractionStrengthAnnotation() - Constructor for class org.apache.ctakes.drugner.type.FractionStrengthAnnotation: Never called.
FractionStrengthAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.FractionStrengthAnnotation: Internal - constructor used by generator
FractionStrengthAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.FractionStrengthAnnotation
FractionStrengthAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.FractionStrengthAnnotation
FractionStrengthAnnotation_Type - Class in org.apache.ctakes.drugner.type: The fraction portion of dosages strength determination for the Drug NER profile.
FractionStrengthAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.FractionStrengthAnnotation_Type: initialize variables to correspond with Cas Type and Features
FractionStrengthCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a FractionStrengthToken.
FractionStrengthCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.FractionStrengthCondition
FractionStrengthFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect fraction strength tokens in the given input of tokens.
FractionStrengthFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM: Constructor
FractionStrengthToken - Class in org.apache.ctakes.drugner.fsm.output.util
FractionStrengthToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.FractionStrengthToken
FractionToken - Class in org.apache.ctakes.core.fsm.output
FractionToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.FractionToken
FractionToken - Class in org.apache.ctakes.drugner.fsm.output.util
FractionToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.FractionToken
frag2tree(String) - Static method in class org.apache.ctakes.utils.tree.FragmentUtils
fragmentMatch(SimpleTree, SimpleTree, boolean) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
FragmentUtils - Class in org.apache.ctakes.utils.tree
FragmentUtils() - Constructor for class org.apache.ctakes.utils.tree.FragmentUtils
frags - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
frags - Variable in class org.apache.ctakes.coreference.util.SvmVectorCreator
frags - Static variable in class org.apache.ctakes.relationextractor.ae.features.TreeFragmentFeatureExtractor
frameSetCategories - Variable in class org.apache.ctakes.temporal.ae.feature.FramesetCategoryExtractor
FramesetCategoryExtractor - Class in org.apache.ctakes.temporal.ae.feature
FramesetCategoryExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.FramesetCategoryExtractor
freqQuery - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
frequency - Variable in class org.apache.ctakes.drugner.DrugMention: e.g.
frequency - Variable in class org.apache.ctakes.drugner.elements.FrequencyElement
FrequencyAnnotation - Class in org.apache.ctakes.drugner.type: The frequency determination for the Drug NER profile.
FrequencyAnnotation() - Constructor for class org.apache.ctakes.drugner.type.FrequencyAnnotation: Never called.
FrequencyAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.FrequencyAnnotation: Internal - constructor used by generator
FrequencyAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.FrequencyAnnotation
FrequencyAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.FrequencyAnnotation
FrequencyAnnotation_Type - Class in org.apache.ctakes.drugner.type: The frequency determination for the Drug NER profile.
FrequencyAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.FrequencyAnnotation_Type: initialize variables to correspond with Cas Type and Features
FrequencyElement - Class in org.apache.ctakes.drugner.elements
FrequencyElement() - Constructor for class org.apache.ctakes.drugner.elements.FrequencyElement
FrequencyElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.FrequencyElement
FrequencyFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect frequency data in the given input of tokens.
FrequencyFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM: Constructor
FrequencyToken - Class in org.apache.ctakes.drugner.fsm.output.elements
FrequencyToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.FrequencyToken
frequencyUnit - Variable in class org.apache.ctakes.drugner.DrugMention: e.g.
frequencyUnit - Variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
FrequencyUnitAnnotation - Class in org.apache.ctakes.drugner.type: The value represents the unit portion of the drug frequency.
FrequencyUnitAnnotation() - Constructor for class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation: Never called.
FrequencyUnitAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation: Internal - constructor used by generator
FrequencyUnitAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation
FrequencyUnitAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation
FrequencyUnitAnnotation_Type - Class in org.apache.ctakes.drugner.type: The value represents the unit portion of the drug frequency.
FrequencyUnitAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type: initialize variables to correspond with Cas Type and Features
FrequencyUnitCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a FrequencyUnitToken.
FrequencyUnitCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.FrequencyUnitCondition
FrequencyUnitElement - Class in org.apache.ctakes.drugner.elements
FrequencyUnitElement() - Constructor for class org.apache.ctakes.drugner.elements.FrequencyUnitElement
FrequencyUnitElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.FrequencyUnitElement
FrequencyUnitFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect frequency unit data in the given input of tokens.
FrequencyUnitFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Constructor
FrequencyUnitToken - Class in org.apache.ctakes.drugner.fsm.output.elements
FrequencyUnitToken(int, int, double) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
fromSet(Set<String>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
fromString(String) - Static method in class org.apache.ctakes.utils.tree.SimpleTree
fs - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
fs2ll(FSList) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
fsGenerator - Variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
fsGenerator - Variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
fsGenerator - Variable in class org.apache.ctakes.assertion.zoner.types.Heading_Type
fsGenerator - Variable in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
fsGenerator - Variable in class org.apache.ctakes.assertion.zoner.types.Zone_Type
fsGenerator - Variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.DemMarkable_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.Markable_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.NEMarkable_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.Pair_Type
fsGenerator - Variable in class org.apache.ctakes.coreference.type.PronounMarkable_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.DosagesAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.DurationAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.FormAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.FrequencyAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.StrengthAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.sideeffect.type.PSESentence_Type
fsGenerator - Variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
fsGenerator - Variable in class org.apache.ctakes.sideeffect.type.SESentence_Type
fsGenerator - Variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
fsGenerator - Variable in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Attribute_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Course_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Entity_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Event_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.Time_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.Affects_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.Contraindicates_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.DegreeOf_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.Diagnoses_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.Indicates_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.LocationOf_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreats_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOf_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.Prevents_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ResultOf_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.TemporalRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.relation.UMLSRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.ADJP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.ADVP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.CONJP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.ContractionToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.INTJ_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.LST_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.NewlineToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.NP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.O_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.PP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.PRT_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.SBAR_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.SymbolToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.UCP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.VP_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.Markable_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textspan.Paragraph_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.util.Pairs_Type
fsGenerator - Variable in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type
fsGenerator - Variable in class org.apache.ctakes.ytex.uima.types.Date_Type
fsGenerator - Variable in class org.apache.ctakes.ytex.uima.types.DocKey_Type
fsGenerator - Variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
FSIteratorToList - Class in org.apache.ctakes.coreference.util: Converts all Annotations that are retrievable from an FSIterator to a sorted LinkedList.
FSIteratorToList() - Constructor for class org.apache.ctakes.coreference.util.FSIteratorToList
FSListIterator<T> - Class in org.apache.ctakes.core.util
FSListIterator(FSList) - Constructor for class org.apache.ctakes.core.util.FSListIterator
FSM - Interface in org.apache.ctakes.core.fsm.machine: Any finate state machine defined must implement this interface
fstem - Variable in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
FSUtil - Class in org.apache.ctakes.core.util
FSUtil() - Constructor for class org.apache.ctakes.core.util.FSUtil
ftParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
ftParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
ftParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
ftParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
ftParams - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
fullPath(File, String) - Static method in class org.apache.ctakes.jdl.common.FileUtil
FullTemporalExtractionPipeline - Class in org.apache.ctakes.temporal.pipelines
FullTemporalExtractionPipeline() - Constructor for class org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline
FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator - Class in org.apache.ctakes.temporal.pipelines
FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator() - Constructor for class org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
FullTemporalExtractionPipeline.FullOptions - Interface in org.apache.ctakes.temporal.pipelines
FullTextDocumentViewBean - Class in org.apache.ctakes.ytex.web.search: Jsf bean to view results of fullTextSearch.jspx.
FullTextDocumentViewBean() - Constructor for class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
fullTextSearch(String) - Method in interface org.apache.ctakes.ytex.web.search.DocumentSearchService: perform full text search
fullTextSearch(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl: perform full text search
FullTextSearchBean - Class in org.apache.ctakes.ytex.web.search: Jsf bean for full text search.
FullTextSearchBean() - Constructor for class org.apache.ctakes.ytex.web.search.FullTextSearchBean
fullWordsNotToBreakAtApostrophe - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
fword - Variable in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
fword - Variable in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
fwordToConceptIdQuery - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl

G

gamma - Variable in class org.apache.ctakes.utils.kernel.RBFKernel
gamma - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
gamma - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
gap() - Method in class org.apache.ctakes.coreference.eval.helpers.Span
GASTRIC - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
GASTRIC - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
geDuration2ndMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM: Gets a finite state machine that detects the following ('once', 'twice', # or text#) a day/week/month/year: for 3 years until gone for-six-months for an additional eight weeks
geDurationMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM: Gets a finite state machine that detects the following ('once', 'twice', # or text#) a day/week/month/year: for 3 years until gone for-six-months for an additional eight weeks
GEL - Static variable in class org.apache.ctakes.drugner.elements.FormElement
generalizeLeaf - Static variable in class org.apache.ctakes.utils.tree.SimpleTree
generateAdditionalNER(JCas, DrugMentionAnnotation, DrugChangeStatusAnnotation, int, int, int, List) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
generateAnnotationMap(JCas) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
generateAnnotationMap(JCas, Integer) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
GenerateDependencyRepresentation - Class in org.apache.ctakes.assertion.pipelines
GenerateDependencyRepresentation() - Constructor for class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
GenerateDependencyRepresentation.Options - Class in org.apache.ctakes.assertion.pipelines
GenerateDependencyRepresentation.Options() - Constructor for class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation.Options
generateDrugMentions(JCas, Segment, boolean) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
generateDrugMentionsAndAnnotations(JCas, List<MedicationMention>, int, int, DrugMentionAnnotation, String[], int, List<DrugMentionAnnotation>) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
generateEvalFiles() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
generateFolds(Set<String>, InstanceData, String, String, int, String, int, int, Random) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl: generate folds for a run
generateFolds(InstanceData, Properties) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil: generate folds from the label to instance map.
generateFolds(InstanceData, Properties) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
generateInstance(<any>, <any>) - Method in class org.apache.ctakes.temporal.utils.SMOTEplus
generateRuns(String, String, String, int, int, Integer, int) - Method in interface org.apache.ctakes.ytex.kernel.FoldGenerator: Generate cross validation folds, store in database.
generateRuns(SortedMap<String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>>, int, int, Integer, int) - Method in interface org.apache.ctakes.ytex.kernel.FoldGenerator: Generate cross validation folds, don't store in database.
generateRuns(String, String, String, int, int, Integer, int) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
generateRuns(SortedMap<String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>>, int, int, Integer, int) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
generateSemilEvalLines() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil: generate command lines for semil
generateSemilEvalParams() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
generateSvmEvalParams(String) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
generateSvmLinParams(String) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
generateTokenNormForms(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator: Generates normalized form for each token annotation.
GenerateTrainingData - Class in org.apache.ctakes.smokingstatus.MLutil
GenerateTrainingData(String, String) - Constructor for class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData
GenerateTreeRepresentation - Class in org.apache.ctakes.assertion.pipelines
GenerateTreeRepresentation() - Constructor for class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
GenerateTreeRepresentation.ATTRIBUTE - Enum in org.apache.ctakes.assertion.pipelines
GenerateTreeRepresentation.ATTRIBUTE() - Constructor for enum org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.ATTRIBUTE
GenerateTreeRepresentation.Options - Class in org.apache.ctakes.assertion.pipelines
GenerateTreeRepresentation.Options() - Constructor for class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
generateUidValues(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator: Generates UID values for all IdentifiedAnnotation objects.
generateUidValues(JCas) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Generates UID values for all MedicationMention objects.
generateUidValues(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Generates UID values for all MedicationMention objects.
generateXMI(SHARPXMI.Options) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
GenericAttributeAnalysisEngine - Class in org.apache.ctakes.assertion.attributes: This class provides a basic generic attribute extraction technique based on dependency parses.
GenericAttributeAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.attributes.GenericAttributeAnalysisEngine
GenericAttributeClassifier - Class in org.apache.ctakes.assertion.attributes.generic
GenericAttributeClassifier() - Constructor for class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
GenericCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
GenericCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
genericExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
genericExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
genericExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
GenericFeaturesExtractor - Class in org.apache.ctakes.assertion.attributes.features: SubjectFeaturesExtractor Ports the features and classification decisions of the first version (logic) of the subject tool
GenericFeaturesExtractor() - Constructor for class org.apache.ctakes.assertion.attributes.features.GenericFeaturesExtractor
GenericMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup
GenericMetaDataHitImpl(Map<String, String>) - Constructor for class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl
GenericModifier - Class in org.apache.ctakes.typesystem.type.textsem: The Generic modifier indicates that a named entity mention is generic, i.e., not related to the instance of a disorder, sign/symptom, etc.
GenericModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.GenericModifier: Never called.
GenericModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.GenericModifier: Internal - constructor used by generator
GenericModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.GenericModifier
GenericModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.GenericModifier
GenericModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: The Generic modifier indicates that a named entity mention is generic, i.e., not related to the instance of a disorder, sign/symptom, etc.
GenericModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type: initialize variables to correspond with Cas Type and Features
get(int) - Method in class org.apache.ctakes.coreference.eval.helpers.Span
get() - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
get(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
get(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
get(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
get(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
get(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
get(Object) - Method in class org.apache.ctakes.utils.struct.CounterMap
get(Object) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap
get1() - Method in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
get1(int) - Method in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
get2() - Method in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
get2(int) - Method in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
getAbnormalInterpretation() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: getter for abnormalInterpretation - gets
getAbnormalInterpretation(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
getAbnormalInterpretation() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: getter for abnormalInterpretation - gets
getAbnormalInterpretation(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
getAdjNegIndicatorMachine() - Method in class org.apache.ctakes.core.fsm.machine.NegationFSM: recognizes "A B ..." where A is unremarkable, unlikely, or negative and B is of, in, for, or with
getAdjNegIndicatorMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
getAdjNegIndicatorMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM
getAdjNegIndicatorMachine() - Method in class org.apache.ctakes.smokingstatus.machine.NegationFSM: recognizes "A B ..." where A is unremarkable, unlikely, or negative and B is of, in, for, or with
getAdjustedWindowSpan(JCas, int, int, boolean) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: return window span to find reasons for the given d
getAE(File) - Static method in class org.apache.ctakes.utils.test.TestUtil
getAlgorithm() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getAllAnnotations(JCas, int) - Method in class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
getAllAnnotations() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile
getAllAuiStr(String) - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao: get all aui, str from mrconso
getAllAuiStr(String) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl: sets up the umls_aui_fword table.
getAllCollections() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
getAllCollections() - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap
getAllCollections() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
getAllCollections() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
getAllCollections() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
getAllCollections() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
getAlleviatingFactor() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for alleviatingFactor - gets
getAlleviatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getAlleviatingFactor() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for alleviatingFactor - gets
getAlleviatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getAlleviatingFactor() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for alleviatingFactor - gets
getAlleviatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getAlleviatingFactor() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for alleviatingFactor - gets
getAlleviatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getAllFiles(File, String) - Static method in class org.apache.ctakes.temporal.eval.I2B2Data
getAllInstanceIds(String, int, int) - Method in class org.apache.ctakes.ytex.kernel.InstanceData: get all the instance ids for the specified scope
getAllKernelEvaluationsForInstance(KernelEvaluation, long) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao
getAllKernelEvaluationsForInstance(KernelEvaluation, long) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
getAllLeaves(ConceptGraph, BufferedWriter) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
getAllowSmallerSystemArguments() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getAllRows() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable
getAllTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getAnalysisBatch() - Method in class org.apache.ctakes.ytex.uima.model.Document
getAnaphor() - Method in class org.apache.ctakes.coreference.type.MarkablePair: getter for anaphor - gets
getAnaphor(int) - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
getAnaphor() - Method in class org.apache.ctakes.coreference.type.MarkablePairSet: getter for anaphor - gets
getAnaphor(int) - Method in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
getAnaphoric_prob() - Method in class org.apache.ctakes.coreference.type.Markable: getter for anaphoric_prob - gets
getAnaphoric_prob(int) - Method in class org.apache.ctakes.coreference.type.Markable_Type
getAnaphoricityFeatures() - Static method in class org.apache.ctakes.coreference.util.FeatureVector
getAnatomicalSites(List<EntityMention>) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getAnatomyKnowtatorClasses() - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
getAncestors(SimpleTree) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getAnnoBaseId() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
getAnnoClassName() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getAnnoFieldName() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getAnnoMappingInfos() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getAnnotation(int) - Method in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
getAnnotation(Annotation) - Method in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
getAnnotation(int) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getAnnotation(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Returns the XcasAnnotation object associated with the specified internal id.
getAnnotationClassNames() - Method in interface org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures.Options
getAnnotationContext(Annotation, int) - Static method in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
getAnnotationContext(Annotation, int) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
getAnnotationId(Annotation) - Method in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
getAnnotationId(int) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getAnnotationIdCount() - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getAnnotationIds() - Method in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
getAnnotationIterator(JCas) - Method in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
getAnnotationKey(Annotation) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
getAnnotations(JCas, int, int, int) - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
getAnnotations() - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Gets a list of Annotation objects that represent annotations based off of document syntactic cues.
getAnnotationsInSpan(JCas, int, int, int, int[]) - Static method in class org.apache.ctakes.core.util.FSUtil
getAnnotationsInSpan(JCas, int, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
getAnnotationsInSpanIterator(JCas, int, int, int) - Static method in class org.apache.ctakes.core.util.FSUtil: Deprecated.
getAnnotationsInSpanWithAdaptToBaseTokenFSM(JCas, int, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
getAnnotationsInWindow(JCas, AnnotationFS, List<FastLookupToken>, Collection<Integer>) - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: For the given lookup window fills two collections with 1) All tokens in the window, and 2) indexes of tokens in the window to be used for lookup
getAnnotationsIteratorInSpan(JCas, int, int, int) - Static method in class org.apache.ctakes.core.util.FSUtil: For correct behavior, requires types to be listed in TypePriorities so that the subiterator works as expected
getAnnotationTree(JCas, Annotation) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
getAnnotatorDescription() - Static method in class org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator
getAnnotatorDescription() - Static method in class org.apache.ctakes.temporal.ae.ClearTKDocumentCreationTimeAnnotator
getAnnotatorDescription() - Static method in class org.apache.ctakes.temporal.ae.ClearTKLinkToTHYMELinkAnnotator
getAnnotatorDescription() - Static method in class org.apache.ctakes.temporal.ae.EventToClearTKEventAnnotator
getAnnotatorDescription(File) - Static method in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
getAnnotatorDescription() - Static method in class org.apache.ctakes.temporal.ae.TimexToClearTKTimexAnnotator
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
getAnnotatorDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
getAnnotatorNames() - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader: Returns the names of the annotators in the Knowtator files that represent the gold standard
getAnnotatorNames() - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader: Returns the names of the annotators in the Knowtator files that represent the gold standard
getAnnotatorNames() - Method in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
getAntecedent() - Method in class org.apache.ctakes.coreference.type.MarkablePair: getter for antecedent - gets Proposed antecedent
getAntecedent(int) - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
getAntecedentList() - Method in class org.apache.ctakes.coreference.type.MarkablePairSet: getter for antecedentList - gets
getAntecedentList(int) - Method in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
getApplicationContext() - Static method in class org.apache.ctakes.ytex.kernel.KernelContextHolder
getApplicationContext() - Static method in class org.apache.ctakes.ytex.kernel.SimSvcContextHolder
getApplicationContext() - Static method in class org.apache.ctakes.ytex.uima.ApplicationContextHolder
getArg1() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
getArg1() - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation: getter for arg1 - gets
getArg1(int) - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
getArg1() - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: getter for arg1 - gets
getArg1(int) - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
getArg1() - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation: getter for arg1 - gets
getArg1(int) - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
getArg2() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
getArg2() - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation: getter for arg2 - gets
getArg2(int) - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
getArg2() - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: getter for arg2 - gets
getArg2(int) - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
getArg2() - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation: getter for arg2 - gets
getArg2(int) - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
getArgFeats(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Static method in class org.apache.ctakes.temporal.ae.feature.ListFeaturesExtractor
getArgument(String, Map<String, Annotation>, String) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
getArgument() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: getter for argument - gets
getArgument(int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
getArgument() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: getter for argument - gets
getArgument(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
getAsCui(Long) - Static method in class org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil
getAsCui(String) - Static method in class org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil
getAsCui(StringBuilder) - Static method in class org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil
getAsEvaluation() - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
getAsNeededMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a fsm that detects every other hour prn.
getAspect() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for aspect - gets
getAspect(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getAspectualNegIndicatorMachine() - Method in class org.apache.ctakes.core.fsm.machine.NegationFSM
getAspectualNegIndicatorMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM: Gets a finite state machine that detects the following: 10/15/2002 10/15 10-15-2002 10-15
getAspectualNegIndicatorMachine() - Method in class org.apache.ctakes.smokingstatus.machine.NegationFSM
getAssertionType() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion: getter for assertionType - gets assertion type -- one of present, absent, possible, conditional, hypothetical, or assocated_with_someone_else
getAssertionType(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
getAssociatedConcept() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion: getter for associatedConcept - gets
getAssociatedConcept(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
getAssociatedSignSymptom() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for associatedSignSymptom - gets
getAssociatedSignSymptom(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getAssociatedSignSymptom() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for associatedSignSymptom - gets
getAssociatedSignSymptom(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getAsStream(String) - Static method in class org.apache.ctakes.core.resource.FileLocator
getAsTui(Integer) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
getAsTui(String) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
getAsTui(StringBuilder) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
getAttribute() - Method in class org.apache.ctakes.typesystem.type.util.Pair: getter for attribute - gets
getAttribute(int) - Method in class org.apache.ctakes.typesystem.type.util.Pair_Type
getAttribute(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Returns the value of the specified attribute.
getAttributeKey() - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
getAttributeName() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue: getter for attributeName - gets
getAttributeName(int) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
getAttributeName() - Method in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
getAttributes(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader: Attributes of each named entity indexed on mention ids.
getAttributes(Document, String[]) - Static method in class org.apache.ctakes.assertion.cr.XMLReader: Attributes of each named entity indexed on mention ids.
getAttributeSelection() - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
getAttributeStringValue() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue: getter for attributeStringValue - gets
getAttributeStringValue(int) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
getAttributeValue(Element, String) - Method in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
getAttrValueString(IdentifiedAnnotation, JudgeAttributeInstances.Selector) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
getAtui() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
getAui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getAui() - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
getAuthorSpecialty() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for authorSpecialty - gets
getAuthorSpecialty(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getBagOfWordsExporter() - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.TempRelOptions
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.TempRelOptions
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.TempRelOptions
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.TempRelOptions
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.TempRelOptions
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.TempRelOptions
getBaseline() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.TempRelOptions
getBatchCount() - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter.TableSqlInfo
getBatchesDirectory() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.Options
getBatchSize() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getBegin() - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
getBegin() - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.AssociatedCodeElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.DosageElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.DurationElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.FormElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.FrequencyElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.RouteElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.StartDateElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.StrengthElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.StrengthUnitElement
getBeginOffset() - Method in class org.apache.ctakes.drugner.elements.TextMentionElement
getBestLCS(Set<String>, boolean, Map<String, Double>) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: get the best lcs
getBestLCS(Set<String>, boolean, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getBestLCS(Set<String>, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getBirthDate() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for birthDate - gets
getBirthDate(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getBloodPressureMachine() - Method in class org.apache.ctakes.core.fsm.machine.MeasurementFSM: Gets a finite state machine that detects the following: 110/80
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getBodyLaterality() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for bodyLaterality - gets
getBodyLaterality(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getBodyLocation() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for bodyLocation - gets
getBodyLocation(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getBodyLocation() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for bodyLocation - gets
getBodyLocation(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getBodyLocation() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for bodyLocation - gets
getBodyLocation(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getBodyLocation() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for bodyLocation - gets
getBodyLocation(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getBodyLocation() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for bodyLocation - gets
getBodyLocation(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getBodyLocation() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for bodyLocation - gets
getBodyLocation(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getBodySide() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for bodySide - gets
getBodySide(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getBooleanConfigParam(UimaContext, String, boolean) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
getBufferedReader(String) - Static method in class org.apache.ctakes.postagger.TagDictionaryCreator
getCacheKey(Method, Object[]) - Method in interface org.apache.ctakes.ytex.kernel.evaluator.CacheKeyGenerator
getCacheKey(Object, Object) - Method in interface org.apache.ctakes.ytex.kernel.evaluator.CacheKeyGenerator
getCacheKey(Method, Object[]) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SymmetricPairCacheKeyGenerator
getCacheKey(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SymmetricPairCacheKeyGenerator
getCacheKeyGenerator() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
getCacheKeyGenerator() - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
getCacheManager() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
getCacheManager() - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
getCacheManager() - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
getCacheManager() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getCacheName() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
getCacheName() - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Selects the relevant mentions/annotations within a covering annotation for relation identification/extraction.
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.baselines.F1BaselineEventTimeRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventEventRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.baselines.TimidBaselineEventTimeRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.baselines.TreeHeightBaseline
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
getCanonical(File, String) - Static method in class org.apache.ctakes.jdl.common.FileUtil
getCanonical(File) - Static method in class org.apache.ctakes.jdl.common.FileUtil
getCanonicalForm() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: getter for canonicalForm - gets
getCanonicalForm(int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
getCanonicalForm(String) - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord: copied from edu.mayo.bmi.uima.lvg.ae.LvgAnnotator
getCapitalization() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: getter for capitalization - gets
getCapitalization(int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
getCaps() - Method in class org.apache.ctakes.core.fsm.adapters.WordTokenAdapter
getCaps() - Method in class org.apache.ctakes.core.fsm.token.adapter.WordTokenAdapter
getCaps() - Method in interface org.apache.ctakes.core.fsm.token.WordToken
getCaps() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Gets the caps state of the token.
getCas() - Method in class org.apache.ctakes.ytex.uima.model.Document
getCategory() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for category - gets Type of Event.
getCategory(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getCategory() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for category - gets
getCategory(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getCategory() - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier: getter for category - gets
getCategory(int) - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
getChangeStatus() - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation: getter for changeStatus - gets Indicates the drug change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.
getChangeStatus(int) - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
getChangeStatusBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getChangeStatusBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for changeStatusBegin - gets
getChangeStatusBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getChangeStatusEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getChangeStatusEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for changeStatusEnd - gets
getChangeStatusEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getChangeStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following: 'tapered' or 'then': taper then
getChar() - Method in class org.apache.ctakes.core.fsm.adapters.CharacterTokenAdapter
getChar() - Method in class org.apache.ctakes.core.fsm.token.adapter.CharacterTokenAdapter
getChar() - Method in interface org.apache.ctakes.core.fsm.token.CharacterToken
getChild(Element, String) - Method in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
getChildAnnoBaseId() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
getChildAnnotationId() - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
getChildren() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for children - gets
getChildren(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: indexed getter for children - gets an indexed value -
getChildren(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getChildren(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getChildren() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getChildren() - Method in class org.apache.ctakes.ytex.kernel.tree.Node
getChildrenArray() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getChildUimaTypeId() - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
getChunkType() - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk: getter for chunkType - gets
getChunkType(int) - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
getClassAuto() - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
getClasses() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getClassFeatureQuery() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getClassGold() - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
getClassIds() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
getClassIds(ClassifierEvaluation, Integer) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getClassification() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: getter for classification - gets Smoking status classification for the given sentence.
getClassification(int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
getClassification() - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: getter for classification - gets represents the document level classification that RecordResolutionAnnotator assigns
getClassification(int) - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
getClassificationOnly() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.TempRelOptions
getClassifierEvaluation() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getClassifierEvaluation() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getClassifierEvaluationDao() - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
getClassifierEvaluationId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getClassifierEvaluationIRStatId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getClassifierInstanceEvaluationId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
getClassifierInstanceEvaluations() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getClassifierInstanceProbabilities() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
getClassOfT() - Method in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
getClosedTlinks(JCas) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.TempRelOptions
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.TempRelOptions
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.TempRelOptions
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.TempRelOptions
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.TempRelOptions
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.TempRelOptions
getClosure() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.TempRelOptions
getCode() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: getter for code - gets
getCode(int) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getCode() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
getCode() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getCodes(ConceptCode) - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
getCodingScheme() - Method in class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
getCodingScheme() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: getter for codingScheme - gets
getCodingScheme(int) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getCodingScheme() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
getCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: gets a collection mapped with key.
getCollection(K) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: gets a collection mapped with key.
getCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: gets a collection mapped with key.
getCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: gets a collection mapped with key.
getCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: gets a collection mapped with key.
getCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: gets a collection mapped with key.
getCollectionReader(List<File>) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
getCollectionReader(File) - Static method in class org.apache.ctakes.relationextractor.data.analysis.Utils: Instantiate an XMI collection reader.
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline
getCollectionReader(List<File>) - Method in class org.apache.ctakes.relationextractor.eval.SHARPXMI.Evaluation_ImplBase
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.duration.Utils: Instantiate an XMI collection reader.
getCollectionReader(List<Integer>) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getCollectionReader(List<File>) - Static method in class org.apache.ctakes.temporal.pipelines.EventPrintingPipeline
getColorsForTypesFromFile(CasAnnotationViewer, File) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: copied from AnnotationViewerDialog.
getColorsForTypesFromFile(CasAnnotationViewer, File) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Reads in annotation-color associations from stylemap file.
getColumnMappingInfos() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getColumnName() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getCombinedTypeConservative(TlinkType, TlinkType) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType
getCombinedTypeLiberal(TlinkType, TlinkType) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType
getCommonAncestor(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
getCommonAncestor(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils: Returns the common ancestor between them
getCommonNode() - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
getComponents() - Static method in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
getConcept() - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
getConcept1() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
getConcept1() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getConcept1Path() - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
getConcept2() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
getConcept2() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getConcept2Path() - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
getConceptByFirstWord(String) - Method in interface org.apache.ctakes.ytex.web.search.ConceptSearchService: get Concepts that start with the specified text.
getConceptByFirstWord(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
getConceptById(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
getConceptDao() - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
getConceptDao() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getConceptDao() - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
getConceptDao() - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
getConceptDao() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getConceptFactories() - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getConceptFactories() - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getConceptFactory(String) - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getConceptFactory(String) - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getConceptGraph(String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ConceptDao: retrieve an existing concept graph.
getConceptGraph(String) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
getConceptGraph() - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService
getConceptGraph() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getConceptGraph() - Method in class org.apache.ctakes.ytex.ws.SimServiceInfo
getConceptGraphName() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getConceptGraphName() - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService
getConceptGraphName() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getConceptGraphName() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getConceptGraphs() - Method in interface org.apache.ctakes.ytex.ws.ConceptSimilarityRestService
getConceptGraphs() - Method in interface org.apache.ctakes.ytex.ws.ConceptSimilarityWebService
getConceptGraphs() - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
getConceptId() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
getConceptID() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getConceptId(FeatureStructure) - Method in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator: get the concept id for the specified concept.
getConceptId() - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
getConceptList() - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
getConceptMap() - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
getConceptPair() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
getConceptPair() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
getConceptPairText() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getConceptSearchService() - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
getConceptSearchService() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
getConceptSetName() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getConceptSetName() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getConceptSimilarityService() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
getConceptSimilarityService() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
getConceptSimilarityService() - Method in class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric
getConceptSimilarityService() - Method in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
getConceptSimilarityService() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
getConceptSimilarityService(String) - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
getConceptText() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: getter for conceptText - gets
getConceptText(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
getConceptType() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: getter for conceptType - gets the concept type -- one of problem, treatment, or test
getConceptType(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
getConditional() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for conditional - gets
getConditional(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getConditional() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for conditional - gets Whether the relation is conditional/hypothetical.
getConditional(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getConditional() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for conditional - gets
getConditional(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getConfidence() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for confidence - gets The confidence of the annotation.
getConfidence(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getConfidence() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for confidence - gets
getConfidence(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getConfidence() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for confidence - gets
getConfidence(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getConfidence() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for confidence - gets The confidence of the annotation.
getConfidence(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getConfidenceScoreElement() - Method in class org.apache.ctakes.drugner.DrugMention
getConfidenceScoreElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getConfidenceScoreElement() - Method in class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
getConfig() - Static method in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
getConfirmSubSectionMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
getConnection() - Method in interface org.apache.ctakes.core.resource.JdbcConnectionResource: Gets the JDBC connection.
getConnection() - Method in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl
getConnection(String, String, String, String) - Method in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory: Get an existing Connection or create and store a new one
getConnection() - Method in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl
getConnectionUrl(String) - Static method in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory: Uses FileLocator to get the canonical path to the database file
getConnTypeBySrcXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getConnTypeByStrXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getConsumer() - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getConsumer() - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getContent() - Method in class org.apache.ctakes.core.util.DocumentSection
getContent() - Method in class org.apache.ctakes.coreference.type.Markable: getter for content - gets The markable instance, i.e., a Named Entity, pronoun Token, etc.
getContent(int) - Method in class org.apache.ctakes.coreference.type.Markable_Type
getContext() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
getContextHit(List, int) - Method in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
getContextMap(JCas, int, int) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl: returns an empty map Gets context for the specified window.
getContextMap(JCas, int, int) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets context for the specified window.
getContextMap(JCas, int, int) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer: Gets context for the specified window.
getContextMap(JCas, int, int) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets context for the specified window.
getContextSize() - Method in interface org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.Options
getContextualAspect() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for contextualAspect - gets
getContextualAspect(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getContextualModality() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for contextualModality - gets
getContextualModality(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getContingencyTable() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
getContractionTokenLen() - Method in class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
getConverter() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getCoreferenceModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.FullOptions
getCorpusCuiTuis(String, String, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getCorpusCuiTuis(String, String, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getCorpusIC() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
getCorpusLcs() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getCorpusLcsIC() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getCorpusLcsTerm() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getCorpusName() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
getCorpusName() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getCorpusName() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getCorpusName() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getCorpusName() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getCorpusName() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getCorrespondingCasThatHasGoldAnnotations(String) - Static method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
getCosineSimilarity(String, String) - Method in class org.apache.ctakes.utils.wiki.WikiIndex: Send two queries to the index.
getCost() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getCourse() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for course - gets
getCourse(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getCourse() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for course - gets
getCourse(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getCourse() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for course - gets
getCourse(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getCourse() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for course - gets
getCourse(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getCoveredText() - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
getCoveredTextColumn() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getCoveredTextMaxLen() - Method in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.baselines.F1BaselineEventTimeRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventEventRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.baselines.TimidBaselineEventTimeRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.baselines.TreeHeightBaseline
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
getCoveringClass() - Method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
getCoveringSentence(EventMention, Map<EventMention, Collection<Sentence>>) - Static method in class org.apache.ctakes.temporal.ae.feature.SpecialAnnotationRelationExtractor
getCoveringSpan() - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: Get a span that approximates KnowtatorAnnotation.spans, giving the earliest begin offset and the latest end offset.
getCpostag() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for cpostag - gets
getCpostag(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getCR(File) - Static method in class org.apache.ctakes.utils.test.TestUtil
getCrossValidationFold(String, String, String, int, int) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getCrossValidationFold(String, String, String, int, int) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getCrossValidationFoldId() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getCrossValidationFoldId() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getCtakesSemantics() - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
getCuePhrase() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: getter for cuePhrase - gets cue phrase itself (from lookup list)
getCuePhrase(int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
getCuePhraseAssertionFamily() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: getter for cuePhraseAssertionFamily - gets which assertion family this cue phrase belongs to (negation, uncertainty, or conditional)
getCuePhraseAssertionFamily(int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
getCuePhraseCategory() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: getter for cuePhraseCategory - gets
getCuePhraseCategory(int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
getCuePhraseFirstWord() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: getter for cuePhraseFirstWord - gets first word of cue phrase
getCuePhraseFirstWord(int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
getCui() - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
getCui() - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
getCui() - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
getCui() - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
getCui() - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: getter for cui - gets
getCui(int) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
getCui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getCui() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
getCui1() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
getCui2() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
getCuiCode() - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
getCuiCode(String) - Static method in class org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil
getCuiCode() - Method in class org.apache.ctakes.drugner.elements.AssociatedCodeElement
getCuiCode() - Method in class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
getCuiCode() - Method in class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
getCuiCodes(Collection<String>) - Static method in class org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil
getCUIs(IdentifiedAnnotation) - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getCuiText() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
getCuiTuiMap() - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: cui - tui map.
getCuiTuiMap() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getCuiTuiQuery() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
getCurrentCUI() - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean: Gets the currently selected city.
getCurrentCUI() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean: Gets the currently selected city.
getCurrentWorkingDirectory() - Method in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
getCustomizedDictionary(String) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer: Read comma separate file containing target CUIs.
getCutoff() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
getCvf() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getCvf() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
getDailyMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects the following which indicates 1 per day: q.d. o.d. h.s. p.m.
getDailySuffixMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects the following which indicates 1 per day via the following: /d
getDashDashMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM: Gets a finite state machine that detects the following: 25.4-30.4 32.1-three
getDashMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM: Gets a finite state machine that detects the following: 25.4-30.4 32.1-three
getDashMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.HyphenatedDrugFSM: Gets a finite state machine that detects the following: zyrtec-d alka-seltzer plus
getDashMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM: Gets a finite state machine that detects the following: 25.4-30.4 32.1-three
getDataFilePrefix(String, String, Integer, Integer, Boolean) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil: construct file name for train/test set, will be like label[label]_run[run]_fold[fold]_train
getDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
getDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
getDataSource() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
getDataSource() - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
getDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
getDataSource() - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
getDataSource() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
getDataSource() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl
getDataSource() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getDataSource() - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
getDataSource() - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
getDataSource() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
getDataSource() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getDataSource() - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
getDataWriterClass() - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
getDataWriterDescription(Class<? extends <any>>, File) - Static method in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
getDataWriterDescription(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
getDate() - Method in class org.apache.ctakes.drugner.elements.StartDateElement
getDate() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: getter for date - gets
getDate(int) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
getDate() - Method in class org.apache.ctakes.ytex.uima.types.Date: getter for date - gets ISO 8601 Formatted Timestamp: yyyy-MM-dd'T'HH:mm:ssZ
getDate(int) - Method in class org.apache.ctakes.ytex.uima.types.Date_Type
getDateFrom() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getDateTo() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getDateValue() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue: getter for dateValue - gets
getDateValue(int) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
getDay() - Method in class org.apache.ctakes.typesystem.type.refsem.Date: getter for day - gets
getDay(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
getDbSchema() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getDbType() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getDeathDate() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for deathDate - gets
getDeathDate(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getDecimalStrengthMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DecimalStrengthFSM: Gets a finite state machine that detects the following: 0.5*
getDecreaseFromAndTheStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following : 'decrease from' or 'lowered from': decrease from
getDecreaseStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following : 'decrease' or 'lowered': decrease
getDefaultAnalysisBatch() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getDefaultCasViewName() - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Gets the name of the CAS View that will be displayed first in the annotation viewer.
getDefaultConceptGraph() - Method in interface org.apache.ctakes.ytex.ws.ConceptSimilarityRestService
getDefaultConceptGraph() - Method in interface org.apache.ctakes.ytex.ws.ConceptSimilarityWebService
getDefaultConceptGraph() - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
getDefaultConceptGraphDir() - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: use value of org.apache.ctakes.ytex.conceptGraphDir if defined.
getDefaultConceptGraphName() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
getDefaultPipeline() - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getDefaultValue() - Method in enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption
getDegree() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for degree - gets
getDegree(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getDegree() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
getDegree() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getDelegateKernel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
getDelegateKernel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
getDelegateKernel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
getDelegateKernel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
getDelegateKernels() - Method in class org.apache.ctakes.ytex.kernel.evaluator.ProductKernel
getDelegateKernels() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SumKernel
getDeltaFlag() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: getter for deltaFlag - gets
getDeltaFlag(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
getDeltaFlag() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: getter for deltaFlag - gets
getDeltaFlag(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
getDemCorefFeatures() - Static method in class org.apache.ctakes.coreference.util.FeatureVector
getDemographics() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: getter for demographics - gets
getDemographics(int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
getDependencyNode(JCas, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Returns the first ConllDependencyNode in the CAS w/ same begin and end as the given Annotation
getDependencyNodes(JCas, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Returns the ConllDependencyNodes in the CAS w/ subsumed begins and ends
getDependingVerbFeature(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor
getDepLCA(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
getDeprel() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for deprel - gets
getDeprel(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getDepth() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
getDepth(String) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService
getDepth(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getDepth() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getDepthMax() - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
getDescription(Object...) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
getDescription() - Static method in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes: Parses and returns the descriptor for this collection reader.
getDescription(Object...) - Static method in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
getDescription(File) - Static method in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
getDescription() - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
getDescription(File) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
getDescription(File) - Static method in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
getDescription(File) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
getDescription(Class<?>...) - Static method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyFromGold
getDescription() - Static method in class org.apache.ctakes.temporal.pipelines.EventPrintingPipeline.PrintEventAnnotations
getDescription() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
getDescription() - Method in class org.apache.ctakes.ytex.ws.SimServiceInfo
getDescriptorsDirectory() - Method in interface org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain.Options
getDescriptorURL() - Static method in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
getDevPatientSets(File) - Static method in class org.apache.ctakes.temporal.eval.I2B2Data
getDevPatientSets(List<Integer>) - Static method in class org.apache.ctakes.temporal.eval.THYMEData: Deprecated.
Use getPatientSets(patientSets, DEV_REMAINDERS)
getDevRemainders() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getDevTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getDialectClassName() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getDictionaries() - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
getDictionaries() - Method in interface org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator
getDictionaries() - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getDictionaries() - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getDictionary(String) - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getDictionary(String) - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getDictionary() - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Initialize WordNet dictionary.
getDictMetaDataHit() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
getDimensionality() - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings
getDirectory1() - Method in interface org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures.Options
getDirectory2() - Method in interface org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures.Options
getDisambiguated() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: getter for disambiguated - gets Word Sense disambiguation: if this named entity is assigned multiple ontologyConcepts, then the OntologyConcept with disambiguated=true is the most likely sense
getDisambiguated(int) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getDiscoveryTechnique() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for discoveryTechnique - gets
getDiscoveryTechnique(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getDiscoveryTechnique() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for discoveryTechnique - gets
getDiscoveryTechnique(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getDiscoveryTechnique() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for discoveryTechnique - gets
getDiscoveryTechnique(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getDiseaseDisorderKnowtatorClasses() - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
getDisplayValue(int, Annotation) - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer: Gets a value to be displayed in table cell for the given annotation object.
getDistance(JCas, RelationExtractorAnnotator.IdentifiedAnnotationPair) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Calculate the distance (in tokens) between two identified annotations.
getDistance() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
getDocLengthMap() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getDocResultInstanceImporter() - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
getDocText() - Method in class org.apache.ctakes.ytex.uima.model.Document
getDocText() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getDocText() - Method in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
getDocTimeRel() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for docTimeRel - gets
getDocTimeRel(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getDoctimerelModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.FullOptions
getDocument(int) - Method in interface org.apache.ctakes.ytex.uima.dao.DocumentDao: Retrieve document by primary key
getDocument(int) - Method in class org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl
getDocument() - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
getDocument() - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
getDocumentAnnotationID() - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
getDocumentAnnotations() - Method in class org.apache.ctakes.ytex.uima.model.Document
getDocumentById(JCas, Map<String, Object>) - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
getDocumentClasses() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getDocumentClasses() - Method in class org.apache.ctakes.ytex.uima.model.Document
getDocumentClassID() - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
getDocumentDate() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
getDocumentID(ResultSet) - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader: Builds a document ID from one or more pieces of query data.
getDocumentID(JCas) - Static method in class org.apache.ctakes.core.util.DocumentIDAnnotationUtil
getDocumentID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID: getter for documentID - gets
getDocumentID(int) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
getDocumentID() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID: getter for documentID - gets
getDocumentID(int) - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
getDocumentID() - Method in class org.apache.ctakes.ytex.uima.model.Document
getDocumentID() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
getDocumentID() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getDocumentID() - Method in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
getDocumentSearchService() - Method in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
getDocumentSearchService() - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
getDocumentSearchService() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getDocumentStandard() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for documentStandard - gets
getDocumentStandard(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getDocumentTitle() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
getDocumentTypeName() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
getDosage() - Method in class org.apache.ctakes.drugner.elements.DosageElement
getDosage() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for dosage - gets Dosage refers to how many of each drug the patient is taking.
getDosage(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getDosageBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getDosageBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for dosageBegin - gets
getDosageBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getDosageElement() - Method in class org.apache.ctakes.drugner.DrugMention
getDosageElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getDosageEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getDosageEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for dosageEnd - gets
getDosageEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getDosageQuantityMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM: - * Gets a finite state machine that detects the following: one milligram one mg 1 milligram 1 mg 10mg 0.5 mg 1-5 milligrams
getDotDashMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM: Gets a finite state machine that detects the following: 250-300 I-IV two-three two-to-three
getDoubleProperty(Properties, String, Double) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil
getDrug() - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: getter for drug - gets
getDrug(int) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
getDrugChangeStatus() - Method in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
getDrugChangeStatus() - Method in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
getDrugChangeStatus() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for drugChangeStatus - gets Status refers to the whether the medication is currently being taken or not.
getDrugChangeStatus(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getDrugChangeStatusElement() - Method in class org.apache.ctakes.drugner.DrugMention
getDrugChangeStatusElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getDrugsInSpan(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return the List of drug IdentifiedAnnotation within the span
getDuratationBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getDuratationEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getDuration() - Method in class org.apache.ctakes.drugner.elements.DurationElement
getDuration() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for duration - gets Duration refers to for how long the patient is expected to take the drug.
getDuration(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getDuration() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for duration - gets
getDuration(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getDuration() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for duration - gets
getDuration(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getDuration() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for duration - gets
getDuration(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getDuration() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for duration - gets
getDuration(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getDuration() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for duration - gets
getDuration(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getDuration() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for duration - gets
getDuration(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getDurationBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for durationBegin - gets
getDurationBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getDurationElement() - Method in class org.apache.ctakes.drugner.DrugMention
getDurationElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getDurationEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for durationEnd - gets
getDurationEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getEmbeddings() - Method in class org.apache.ctakes.utils.distsem.WordVectorReader
getEmbeddings(String) - Static method in class org.apache.ctakes.utils.distsem.WordVectorReader
getEmbeddings(InputStream) - Static method in class org.apache.ctakes.utils.distsem.WordVectorReader
getEmptyDocument() - Static method in class org.apache.ctakes.jdl.data.xml.DomUtil
getEmptyString() - Static method in class org.apache.ctakes.ytex.dao.DBUtil
getEnclosingNP(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
getEncounterNum(SourceData) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil
getEnd() - Method in class org.apache.ctakes.core.sentence.SentenceSpan
getEnd() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
getEnd() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
getEnd() - Method in interface org.apache.ctakes.dictionary.lookup2.textspan.TextSpan
getEnd() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
getEnd() - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
getEnd() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
getEnd() - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
getEnd() - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
getEndDate() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for endDate - gets
getEndDate(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getEndDate() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for endDate - gets
getEndDate(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getEndDate() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for endDate - gets
getEndDate(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getEndDateElement() - Method in class org.apache.ctakes.drugner.DrugMention
getEndDateElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getEndLine() - Method in class org.apache.ctakes.core.util.DocumentSection
getEndOffset() - Method in class org.apache.ctakes.core.fsm.adapters.BaseTokenAdapter
getEndOffset() - Method in class org.apache.ctakes.core.fsm.output.BaseTokenImpl
getEndOffset() - Method in class org.apache.ctakes.core.fsm.token.adapter.BaseTokenAdapter
getEndOffset() - Method in interface org.apache.ctakes.core.fsm.token.BaseToken
getEndOffset() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Gets the end offset.
getEndOffset() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter: Gets the end offset.
getEndOffset() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation: Gets the end offset.
getEndOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
getEndOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.AssociatedCodeElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.ConfidenceScoreElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.DosageElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.DurationElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.FormElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.FrequencyElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.RouteElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.StartDateElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.StrengthElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.StrengthUnitElement
getEndOffset() - Method in class org.apache.ctakes.drugner.elements.TextMentionElement
getEndOffset() - Method in class org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl
getEndOffset() - Method in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
getEndOfLineTokens(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Gets a list of tokens that mark end of a line.
getEndOfSentenceCharacters() - Method in class org.apache.ctakes.core.sentence.EndOfSentenceScannerImpl
getEndTime() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for endTime - gets
getEndTime(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getEndTime() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for endTime - gets
getEndTime(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getEndTime() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for endTime - gets
getEndTime(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getEndTime() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for endTime - gets
getEndTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getEndTime() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for endTime - gets
getEndTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getEndTime() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for endTime - gets
getEndTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getEntitiesSuitableForDegreeOf(List<EntityMention>) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
getEntitiesSuitableForLocationOf(List<EntityMention>) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getEntity() - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention: getter for entity - gets
getEntity(int) - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
getEntityAttributes(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader: Attribute mention IDs of each named entity, indexed on mention ids Filter based on entity types, so non-NE get left out.
getEntityFeats(JCas, IdentifiedAnnotation, Sentence) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SRLFeatureExtractor
getEntityMentions(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader: Get spans of named entity annotations indexed on knowtator mention id
getEntityMentions(Document) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader: Get spans of named entity annotations indexed on knowtator mention id
getEntityStats(String) - Static method in class org.apache.ctakes.relationextractor.data.Stats
getEntityType(int) - Static method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
getEntityTypeId(String) - Static method in class org.apache.ctakes.core.util.Mapper: Map entity type to its integer id.
getEntityTypes(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader: Type of each named entity indexed on mention ids
getEntityTypes(Document) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader: Type of each named entity indexed on mention ids
getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl: Deprecated.
getEntries(String) - Method in interface org.apache.ctakes.dictionary.lookup.Dictionary: Gets any meta data entries associated with the specified input text.
getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl: Gets any meta data entries associated with the specified input text.
getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl: Gets any meta data entries associated with the specified input text.
getEntries(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl: Gets any meta data entries associated with the specified input text.
getEntropyX() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
getEntropyXY() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
getEnv(String, UimaContext) - Static method in class org.apache.ctakes.utils.env.EnvironmentVariable: Get the value of some variable in the full (os, user, java, ctakes) environment.
getEnv(String) - Static method in class org.apache.ctakes.utils.env.EnvironmentVariable: Get the value of some variable in the full (os, user, java, ctakes) environment.
getError() - Method in class org.apache.ctakes.jdl.data.xml.Validation
getEscapeBegin() - Static method in class org.apache.ctakes.ytex.dao.DBUtil
getEscapeEnd() - Static method in class org.apache.ctakes.ytex.dao.DBUtil
getEvaluation() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
getEvaluationType() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getEvaluteOn() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluationOptions
getEvent() - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention: getter for event - gets
getEvent(int) - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
getEventEventRelationModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.FullOptions
getEventFeats(String, EventMention) - Static method in class org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor
getEventModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.EventAndTimeExtractionPipeline.ETOptions
getEventModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.FullOptions
getEventOutputFile() - Method in interface org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.Options
getEventOutputFile() - Method in interface org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.Options
getEventOutputFile() - Method in interface org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.Options
getEventTimeRelationModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.FullOptions
getEveryOtherDayMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a fsm that detects every other day q.a.d.
getEveryOtherHourMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a fsm that detects every other hour q.o.d.
getExacerbatingFactor() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for exacerbatingFactor - gets
getExacerbatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getExacerbatingFactor() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for exacerbatingFactor - gets
getExacerbatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getExacerbatingFactor() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for exacerbatingFactor - gets
getExacerbatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getExacerbatingFactor() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for exacerbatingFactor - gets
getExacerbatingFactor(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getExpandedEvent(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor
getExpandedEvent(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor
getExperiment() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getExperiment() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getExperiment() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getExportType() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getExternalId() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: getter for externalId - gets
getExternalId(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
getF1() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getF1() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getFamilyHistoryMachine() - Method in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM: Gets a finite state machine that detects the following: fh fx family history
getFamilyHistoryMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM: Gets a finite state machine that detects the following: fh fx family history
getFastPipeline() - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getFeats() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for feats - gets
getFeats(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getFeature(TOP) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
getFeature(TOP) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
getFeature() - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS: getter for feature - gets
getFeature(int) - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
getFeature() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
getFeatureEval() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
getFeatureEvaluationId() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getFeatureExtractors() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Defines the list of feature extractors used by the classifier.
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.baselines.TreeHeightBaseline
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
getFeatureExtractors() - Method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
getFeatureName(Feature) - Method in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
getFeatureName(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
getFeatureName(Feature) - Method in class org.apache.ctakes.temporal.utils.SMOTEplus
getFeatureName() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
getFeatureParentChildId() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
getFeatureRankChild() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
getFeatureRankEvaluations(String, String, String, String, Integer, double, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getFeatureRankEvaluations(Set<String>, String, String, String, String, Integer, double, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getFeatureRankEvaluations(Set<String>, String, String, String, String, Integer, double, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getFeatureRankEvaluations(String, String, String, String, Integer, double, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getFeatureRankId() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
getFeatureRankParent() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
getFeatureRanks(Set<String>, String, String, String, String, Integer, double, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getFeatureRanks(Set<String>, String, String, String, String, Integer, double, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getFeatures() - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: getter for features - gets
getFeatures(int) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: indexed getter for features - gets an indexed value -
getFeatures(int) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
getFeatures(int, int) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
getFeatureSelectionThreshold() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventSpans.Options
getFeatureSelectionThreshold() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getFeatureSetName() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getFeatureStructureAtIndex(JCas, Class<T>, int) - Static method in class org.apache.ctakes.utils.test.TestUtil
getFeatureStructureSize(JCas, Class<T>) - Static method in class org.apache.ctakes.utils.test.TestUtil
getFeatureValue(Feature, Class<? extends Object>, Annotation) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
getFieldIndex() - Method in interface org.apache.ctakes.core.cc.AbstractJdbcWriter.FieldInfo
getFieldIndex() - Method in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
getFieldInfos() - Method in interface org.apache.ctakes.core.cc.AbstractJdbcWriter.TableInfo
getFieldName() - Method in interface org.apache.ctakes.core.cc.AbstractJdbcWriter.FieldInfo
getFieldName() - Method in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
getFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow
getFile() - Method in interface org.apache.ctakes.core.resource.FileResource
getFile() - Method in class org.apache.ctakes.core.resource.FileResourceImpl
getFile(String) - Static method in class org.apache.ctakes.jdl.common.FileUtil
getFileBaseName(Properties) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
getFileInExistingDir(String) - Static method in class org.apache.ctakes.core.ae.SentenceDetector
getFileInExistingDir(String) - Static method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
getFileName() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile
getFilesFor(List<Integer>, File) - Static method in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline
getFilesFor(List<Integer>, File) - Static method in class org.apache.ctakes.temporal.duration.Utils: Get files for specific sets of patients.
getFilesFor(List<Integer>) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getFilesFor(List<Integer>, File) - Static method in class org.apache.ctakes.temporal.eval.THYMEData
getFilesFor(File, List<Integer>) - Static method in class org.apache.ctakes.temporal.utils.RunCorpusDiagnostics
getFirstChildByName(Node, String) - Static method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Gets the first child with a given name.
getFirstChildByName(Node, String) - Static method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Gets the first child with a given name.
getFirstInsidePunctSymbol(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
getFirstName() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for firstName - gets
getFirstName(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getFirstNameSoundex() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for firstNameSoundex - gets
getFirstNameSoundex(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getFirstNonWS(String, int) - Method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
getFirstTokenHits(LookupToken) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Gets the hits for the specified LookupToken.
getFirstWS(String, int) - Method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
getFiveTimesADayMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a fsm that detects five times a day five X
getFixedWindowEndOffset(int, LookupToken, List<LookupToken>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
getFn() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getFn() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getFocusText() - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: getter for FocusText - gets
getFocusText(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
getFold() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getFold() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getFoldFilePrefix(String, String, Integer, Integer) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil: construct file name with label, run, fold with format label[label]_run[run]_fold[fold]_ only put in the non-null pieces.
getFoldGenerator() - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
getFoldId() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getFoldId(ImputedFeatureEvaluatorImpl.Parameters, String, int, int) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getFoldId() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getFoldYMargin(InstanceData, String, int, int) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getForm() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for form - gets Form refers to the physical appearance of the drug.
getForm(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getForm() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for form - gets
getForm(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getFormatter() - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory
getFormatter() - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory
getFormBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getFormBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for formBegin - gets
getFormBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFormElement() - Method in class org.apache.ctakes.drugner.DrugMention
getFormElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getFormEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getFormEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for formEnd - gets
getFormEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFormMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FormFSM: - * Gets a finite state machine that detects the following: tablet caps
getFormMention() - Method in class org.apache.ctakes.drugner.elements.FormElement
getFormMethod() - Method in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
getFourTimesADayMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a fsm that detects four times a day q.i.d. 6-8 hours
getFp() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getFp() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getFrameSet() - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate: getter for frameSet - gets
getFrameSet(int) - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
getFreqQuery() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getFrequencies(String) - Method in interface org.apache.ctakes.ytex.kernel.InfoContentEvaluator
getFrequencies(String) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl: get the frequency of each term in the corpus.
getFrequency() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for frequency - gets Frequency refers to how often the patient needs to take the drug.
getFrequency(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFrequency(ConcRel, Map<String, Double>, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl: recursively sum frequency of parent and all its childrens' frequencies
getFrequencyBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getFrequencyBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for frequencyBegin - gets
getFrequencyBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFrequencyElement() - Method in class org.apache.ctakes.drugner.DrugMention
getFrequencyElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getFrequencyEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getFrequencyEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for frequencyEnd - gets
getFrequencyEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFrequencyMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM: Gets a finite state machine that detects the following ('once', 'twice', # or text#) a day/week/month/year: once a day three times a day once-a-day
getFrequencyMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM: Gets a finite state machine that detects the following ('once', 'twice', # or text#) a day/week/month/year: once a day three times a day once-a-day
getFrequencyMention() - Method in class org.apache.ctakes.drugner.elements.FrequencyElement
getFrequencyUnit() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for frequencyUnit - gets
getFrequencyUnit(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFrequencyUnitElement() - Method in class org.apache.ctakes.drugner.DrugMention
getFrequencyUnitElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getFrequencyUnitMention() - Method in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
getFrequencyUnitQuantity() - Method in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
getFs() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
getFSGenerator() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
getFSGenerator() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
getFSGenerator() - Method in class org.apache.ctakes.assertion.zoner.types.Heading_Type
getFSGenerator() - Method in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
getFSGenerator() - Method in class org.apache.ctakes.assertion.zoner.types.Zone_Type
getFSGenerator() - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.DemMarkable_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.Markable_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.NEMarkable_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.Pair_Type
getFSGenerator() - Method in class org.apache.ctakes.coreference.type.PronounMarkable_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.DosagesAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.DurationAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.FormAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.FrequencyAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.StrengthAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.sideeffect.type.PSESentence_Type
getFSGenerator() - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
getFSGenerator() - Method in class org.apache.ctakes.sideeffect.type.SESentence_Type
getFSGenerator() - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
getFSGenerator() - Method in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Attribute_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Course_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Entity_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Event_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.Time_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.Affects_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.Contraindicates_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.DegreeOf_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.Diagnoses_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.Indicates_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.LocationOf_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ManagesTreats_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ManifestationOf_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.Prevents_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ResultOf_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.TemporalRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.relation.UMLSRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.ADJP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.ADVP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.CONJP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.ContractionToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.INTJ_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.LST_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.NewlineToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.NP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.O_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.PP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.PRT_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.SBAR_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.SymbolToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.UCP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.VP_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.Markable_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textspan.List_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textspan.Paragraph_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.util.Pair_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.util.Pairs_Type
getFSGenerator() - Method in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type
getFSGenerator() - Method in class org.apache.ctakes.ytex.uima.types.Date_Type
getFSGenerator() - Method in class org.apache.ctakes.ytex.uima.types.DocKey_Type
getFSGenerator() - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
getFstem() - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
getFUBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getFuBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for fuBegin - gets
getFuBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFUENd() - Method in class org.apache.ctakes.drugner.DrugMention
getFuEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for fuEnd - gets
getFuEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getFullPath(String) - Static method in class org.apache.ctakes.core.resource.FileLocator: Attempts to discover the real location of a file pointed to by relativePath.
getFullTextSearchDocument(int) - Method in interface org.apache.ctakes.ytex.web.search.DocumentSearchService: retrieve note for specified document id, retrieved via full text search
getFullTextSearchDocument(int) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl: retrieve note for specified document id, retrieved via full text search
getFword() - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
getFword() - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
getGamma() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
getGamma() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getGastricMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Gets a finite state machine that detects the following medications given through a gastric or duodenal tube.
getGender() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for gender - gets
getGender(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getGenerateXMI() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.Options
getGeneric(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
getGeneric() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for generic - gets
getGeneric(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getGeneric() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for generic - gets
getGeneric(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
getGoldAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
getGrid() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getGridSearch() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluationOptions
getHead(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
getHead(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.MarkableTreeUtils
getHead() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for head - gets
getHead(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getHeadIndex() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for headIndex - gets The head index tracks the index into the word tokens which is the syntactic head of a phrase.
getHeadIndex(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getHeadWord(String) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: A simple way to get the head word of a phrase.
getHighestIndexTerm(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
getHistory(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
getHistoryMachine() - Method in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM: Gets a finite state machine that detects the following: history hx h/o
getHistoryMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM: Gets a finite state machine that detects the following: history hx h/o
getHistoryOf() - Static method in class org.apache.ctakes.core.util.SHARPKnowtatorXMLDefaults
getHistoryOf() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for historyOf - gets
getHistoryOf(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getHistoryOf() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for historyOf - gets
getHistoryOf(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getHistorySubSectionMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
getHits(String[]) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl
getHourlySuffixMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects the following which indicates 1 per hour via the following: /h
getHyperHypernyms(IDictionary, String, String, boolean) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils
getHypernyms(IDictionary, String, String, boolean) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Retrieve a set of hypernyms for a word.
getI2B2Output() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getIC(String, boolean) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService
getIC(String, boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getICOnDemand(Set<String>, boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getId() - Method in class org.apache.ctakes.coreference.type.Markable: getter for id - gets
getId(int) - Method in class org.apache.ctakes.coreference.type.Markable_Type
getId() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getId() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getId() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
getId() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for id - gets The token's position in the sentence.
getId(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getId() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
getId() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getId() - Method in class org.apache.ctakes.typesystem.type.textspan.List: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.textspan.List_Type
getId() - Method in class org.apache.ctakes.typesystem.type.textspan.Segment: getter for id - gets
getId(int) - Method in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
getIdByAnnotationEqual(Annotation) - Method in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
getIdByTextSpan(int, int) - Method in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
getIdfMap() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getIgnoreEventEvent() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations.EvalOptions
getIgnoreEventTime() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations.EvalOptions
getIgnoreImpossibleGoldRelations() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getImputedFeaturesByPropagatedCutoff(String, String, String, String, String, String, int) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getImputedFeaturesByPropagatedCutoff(String, String, String, String, String, String, int) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getImputeWeight() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getIncreaseFromAndTheStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following : 'increase from': increase from
getIncreaseStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following : 'increase': increase
getIndex() - Method in enum org.apache.ctakes.temporal.utils.TlinkType
getIndex() - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: getter for index - gets The index of this node in the top node's list of terminals.
getIndex(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
getIndex() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
getIndexAfterLastNonDigit(String) - Static method in class org.apache.ctakes.core.util.DateParser
getIndexFirstNonLetter(String) - Static method in class org.apache.ctakes.core.util.DateParser
getIndexReader() - Method in interface org.apache.ctakes.core.resource.LuceneIndexReaderResource
getIndexReader() - Method in class org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
getIndicated() - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier: getter for indicated - gets
getIndicated(int) - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
getInfoContent(String, String, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getInfoContent(String, String, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getInfoContentEvaluator() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getInfoGain() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
getInitialNegIndicatorMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
getInitialNegIndicatorMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM
getInjectionMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Gets a finite state machine that detects the following Drugs in inject or intervenous form.
getInputDirectory() - Method in interface org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer.Options
getInputDirectory() - Method in interface org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.GoldRelationViewer.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.duration.EventEventDurationStatistics.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.EventPrintingPipeline.Options
getInputDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.TemporalExtractionPipeline_ImplBase.Options
getInstance() - Static method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator
getInstance() - Static method in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
getInstance() - Static method in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
getInstanceDataExporter() - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
getInstanceDataExporter() - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
getInstanceId() - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
getInstanceId() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
getInstanceId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
getInstanceId() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
getInstanceID() - Method in class org.apache.ctakes.ytex.uima.model.Document
getInstanceId1() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
getInstanceId2() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
getInstanceIdClass(String, List<Integer>) - Method in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
getInstanceIDField() - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
getInstanceIDQuery() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getInstanceIds() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getInstanceIds() - Method in class org.apache.ctakes.ytex.kernel.SparseData
getInstanceKernel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getInstanceKey() - Method in class org.apache.ctakes.ytex.uima.model.Document
getInstanceNominalWords() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getInstanceNominalWords() - Method in class org.apache.ctakes.ytex.kernel.SparseData
getInstanceNum(SourceData) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil
getInstanceNumericWords() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getInstanceNumericWords() - Method in class org.apache.ctakes.ytex.kernel.SparseData
getInstanceQueryMappingInfo() - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
getInstances(String, String) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
getInstances(String, BagOfWordsData) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
getInstanceTreeBuilder() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getIntakeMethod() - Method in class org.apache.ctakes.drugner.type.RouteAnnotation: getter for intakeMethod - gets Means by which the drug was taken.
getIntakeMethod(int) - Method in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
getIntAsTuis(Collection<Integer>) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
getIntegerProperty(Properties, String, Integer) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil
getIntrinsicIC() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
getIntrinsicICMax() - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
getIntrinsicInfoContent(String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getIntrinsicInfoContent(String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getIntrinsicInfoContent() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getIntrinsicInfoContentEvaluator() - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
getIntrinsicLcs() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getIntrinsicLcsIC() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getIntrinsicLcsTerm() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getIrClass() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getIrClassId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getIspref() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getIstance() - Static method in class org.apache.ctakes.jdl.common.Singleton
getItems() - Method in class org.apache.ctakes.typesystem.type.textspan.List: getter for items - gets
getItems(int) - Method in class org.apache.ctakes.typesystem.type.textspan.List_Type
getJavaClassPaths() - Static method in class org.apache.ctakes.jdl.common.FileUtil
getJAXBElement(Object) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getJAXBElementBySrcXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getJAXBElementByStrXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getJcas(File) - Static method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
getJcas() - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
getJcas() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
getJcas() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
getJCasViewWithDefault(CAS, String) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: helper to look for plain text view for CDA processing or else use the default view.
getJdbcTypeBySrcXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getJdbcTypeByStrXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getJxpath() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getKernel(KernelEvaluation, long, long) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao
getKernel(KernelEvaluation, long, long) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
getKernel() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getKernelEval(String, String, String, int, double, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao
getKernelEval(String, String, String, int, double, String) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
getKernelEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getKernelEvaluationDao() - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
getKernelEvaluationDao() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
getKernelEvaluationDao() - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
getKernelEvaluationDao() - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
getKernelEvaluationId() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getKernelEvaluationId() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
getKernelParams() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getKernelUtil() - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
getKernelUtil() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getKernelUtil() - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
getKernelUtil() - Method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory
getKernelUtil() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory
getKernelUtil() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
getKernelUtil() - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
getKernelUtil() - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory
getKernelUtil() - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
getKernelUtil() - Method in class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory
getKernelUtil() - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory
getKernelUtil() - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
getKernelUtil() - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory
getKey(Annotation) - Static method in class org.apache.ctakes.temporal.ae.feature.ListFeaturesExtractor
getKey() - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma: getter for key - gets
getKey(int) - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
getKey() - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: getter for key - gets
getKey(int) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
getKeyValuePairs() - Method in class org.apache.ctakes.ytex.uima.types.DocKey: getter for keyValuePairs - gets
getKeyValuePairs(int) - Method in class org.apache.ctakes.ytex.uima.types.DocKey: indexed getter for keyValuePairs - gets an indexed value -
getKeyValuePairs(int) - Method in class org.apache.ctakes.ytex.uima.types.DocKey_Type
getKeyValuePairs(int, int) - Method in class org.apache.ctakes.ytex.uima.types.DocKey_Type
getKnowtatorURI(JCas) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader: Get the URI for the Knowtator XML file that should be loaded
getKnowtatorURI(JCas) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader: Get the URI for the Knowtator XML file that should be loaded
getKnowtatorURI(JCas) - Method in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
getKnowtatorXMLDirectory() - Method in interface org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader.Options
getKnowtatorXMLDirectory() - Method in interface org.apache.ctakes.temporal.eval.PrintRelations.Options
getKnowtatorXMLDirectory() - Method in interface org.apache.ctakes.temporal.utils.CheckKnowtatorAnnotations.Options
getLabel() - Method in class org.apache.ctakes.assertion.zoner.types.Heading: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.assertion.zoner.types.Heading_Type
getLabel() - Method in class org.apache.ctakes.assertion.zoner.types.Subzone: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
getLabel() - Method in class org.apache.ctakes.assertion.zoner.types.Zone: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.assertion.zoner.types.Zone_Type
getLabel() - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
getLabel(String) - Method in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
getLabel() - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
getLabel() - Method in class org.apache.ctakes.coreference.type.MarkablePair: getter for label - gets Is this pair coreferent?
getLabel(int) - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
getLabel() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
getLabel() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: getter for label - gets
getLabel(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
getLabel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getLabel() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
getLabel() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getLabel() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getLabel() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getLabel() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getLabelQuery() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getLabelToClassMap() - Method in class org.apache.ctakes.ytex.kernel.InstanceData
getLabelToInstanceMap() - Method in class org.apache.ctakes.ytex.kernel.InstanceData
getLabValue() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: getter for labValue - gets
getLabValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
getLabValue() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: getter for labValue - gets
getLabValue(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
getLambda() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
getLargestWindowAnnotation(int, LookupToken, Map<Integer, List<LookupToken>>, Map<Integer, List<LookupToken>>, Map<LookupToken, Integer>, Map<Integer, List<LookupAnnotation>>, Map<Integer, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Determines the largest overlapping window annotation for the specified LookupToken.
getLastAui() - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao: Get the 'last' UmlsAuiFirstWord.
getLastAui() - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
getLastName() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for lastName - gets
getLastName(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getLastNameSoundex() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for lastNameSoundex - gets
getLastNameSoundex(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getLastWord(JCas, Annotation) - Static method in class org.apache.ctakes.relationextractor.data.analysis.Utils: Given an annotation, retrieve its last word.
getLat() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getLatin2AbbreviationMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM: Gets a finite state machine that detects the following: 40mg/d 32.1-47.3mg/wk
getLatin3AbbreviationMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM: Gets a finite state machine that detects the following: 40mg/d 32.1-47.3mg/wk
getLCA(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
getLCS(String, String, Set<String>, List<LCSPath>) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: get the lcs(s) for the specified concepts
getLCS(String, String, Set<String>, List<LCSPath>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getLcs() - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
getLcsCache() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getLcsDist() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getLcses() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getLCSFromCache(ConcRel, ConcRel, Set<String>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getLcsImputedType() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getLcsPathMap() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getLcsPaths() - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
getLeaf() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for leaf - gets
getLeaf(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getLeafAttributes(String, HashMap<String, List<String>>, HashMap<String, ArgumentInfo>, HashMap<String, ArgumentInfo>, List<ArgumentInfo>) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
getLeafCount() - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
getLeastCommonConcept(ConcRel, ConcRel) - Static method in class org.apache.ctakes.ytex.kernel.model.ConcRel: Deprecated.
getLeastCommonConcept(ConcRel, ConcRel, Set<ConcRel>, Map<ConcRel, LCSPath>) - Static method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getLeaves(ConcRel, SoftReference<HashSet<Integer>>[], Map<String, IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo>, ConceptGraph, BufferedWriter, HashSet<Integer>) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl: recursively compute the number of leaves.
getLeftmostNode(SimpleTree, Set<String>) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getLeftScopeContextAnnotations(JCas, Annotation, Annotation) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
getLeftSibProgeny(ConllDependencyNode, List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getLeftSibs(ConllDependencyNode, List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getLemma() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for lemma - gets
getLemma(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getLemmaEntries() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: getter for lemmaEntries - gets
getLemmaEntries(int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
getLenContractionToken(int, String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
getLength() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter: Gets the length of this annotation based on offsets.
getLength() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation: Gets the length of this annotation based on offsets.
getLength() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
getLength() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
getLength() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan: return the length of the full span minus the lengths of the missing spans
getLength() - Method in interface org.apache.ctakes.dictionary.lookup2.textspan.TextSpan
getLength() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
getLength() - Method in class org.apache.ctakes.utils.distsem.WordVector
getLength() - Method in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
getLengthIfIsNumberThatStartsWithPeriod(int, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
getLengthIfNameStartingWithApostrophe(int, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
getLengthIfNextApostIsMiddleOfContraction(int, int, String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB: Determine if the text starting at 'position' within 'text' is the start of a contraction such as "should've" or "hasn't" or "it's" by looking at whether there is a letter before the apostrophe, and the appropriate letters after the apostrophe (or in the case of "n't", verify the letter before is an 'n' Note that if the text starting at 'position' is something like "n't" which isn't a complete word, returns null.
getLenToNextNonDigit(String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
getLibsvmUtil() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
getLightweightPreprocessorAggregateBuilder() - Static method in class org.apache.ctakes.temporal.pipelines.TemporalExtractionPipeline_ImplBase
getLinearPermutations(List<Integer>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil: Gets a collection of lists, each list represents a single permutation.
getLinearPermutations(Collection<List<Integer>>, List<Integer>, List<Integer>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil: Recursively builds permutations from the number list.
getList() - Method in class org.apache.ctakes.temporal.eval.CommandLine.IntegerRanges
getList() - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean: The list of possible matches for the given SelectInputText value
getList() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean: The list of possible matches for the given SelectInputText value
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog.MyListCellRenderer
getListIndexMap(List<LookupToken>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Creates a map that binds an object from a list to its index position.
getLoadTypeBySrcXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getLoadTypeByStrXml(String) - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getLocationFeaturesFromMetaKeywords(JCas, PSESentence) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator: Return the List of location features of meta keywords metaKeywords - key:metakeyword, value:actual keyword
getLongCodes(PreparedStatement, Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
getLookupAlgorithm(DictionaryEngine) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl: Gets the LookupAlgorithm to be used to perform the lookup operations.
getLookupAlgorithm(DictionaryEngine) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets the LookupAlgorithm to be used to perform the lookup operations.
getLookupAlgorithm(DictionaryEngine) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer: Gets the LookupAlgorithm to be used to perform the lookup operations.
getLookupAlgorithm() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
getLookupAlgorithm(DictionaryEngine) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets the LookupAlgorithm to be used to perform the lookup operations.
getLookupConsumer() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
getLookupData(JCas, LookupSpec) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
getLookupHits(Collection<MetaDataHit>, List<LookupToken>, int) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
getLookupInitializer() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
getLookupTokenIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl: Gets an iteration of tokens that represent the finest grain used for a lookup operation.
getLookupTokenIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets an iteration of tokens that represent the finest grain used for a lookup operation.
getLookupTokenIterator(JCas) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer: Gets an iteration of tokens that represent the finest grain used for a lookup operation.
getLookupTokenIterator(JCas) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets an iteration of tokens that represent the finest grain used for a lookup operation.
getLookupTokenList(int, Map<Integer, List<LookupToken>>, boolean) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Attempts to get a list of LookupToken objects at the specified offset.
getLookupWindowIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl: Gets an iteration of windows.
getLookupWindowIterator(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets an iteration of windows.
getLookupWindowIterator(JCas) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer: Gets an iteration of windows.
getLookupWindowIterator(JCas) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets an iteration of windows.
getLui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getLvg() - Method in interface org.apache.ctakes.lvg.resource.LvgCmdApiResource
getLvg() - Method in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl: An LvgCmdApi takes a term from the input and returns a vector of strings.
getLvgDir(File) - Method in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl: Get the path to the root directory of the installation of NLMs lvg lexical tools.
getLvgLex() - Method in interface org.apache.ctakes.lvg.resource.LvgCmdApiResource
getLvgLex() - Method in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl: The thing to run through Lvg
getMachine() - Method in class org.apache.ctakes.core.fsm.machine.FractionFSM: Gets a finite state machine that detects the following: 1/2 0.5 half one half 1 half
getMachine() - Method in class org.apache.ctakes.core.fsm.machine.RangeFSM: Gets a finite state machine that detects the following: 250-300 I-IV two-three
getMachine() - Method in class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM: Gets a finite state machine that detects the following: III iii
getMachine() - Method in class org.apache.ctakes.core.fsm.machine.TimeFSM: Gets a finite state machine that detects the following: 3 PM 3 P.M. 3:05 PM 3:05 P.M.
getMainSem(int) - Static method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
getMap() - Method in interface org.apache.ctakes.core.resource.StringIntegerMapResource: Gets a map of the String/Integer values.
getMap() - Method in class org.apache.ctakes.core.resource.StringIntegerMapResourceImpl: Gets a map of the String/Integer values.
getMap() - Method in interface org.apache.ctakes.core.resource.StringMapResource: Gets a map of String/String values.
getMap() - Method in class org.apache.ctakes.core.resource.StringMapResourceImpl: Gets a map of the String/Integer values.
getMapAnnoMappingInfo() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getMapField() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getMapIndexWeight() - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
getMapInfo(FeatureStructure) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getMappedCategory(String) - Static method in class org.apache.ctakes.temporal.ae.ClearTKLinkToTHYMELinkAnnotator
getMatch(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
getMatch(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getMaxDepth(String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getMaxDepth(String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getMaxFeatureEvaluation(String, String, String, String, Integer, double, String) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getMaxFeatureEvaluation(String, String, String, String, Integer, double, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getMaxID() - Method in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
getMaximumStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following: 'maximum' or 'total': max of totaling
getMaxSizeList() - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities: Get the maximum list size to be returned from a lucene index
getMeasure() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getMedicationAllergy() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationAllergy - gets
getMedicationAllergy(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationDosage() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationDosage - gets
getMedicationDosage(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationDosage() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationDosage - gets
getMedicationDosage(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationDosage() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationDosage - gets
getMedicationDosage(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationDuration() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationDuration - gets
getMedicationDuration(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationDuration() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationDuration - gets
getMedicationDuration(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationDuration() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationDuration - gets
getMedicationDuration(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationForm() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationForm - gets
getMedicationForm(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationForm() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationForm - gets
getMedicationForm(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationForm() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationForm - gets
getMedicationForm(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationFrequency() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationFrequency - gets
getMedicationFrequency(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationFrequency() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationFrequency - gets
getMedicationFrequency(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationFrequency() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationFrequency - gets
getMedicationFrequency(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationKnowtatorClasses() - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
getMedicationRoute() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationRoute - gets
getMedicationRoute(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationRoute() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationRoute - gets
getMedicationRoute(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationRoute() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationRoute - gets
getMedicationRoute(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationStatusChange() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationStatusChange - gets
getMedicationStatusChange(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationStatusChange() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationStatusChange - gets
getMedicationStatusChange(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationStatusChange() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationStatusChange - gets
getMedicationStatusChange(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMedicationStrength() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for medicationStrength - gets
getMedicationStrength(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getMedicationStrength() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for medicationStrength - gets
getMedicationStrength(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getMedicationStrength() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for medicationStrength - gets
getMedicationStrength(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getMembers() - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation: getter for members - gets A super-type for relationships between multiple spans of text.
getMembers(int) - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
getMentions() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for mentions - gets
getMentions(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: indexed getter for mentions - gets an indexed value -
getMentions(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getMentions(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getMentionTypes(List<EventMention>) - Static method in class org.apache.ctakes.temporal.ae.feature.UmlsFeatureExtractor
getMentionTypes(List<EventMention>) - Static method in class org.apache.ctakes.temporal.ae.feature.UmlsSingleFeatureExtractor
getMetadata(JCas) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil
getMetaData(Object) - Method in class org.apache.ctakes.necontexts.ContextHit
getMetaData() - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Gets a map of meta data about the document.
getMetaDataValue(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl
getMetaDataValue(MetaDataHit) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary: TODO - get rid of the using class iterators and use Collection foreach
getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl: Deprecated.
getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl
getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
getMetaFieldNames() - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit
getMetaFieldNames() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl
getMetaFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl
getMetaFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
getMetaFieldValue(String) - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit
getMetaFieldValue(String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl
getMetaFieldValues() - Method in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl
getMetaFieldValues() - Method in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
getMetaFieldValues() - Method in interface org.apache.ctakes.dictionary.lookup.MetaDataHit
getMetaFieldValues() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl
getMethod() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for method - gets
getMethod(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getMethod() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for method - gets
getMethod(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getMethodName() - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
getMetricNames() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
getMetrics() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getMetricSelectCorpusIC() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getMetricSelectIntrinsicIC() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getMetricSelectTaxonomy() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getMiddleName() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: getter for middleName - gets
getMiddleName(int) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
getMiddleScopeContextAnnotations(JCas, Annotation) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
getMinInfo() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getMissingSpans() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
getMode() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
getModel() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getModelDirectory(File) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
getModelDirectory(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
getModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.EventExtractionPipeline.EventOptions
getModifierTypeId(String) - Static method in class org.apache.ctakes.core.util.Mapper: Map modifier type to its integer id.
getMonth() - Method in class org.apache.ctakes.typesystem.type.refsem.Date: getter for month - gets
getMonth(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
getMonthlySuffixMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects the following which indicates 1 per month via the following: /m
getMu() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
getMultipleEndOffsetMap(List<T>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Creates a map that uses the end offset to index the LookupAnnotation objects.
getMultipleStartOffsetMap(List<T>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Creates a map that uses the start offset to index the LookupAnnotation objects.
getMutualInformation(double) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
getName() - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
getName() - Method in class org.apache.ctakes.dictionary.lookup2.concept.AbstractConceptFactory: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in interface org.apache.ctakes.dictionary.lookup2.concept.ConceptFactory: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in class org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.AbstractRareWordDictionary: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName(String, Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
getName() - Method in interface org.apache.ctakes.dictionary.lookup2.dictionary.RareWordDictionary: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary: The Type identifier and Name are used to maintain a collection of dictionaries, so the combination of Type and Name should be unique for each dictionary if possible.
getName() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getName() - Method in enum org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator.MeasureType
getName() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getNamedEntityRegexID() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
getNamedEntityRegexs() - Method in interface org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDao
getNamedEntityRegexs() - Method in class org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDaoImpl
getNamedEntityType(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
getNamedMetaDataHits(Collection<MetaDataHit>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
getNames() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow
getNames(List<String>) - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao
getNames(List<String>) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
getNameToFormatterMap() - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
getNameToParserMap() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
getNarrativeSpansContainingGivenSpanType(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
getNearestEntity(JCas, Modifier, List<EntityMention>) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
getNearestEntity(JCas, EntityMention, List<EntityMention>) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getNearestTimeMention(JCas, EventMention) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor: Find nearest time mention on the right that is within allowable distance.
getNECorefFeatures() - Static method in class org.apache.ctakes.coreference.util.FeatureVector
getNegatedSpans(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator: get all negated spans
getNegationStatus() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getNegationTree(JCas, IdentifiedAnnotation, SemanticClasses) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
getNegConCount(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator: This is to count contradiction words -- if appears do not negate eg) Tobacco: no quit in 1980 -- "quit" is contradiction words.
getNewEndOffset() - Method in class org.apache.ctakes.core.ci.TextModification
getNewStartOffset() - Method in class org.apache.ctakes.core.ci.TextModification
getNewText() - Method in class org.apache.ctakes.core.ci.TextModification
getNext(CAS) - Method in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
getNext(CAS) - Method in class org.apache.ctakes.assertion.cr.NegExCorpusReader: Does more than a typical reader - also creates an IdentifiedAnnotation and a DocumentID annotation
getNext(CAS) - Method in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
getNext(JCas) - Method in class org.apache.ctakes.assertion.eval.XMIReader
getNext(CAS) - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
getNext(CAS) - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
getNext(CAS) - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader
getNext(CAS) - Method in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
getNext(JCas) - Method in class org.apache.ctakes.core.cr.TextReader
getNext(CAS) - Method in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
getNext(JCas) - Method in class org.apache.ctakes.core.cr.XMIReader
getNext(JCas) - Method in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
getNext(CAS) - Method in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader: Some of the code in this method is based loosely on opennlp.tools.postag.POSEventCollector
getNext(CAS) - Method in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader: Some of the code in this method is based loosely on opennlp.tools.postag.POSEventCollector
getNext(JCas) - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
getNext(CAS) - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
getNext(JCas) - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
getNextCharTerm(String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
getNextNonEOLToken(<any>) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
getNGrams() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
getNoChangeStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following 'current': current medications
getNodeFeatures(Markable, Markable, JCas) - Method in class org.apache.ctakes.coreference.util.SvmVectorCreator
getNodeFeatures(Markable, Markable, JCas, boolean) - Method in class org.apache.ctakes.coreference.util.SvmVectorCreator
getNodeForIndex(int, Node) - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
getNodeIndex() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getNodeList(TopTreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
getNodeList(Parse) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
getNodeQueryMappingInfos() - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
getNodes(String) - Static method in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
getNodes(String) - Static method in class org.apache.ctakes.coreference.util.SvmUtils
getNodeTags() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for nodeTags - gets
getNodeTags(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: indexed getter for nodeTags - gets an indexed value -
getNodeTags(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getNodeTags(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getNodeTreeMap(List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getNodeType() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for nodeType - gets
getNodeType(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getNodeType() - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
getNodeType() - Method in class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
getNodeTypes() - Method in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
getNodeValue() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for nodeValue - gets
getNodeValue(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getNominalHeadNode(JCas, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Returns the first ConllDependencyNode in the CAS w/ same begin and end as the given Annotation
getNominalHeadNode(List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Finds the head node out of a few ConllDependencyNodes.
getNominalInstanceWords(String, BagOfWordsData) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
getNominalInstanceWords(String, String, String, SparseData, Map<String, Object>) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
getNominalNegIndicatorMachine() - Method in class org.apache.ctakes.core.fsm.machine.NegationFSM: should recognize: A B B C B D* C
getNominalNegIndicatorMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
getNominalNegIndicatorMachine() - Method in class org.apache.ctakes.smokingstatus.machine.NegationFSM: should recognize: A B B C B D* C
getNominalValue() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue: getter for nominalValue - gets
getNominalValue(int) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
getNominalWordValueMap() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getNominalWordValueMap() - Method in class org.apache.ctakes.ytex.kernel.SparseData
getNonSmokerNegatedCount(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
getNorm(KernelEvaluation, long) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao
getNorm(KernelEvaluation, long) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
getNorm(Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel: compute the norm.
getNorm() - Method in class org.apache.ctakes.ytex.kernel.tree.Node
getNormalizedForm() - Method in class org.apache.ctakes.typesystem.type.refsem.Time: getter for normalizedForm - gets
getNormalizedForm(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Time_Type
getNormalizedForm() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: getter for normalizedForm - gets
getNormalizedForm(int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
getNormalizedForm() - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier: getter for normalizedForm - gets
getNormalizedForm(int) - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
getNoteSubTypeCode() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for noteSubTypeCode - gets
getNoteSubTypeCode(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getNoteTypeCode() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for noteTypeCode - gets
getNoteTypeCode(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getNounPhrases(JCas, Sentence) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Get all noun phrases in a sentence.
getNpChunkerPipeline() - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getNpv() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getNumber() - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue: getter for number - gets
getNumber(int) - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
getNumber() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: getter for number - gets
getNumber(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
getNumber() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: getter for number - gets
getNumber(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
getNumberOfDocuments() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Gets the total number of documents that will be returned by this collection reader.
getNumberOfDocuments() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader: Gets the total number of documents that will be returned by this collection reader.
getNumberOfDocuments() - Method in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader: Gets the total number of documents that will be returned by this collection reader.
getNumberOfListTokens(Map<Integer, List<LookupToken>>, Map<Integer, List<LookupToken>>, Map<LookupToken, Integer>, int, int) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Determines the number of ListTokens are contained within the specified start and end offsets;
getNumDemFeats() - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
getNumericDateMachine() - Method in class org.apache.ctakes.core.fsm.machine.DateFSM: Gets a finite state machine that detects the following: 10/15/2002 10/15 10-15-2002 10-15
getNumericInstanceWords(String, BagOfWordsData) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
getNumericInstanceWords(String, String, String, SparseData, Map<String, Object>) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
getNumericValue() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue: getter for numericValue - gets
getNumericValue(int) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
getNumericWords() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
getNumericWords() - Method in class org.apache.ctakes.ytex.kernel.SparseData
getNumFeatures() - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
getNumLists(int, List<Integer>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil
getNumNEFeats() - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
getNumOfWordTokensInSpan(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: return the number of words except for "and" "or" in span
getNumOfWordTokensInSpanExceptGivenNE(JCas, int, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: return the number of words in span except for "and" "or" and given NE
getNumPosition() - Method in class org.apache.ctakes.core.fsm.adapters.WordTokenAdapter
getNumPosition() - Method in class org.apache.ctakes.core.fsm.token.adapter.WordTokenAdapter
getNumPosition() - Method in interface org.apache.ctakes.core.fsm.token.WordToken
getNumPosition() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Gets the position of a number inside a Token.
getNumPosition() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: getter for numPosition - gets
getNumPosition(int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
getNumPronFeats() - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
getNumType() - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken: getter for numType - gets
getNumType(int) - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
getObjectFactoryMapping() - Static method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
getOffsetKey(LookupHit) - Static method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
getOid() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: getter for oid - gets
getOid(int) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getOid() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
getOntologyConcept() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for ontologyConcept - gets
getOntologyConcept(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getOntologyConceptArr() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for ontologyConceptArr - gets
getOntologyConceptArr(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: indexed getter for ontologyConceptArr - gets an indexed value -
getOntologyConceptArr(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getOntologyConceptArr(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getOntologyConceptCodes(IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer: Get the CUIs, RxNorm codes specified for this entity.
getOntologyConcepts(IdentifiedAnnotation) - Static method in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
getOpenConnection() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection
getOprions() - Static method in class org.apache.ctakes.jdl.AppMain
getOptionKey() - Method in enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption
getOptions() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getOralMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Gets a finite state machine that detects the following Most drugs taken by mouth such as tablets or capsules.
getOrdinalInterpretation() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: getter for ordinalInterpretation - gets
getOrdinalInterpretation(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
getOrdinalInterpretation() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: getter for ordinalInterpretation - gets
getOrdinalInterpretation(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
getOrigEndOffset() - Method in class org.apache.ctakes.core.ci.TextModification
getOriginalEntityExternalId() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: getter for originalEntityExternalId - gets
getOriginalEntityExternalId(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
getOriginalText() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for originalText - gets The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation.
getOriginalText(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: indexed getter for originalText - gets an indexed value - The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation.
getOriginalText(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getOriginalText(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getOrigStartOffset() - Method in class org.apache.ctakes.core.ci.TextModification
getOui() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: getter for oui - gets holds the rxnorm unique identifier for a given drug mention.
getOui(int) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getOutputDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.TemporalExtractionPipeline_ImplBase.Options
getOutputFile() - Method in interface org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.Options
getOutputFile() - Method in interface org.apache.ctakes.temporal.duration.EventEventDurationStatistics.Options
getOutputFile() - Method in interface org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.Options
getOutputFile(String, String, String) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
getOutputXml() - Method in interface org.apache.ctakes.core.cc.NonTerminalConsumer: Gets the generated output from a CasConsumer in XML form.
getOverlapTerm(List<FastLookupToken>, int, RareWordTerm, int, int) - Static method in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator: Check to see if a given term overlaps a set of tokens
getOverlapType(Annotation, Annotation) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator: Determines the type of overlap between annotations A and B.
getP1() - Method in class org.apache.ctakes.coreference.type.Pair: getter for p1 - gets
getP1(int) - Method in class org.apache.ctakes.coreference.type.Pair_Type
getP2() - Method in class org.apache.ctakes.coreference.type.Pair: getter for p2 - gets
getP2(int) - Method in class org.apache.ctakes.coreference.type.Pair_Type
getPageRankService() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getPairedConceptFactories(String) - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getPairedConceptFactories(String) - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getPairedDictionaries(String) - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getPairedDictionaries(String) - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getPairNames() - Method in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
getPairNames() - Method in interface org.apache.ctakes.dictionary.lookup2.util.DictionarySpec
getPairs() - Method in class org.apache.ctakes.typesystem.type.util.Pairs: getter for pairs - gets
getPairs(int) - Method in class org.apache.ctakes.typesystem.type.util.Pairs: indexed getter for pairs - gets an indexed value -
getPairs(int) - Method in class org.apache.ctakes.typesystem.type.util.Pairs_Type
getPairs(int, int) - Method in class org.apache.ctakes.typesystem.type.util.Pairs_Type
getParam1() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getParam1() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getParam1() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getParam1() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getParam2() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getParam2() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getParam2() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
getParam2() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
getParent() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: getter for parent - gets
getParent(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
getParentAnnoBaseId() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
getParentAnnotationId() - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
getParentConceptEvalThreshold() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getParentConceptTopThreshold() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getParents() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getParentsArray() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
getParentSectionId() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: getter for parentSectionId - gets The section in which the subsection was found.
getParentSectionId(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getParentUimaTypeId() - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
getParser(CommandLine) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
getParseString(FSIterator) - Method in class org.apache.ctakes.constituency.parser.MaxentParserWrapper
getParseString(FSIterator) - Method in interface org.apache.ctakes.constituency.parser.ParserWrapper
getParsingPipeline() - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getParticipatesIn() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: getter for participatesIn - gets
getParticipatesIn(int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
getPartOfSpeech() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: getter for partOfSpeech - gets
getPartOfSpeech(int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
getPatchesMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Gets a finite state machine that detects the following Such as patches patches
getPath(List<ConllDependencyNode>, ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Given a set of ConllDependencyNodes, find the path between two nodes
getPath(JCas, ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Given a CAS, find the path between two nodes in a sentence
getPath(List<ConcRel>, List<List<ConcRel>>, int, int) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel: recursively build all paths to root from a concept - add elements from set of parents.
getPathBetweenNodes(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: Finds the path between two dependency nodes
getPathBetweenNodes(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils: Finds the path between two dependency nodes
getPathEnclosedTree(SimpleTree, List<SimpleTree>, SimpleTree, SimpleTree) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getPathLength() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
getPathsToCommonAncestor(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: Returns the paths from each node to the common ancestor between them
getPathsToCommonAncestor(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils: Returns the paths from each node to the common ancestor between them
getPathToSentenceHead(ConllDependencyNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils
getPathToSentenceHead(ConllDependencyNode) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils
getPathToTop(JCas, ConllDependencyNode) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getPatientID() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: getter for patientID - gets
getPatientID(int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
getPatientId() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getPatientNum(JCas) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil
getPatients() - Method in interface org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader.Options
getPatients() - Method in interface org.apache.ctakes.temporal.data.analysis.GoldRelationViewer.Options
getPatients() - Method in interface org.apache.ctakes.temporal.data.analysis.PrintFailedTimeNormalizations.Options
getPatients() - Method in interface org.apache.ctakes.temporal.data.analysis.PrintInconsistentAnnotations.Options
getPatients() - Method in interface org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.Options
getPatients() - Method in interface org.apache.ctakes.temporal.data.analysis.TimexTreeAlignmentStatistics.Options
getPatients() - Method in interface org.apache.ctakes.temporal.duration.EventEventDurationStatistics.Options
getPatients() - Method in interface org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.Options
getPatients() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getPatients() - Method in interface org.apache.ctakes.temporal.eval.PrintRelations.Options
getPatients() - Method in interface org.apache.ctakes.temporal.utils.CheckKnowtatorAnnotations.Options
getPatients() - Method in interface org.apache.ctakes.temporal.utils.RunCorpusDiagnostics.Options
getPatientSets(List<Integer>, Collection<Integer>) - Static method in class org.apache.ctakes.temporal.eval.THYMEData
getPattern() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
getPdeprel() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for pdeprel - gets
getPdeprel(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getPercentLabeled() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
getPeriod() - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation: getter for period - gets The periodic unit used, e.g day, month, hour, etc.
getPeriod(int) - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
getPermanence() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for permanence - gets
getPermanence(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getPermutationList(int) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil: Gets all permutations for the given level and all sub-levels.
getPhead() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for phead - gets
getPhead(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getPhrases(List<LookupToken>) - Method in interface org.apache.ctakes.dictionary.lookup.phrasebuilder.PhraseBuilder: Given a list of LookupTokens, one or more phrases are built.
getPhrases(List<LookupToken>) - Method in class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl
getPlaintextAggregateBuilder() - Static method in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors: Builds the plaintext prepreprocessing pipeline for ClearNLP
getPolarity() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for polarity - gets
getPolarity(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getPolarity() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: getter for polarity - gets
getPolarity(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
getPolarity() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for polarity - gets
getPolarity(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getPolarity() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for polarity - gets
getPolarity(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getPOS() - Method in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
getPosition(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Returns the line and column numbers of the specified XcasAnnotation.
getPositionOther(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Finds an XcasAnnotation with the same attributes as specified, and returns its line and column numbers.
getPositionOwn(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Returns the line and column numbers of the specified XcasAnnotation, which is included in this XcasFile object.
getPositionOwn(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Returns the line and column numbers of the XcasAnnotation, specified by the original XCAS internal _id field.
getPositions(String) - Method in class org.apache.ctakes.core.sentence.EndOfSentenceScannerImpl
getPositions(StringBuffer) - Method in class org.apache.ctakes.core.sentence.EndOfSentenceScannerImpl
getPositions(char[]) - Method in class org.apache.ctakes.core.sentence.EndOfSentenceScannerImpl
getPositionSimilar(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Finds an XcasAnnotation of the same type as specified, and a same text span, then returns its line and column number.
getPositive() - Method in class org.apache.ctakes.core.fsm.adapters.NumberTokenAdapter
getPositive() - Method in class org.apache.ctakes.core.fsm.token.adapter.NumberTokenAdapter
getPositive() - Method in interface org.apache.ctakes.core.fsm.token.NumberToken
getPosTag(JCas, Annotation) - Static method in class org.apache.ctakes.temporal.duration.Utils: Return system generated POS tag or null if none available.
getPostag() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: getter for postag - gets
getPostag(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
getPosTag() - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma: getter for posTag - gets
getPosTag(int) - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
getPotentialSideEffects(JCas) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return List of PotentialSideEffect classes - get NEs from getSideEffectNEs() - drug must appear in the same or previous sentence - but in Allergy section drug must appear in the same sentence - don't include the sentence in different line
getPow() - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
getPow() - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
getPpv() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getPrecision() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getPredicate() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: getter for predicate - gets
getPredicate(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
getPredictedClassId() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
getPredictedClassId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
getPredictedClassIds() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
getPreferredSize() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
getPreferredTerm(Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
getPreferredText() - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
getPreferredText() - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
getPreferredText() - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: getter for preferredText - gets preferredText is the preferred term.
getPreferredText(int) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
getPreferredText() - Method in class org.apache.ctakes.typesystem.type.textspan.Segment: getter for preferredText - gets preferredText is the normalized/resolved section name.
getPreferredText(int) - Method in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
getPrefTerm() - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
getPreparedStatement() - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter.TableSqlInfo
getPrepareScript() - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
getPrepareScriptStatementDelimiter() - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
getPreprocessorAggregateBuilder() - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getPreprocessorAggregateBuilder() - Static method in class org.apache.ctakes.temporal.pipelines.TemporalExtractionPipeline_ImplBase: Preprocessing needed for relation extraction.
getPrimaryAssociatedCodeElement() - Method in class org.apache.ctakes.drugner.DrugMention
getPrimaryAssociatedCodeElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getPrintContext() - Method in interface org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.Options
getPrintErrors() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getPrintErrors() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.TempRelOptions
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.TempRelOptions
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.TempRelOptions
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.TempRelOptions
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.TempRelOptions
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.TempRelOptions
getPrintFormattedRelations() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.TempRelOptions
getPrintOverlappingSpans() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getProbabilities() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
getProbabilities() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
getProbabilityOfKeepingANegativeExample() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventSpans.Options
getProbableMachine() - Method in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM: Gets a finite state machine that detects the following: probable probably likely
getProbableMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM: Gets a finite state machine that detects the following: probable probably likely
getProbableMachineNonTerm() - Method in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM: Gets a finite state machine that detects the following: probable probably likely
getProbableSubSectionMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
getProcedureDevice() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for procedureDevice - gets
getProcedureDevice(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getProcedureDevice() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for procedureDevice - gets
getProcedureDevice(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getProcedureKnowtatorClasses() - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
getProgeny(ConllDependencyNode, List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getProgeny(List<ConllDependencyNode>, List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getProgress() - Method in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
getProgress() - Method in class org.apache.ctakes.assertion.cr.NegExCorpusReader
getProgress() - Method in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
getProgress() - Method in class org.apache.ctakes.assertion.eval.XMIReader
getProgress() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
getProgress() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
getProgress() - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader
getProgress() - Method in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
getProgress() - Method in class org.apache.ctakes.core.cr.TextReader
getProgress() - Method in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
getProgress() - Method in class org.apache.ctakes.core.cr.XMIReader
getProgress() - Method in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
getProgress() - Method in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
getProgress() - Method in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
getProgress() - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
getProgress() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
getPronCorefFeatures() - Static method in class org.apache.ctakes.coreference.util.FeatureVector
getProperties(String, boolean) - Static method in class org.apache.ctakes.jdl.common.PropFile
getProperties() - Method in class org.apache.ctakes.typesystem.type.refsem.Event: getter for properties - gets
getProperties(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Event_Type
getProperty(String) - Method in class org.apache.ctakes.jdl.common.PropertiesFile
getProperty(Properties, String) - Static method in class org.apache.ctakes.jdl.common.PropFile
getPropertyGetter(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
getPropertyGetter(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
getProviderId(SourceData) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil
getProviderID() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: getter for providerID - gets
getProviderID(int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: indexed getter for providerID - gets an indexed value -
getProviderID(int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
getProviderID(int, int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
getPseSen() - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: getter for pseSen - gets
getPseSen(int) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
getQuery() - Method in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
getQuery() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getQueryArgs() - Method in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
getRank() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
getRankCutoff() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
getRareWord(String, Map<String, Integer>) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
getRareWord() - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
getRareWordHits(FastLookupToken) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.AbstractRareWordDictionary: Any single token can exist in zero or more terms in the dictionary.
getRareWordHits(FastLookupToken) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary: Any single token can exist in zero or more terms in the dictionary.
getRareWordHits(String) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary: Get all terms within the dictionary that contain a given rare word
getRareWordHits(String) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary: Get all terms within the dictionary that contain a given rare word
getRareWordHits(String) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.MemRareWordDictionary: Get all terms within the dictionary that contain a given rare word
getRareWordHits(FastLookupToken) - Method in interface org.apache.ctakes.dictionary.lookup2.dictionary.RareWordDictionary: Any single token can exist in zero or more terms in the dictionary.
getRareWordHits(String) - Method in interface org.apache.ctakes.dictionary.lookup2.dictionary.RareWordDictionary: Get all terms within the dictionary that contain a given rare word
getRareWordHits(FastLookupToken) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary: Any single token can exist in zero or more terms in the dictionary.
getRareWordHits(String) - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary: Get all terms within the dictionary that contain a given rare word
getRareWordIndex() - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
getRareWordTerm() - Method in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
getRawText() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.PrintFailedTimeNormalizations.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.PrintInconsistentAnnotations.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.TimexTreeAlignmentStatistics.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.eval.PrintRelations.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.utils.CheckKnowtatorAnnotations.Options
getRawTextDirectory() - Method in interface org.apache.ctakes.temporal.utils.RunCorpusDiagnostics.Options
getRawTokens(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Text is split based on whitespace into raw tokens.
getReadableFile(String) - Static method in class org.apache.ctakes.core.ae.SentenceDetector
getReadableFile(String) - Static method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
getReason() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for reason - gets
getReason(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: indexed getter for reason - gets an indexed value -
getReason(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getReason(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getRecall() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getReciprocal() - Method in enum org.apache.ctakes.temporal.utils.TlinkType
getRecordID() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: getter for recordID - gets ID of record that this sentence belongs to.
getRecordID(int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
getRecordID() - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: getter for recordID - gets Represents the document record id
getRecordID(int) - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
getRecordTextBegin() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: getter for recordTextBegin - gets Begin offset of the sentence relative to the entire record text.
getRecordTextBegin(int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
getRecordTextEnd() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: getter for recordTextEnd - gets End offset of the sentence relative to the entire record text.
getRecordTextEnd(int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
getRectalMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Gets a finite state machine that detects the following Drugs in suppositories or enema form.
getReference(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Returns the referenced XcasAnnotations of the specified attribute.
getReferenceRangeNarrative() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: getter for referenceRangeNarrative - gets
getReferenceRangeNarrative(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
getReferenceRangeNarrative() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: getter for referenceRangeNarrative - gets
getReferenceRangeNarrative(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
getRegex() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
getRegex() - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
getRegexInput(JCas, SideEffectAnnotator.PotentialSideEffect) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return a string to be used for regular expression pattern matching Replace a target sign/symptom or disorder/diseas with <@PSE>, a target drug with <@DRUG>, and the other pse and drug with and respectively, and lower cased the rest text.
getRegexName(int) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
getRel() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
getRela() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
getRelation() - Method in interface org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.Options
getRelation() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: getter for relation - gets
getRelation(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Looks up the arguments in the specified lookup table and converts the relation into a label for classification
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
getRelations(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader
getRelations() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getRelations(Document) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader
getRelations() - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate: getter for relations - gets
getRelations(int) - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
getRelationStats(String) - Static method in class org.apache.ctakes.relationextractor.data.Stats
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getRelativeTemporalContext() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for relativeTemporalContext - gets
getRelativeTemporalContext(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getResourcesDirectory() - Method in interface org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain.Options
getResult() - Method in class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
getResult() - Method in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor.StringToDoublesProcessor
getResult() - Method in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor
getResult() - Method in class org.apache.ctakes.temporal.duration.Utils.Callback
getResults() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
getRightmostNode(SimpleTree, Set<String>) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getRightScopeContextAnnotations(JCas, Annotation, Annotation) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
getRightSibProgeny(ConllDependencyNode, List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getRightSibs(ConllDependencyNode, List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility
getRole() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: getter for role - gets
getRole(int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
getRoot(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
getRoot(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.MarkableTreeUtils
getRoot() - Method in class org.apache.ctakes.jdl.data.xml.DomParser
getRoot() - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
getRoute() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for route - gets Medication route refers to the way that a drug is introduced into the body.
getRoute(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getRouteBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getRouteBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for routeBegin - gets
getRouteBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getRouteElement() - Method in class org.apache.ctakes.drugner.DrugMention
getRouteElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getRouteEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getRouteEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for routeEnd - gets
getRouteEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getRouteMention() - Method in class org.apache.ctakes.drugner.elements.RouteElement
getRowCount(Connection, String) - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader: Slice up the query SQL and rebuild a SQL statement that gets a row count;
getRowNum() - Method in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
getRows(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable
getRui() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
getRule() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
getRun() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
getRun() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getRunBackwards() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getRunCrfBased() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getRunForwards() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getRunParserBased() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getRxNormCodes(IdentifiedAnnotation) - Static method in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
getRXNORMCuis() - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao: get a set of all cuis in RXNORM.
getRXNORMCuis() - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
getSab() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getSab() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
getSaui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getScope() - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: getter for Scope - gets
getScope(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
getScope() - Method in enum org.apache.ctakes.ytex.kernel.SparseDataExporter.ScopeEnum
getScopeContextAnnotations(JCas, Annotation, Annotation, int) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
getScopedFileName(String, String, Integer, Integer, String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil: generate file name for given outdir and 'scope'
getScore() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: getter for score - gets Word Sense disambiguation: if this named entity is assigned multiple ontologyConcepts, the score represents how similar this sense is to surrounding senses (higher scores = more likely to be the correct sense)
getScore(int) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
getScoreFunction(MutualInformationFeatureSelection.CombineScoreMethod) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
getScoreFunction(MutualInformationFeatureSelection.CombineScoreMethod) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
getScui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getSdui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getSearchCUI() - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
getSearchCUI() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getSearchProperties() - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
getSearchProperties() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
getSearchProperties() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getSearchProperties() - Method in class org.apache.ctakes.ytex.web.search.SearchConfigBean
getSearchResultList() - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
getSearchResultList() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getSearchTerm() - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
getSecondaryAssociatedCodeElement() - Method in class org.apache.ctakes.drugner.DrugMention
getSecondaryAssociatedCodeElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getSectionEndMarker(String) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
getSectionName() - Method in class org.apache.ctakes.core.util.DocumentSection
getSectionStartMarker(String) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
getSegment(String) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Gets meta data about the specified segment.
getSegment(ClassifiableEntry) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
getSegmentContainingOffsets(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
getSegmentID(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return segmentID contain the given span
getSegmentID() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for segmentID - gets
getSegmentID(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getSegmentId() - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence: getter for segmentId - gets
getSegmentId(int) - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
getSegmentID() - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
getSegmentIdentifiers() - Method in class org.apache.ctakes.preprocessor.DocumentMetaData: Gets a set of segment identifiers.
getSegmentIDOfSpan(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return segmentID of the sentence containing the given span
getSegmentRegexID() - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
getSegmentRegexs() - Method in interface org.apache.ctakes.ytex.uima.dao.SegmentRegexDao
getSegmentRegexs() - Method in class org.apache.ctakes.ytex.uima.dao.SegmentRegexDaoImpl
getSemanticSimDescriptionMap() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
getSemanticSimRegistryBean() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getSemanticSimRegistryBean() - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
getSemanticSimServiceList() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
getSemanticSimServiceMap() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
getSemilDistFilesForLabel(File, File) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
getSensitivity() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getSentence(FSArray) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
getSentence(JCas, Annotation) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility: Find the sentence in which an Annotation lives
getSentence() - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: getter for sentence - gets sentence containing side effect
getSentence(int) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
getSentenceDistance() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
getSentenceID() - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation: getter for sentenceID - gets
getSentenceID(int) - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
getSentenceID() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for sentenceID - gets contains the sentence id of the sentence that contains the NE's text span
getSentenceID(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getSentenceNumber() - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence: getter for sentenceNumber - gets
getSentenceNumber(int) - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
getSentenceNumContainingGivenSpan(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return sentenceNumber of the sentence containing the given span
getSentenceProbabilities() - Method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Returns the probabilities associated with the most recent calls to sentDetect().
getSentencesOrderById(Iterator<?>) - Method in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
getSentenceSpanContainingGivenSpan(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
getSentenceSpanContainingGivenSpan(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return sentence span containing the span (begin & end)
getSentenceSpanOfGivenSentenceNum(JCas, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return sentence span of the given sentence number
getSentenceText() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
getSentenceTextContainingGivenSpan(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return sentence text containing the span (begin & end)
getSentenceTokens(JCas, Annotation) - Static method in class org.apache.ctakes.core.cc.SentenceTokensPrinter
getSessionFactory() - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.uima.dao.SegmentRegexDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
getSessionFactory() - Method in class org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter
getSessionFactory() - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
getSeverity() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for severity - gets
getSeverity(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getSeverity() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for severity - gets
getSeverity(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getSeverity() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for severity - gets
getSeverity(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getSideEffect() - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: getter for sideEffect - gets side effect mention in NamedEntity
getSideEffect(int) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
getSideEffectNEs(JCas) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return List of NEs (signs/symptoms & diseases/disorders) if they are NOT negated -- ignore sections in setionsToIgnore -- only get the longest NE if it contains the shorter (eg.
getSideEffectsWithPrioritizedRule(JCas, List<SideEffectAnnotator.PotentialSideEffect>) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return a list of SideEffect found by rules.
getSignSymptomKnowtatorClasses() - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
getSimilarities() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
getSimilarity(String, String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings
getSimilarity() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
getSimilarityInfo() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
getSimilarityList() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getSimilarityMap() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getSimilarityMap() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
getSimilarityMetricMap() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getSimilarWords(String, int) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings
getSimInfo() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
getSimpleClone(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
getSingleChild(Element, String, String) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
getSingleEndOffsetMap(List<T>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Creates a map that uses the end offset to index the LookupAnnotation objects.
getSingleStartOffsetMap(List<T>) - Static method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Creates a map that uses the start offset to index the LookupAnnotation objects.
getSixTimesADayMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a fsm that detects four times a day four hours 6-8 hours
getSize() - Method in class org.apache.ctakes.coreference.util.ParentPtrTree
getSize() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.TempRelOptions
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.TempRelOptions
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.TempRelOptions
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.TempRelOptions
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.TempRelOptions
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.TempRelOptions
getSkipTrain() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getSkipTrainComponents() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor.MetaOptions
getSmokerNegatedCount(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
getSMOTENeighborNumber() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventSpans.Options
getSMOTENeighborNumber() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans.Options
getSnomedCodes(IdentifiedAnnotation) - Static method in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
getSnomedCodes(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl: Searches for the Snomed codes that are synonyms of the UMLS concept with CUI umlsCode
getSnomedCodes(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl: Queries the given UMLS CUI against the DB.
getSnomedCodes(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl: Find all Snomed codes that map to the given UMLS code (CUI), by looking in a lucene index
getSortedLookupTokens(JCas, Annotation) - Method in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl: Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.
getSortedLookupTokens(JCas, Annotation) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.
getSortedLookupTokens(JCas, Annotation) - Method in interface org.apache.ctakes.dictionary.lookup.ae.LookupInitializer: Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.
getSortedLookupTokens(JCas, Annotation) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl: Gets a list of tokens that we promise to return in sorted order that are constrained by the input annotation.
getSourceApplication() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceApplication - gets
getSourceApplication(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSourceData(JCas) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil: The first step in utilizing SourceData is getting it!
getSourceData() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: getter for sourceData - gets
getSourceData(int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
getSourceEncounterId() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceEncounterId - gets
getSourceEncounterId(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSourceInstanceId() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceInstanceId - gets
getSourceInstanceId(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSourceInstitution() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceInstitution - gets
getSourceInstitution(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSourceOriginalDate() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceOriginalDate - gets
getSourceOriginalDate(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSourceRevisionDate() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceRevisionDate - gets
getSourceRevisionDate(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSourceRevisionNbr() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: getter for sourceRevisionNbr - gets
getSourceRevisionNbr(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
getSparseDataExporter() - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
getSparseLineValues(SparseData, Map<String, Integer>, Map<String, Map<String, Integer>>, long) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: create a map of attribute index - attribute value for the given instance.
getSparseLineValues(SparseData, Map<String, Integer>, Map<String, Map<String, Integer>>, long) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter: add instance_id to sparse line values
getSpecificity() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getSplitName() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getSplitName() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
getSql() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getSqlInsert(CsvLoadType) - Method in class org.apache.ctakes.jdl.data.loader.CsvLoader
getSqlInsert(XmlLoadType) - Method in class org.apache.ctakes.jdl.data.loader.XmlLoader
getSqlType() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getSrcXml() - Method in class org.apache.ctakes.jdl.data.xml.DomParser
getSrcXml() - Method in class org.apache.ctakes.jdl.data.xml.SaxParser
getSrl() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getStandardChunkAdjusterAnnotator() - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getStandardMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM: Gets a finite state machine that detects the following: 1/2 0.5 half one half 1 half
getStart() - Method in class org.apache.ctakes.core.sentence.SentenceSpan
getStart() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
getStart() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
getStart() - Method in interface org.apache.ctakes.dictionary.lookup2.textspan.TextSpan
getStart() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
getStart() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
getStart() - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
getStartDate(SourceData) - Static method in class org.apache.ctakes.core.util.SourceMetadataUtil
getStartDate() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for startDate - gets
getStartDate(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getStartDate() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: getter for startDate - gets
getStartDate(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
getStartDate() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: getter for startDate - gets
getStartDate(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
getStartDate() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: getter for startDate - gets
getStartDate(int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
getStartDateElement() - Method in class org.apache.ctakes.drugner.DrugMention
getStartDateElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getStartLine() - Method in class org.apache.ctakes.core.util.DocumentSection
getStartOffset() - Method in class org.apache.ctakes.core.fsm.adapters.BaseTokenAdapter
getStartOffset() - Method in class org.apache.ctakes.core.fsm.output.BaseTokenImpl
getStartOffset() - Method in class org.apache.ctakes.core.fsm.token.adapter.BaseTokenAdapter
getStartOffset() - Method in interface org.apache.ctakes.core.fsm.token.BaseToken
getStartOffset() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Gets the start offset.
getStartOffset() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter: Gets the start offset.
getStartOffset() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation: Gets the start offset.
getStartOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
getStartOffset() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
getStartOffset() - Method in class org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl
getStartOffset() - Method in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
getStartStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following: 'start' or 'restarted': started restart
getStartTime() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: getter for startTime - gets
getStartTime(int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
getStartTime() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: getter for startTime - gets
getStartTime(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
getStartTime() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: getter for startTime - gets
getStartTime(int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
getStartTime() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: getter for startTime - gets
getStartTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
getStartTime() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: getter for startTime - gets
getStartTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
getStartTime() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: getter for startTime - gets
getStartTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
getStatus() - Method in class org.apache.ctakes.core.fsm.output.StatusIndicator
getStatus() - Method in class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
getStatus() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for status - gets
getStatus(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getStatus() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: getter for status - gets Status of 'possible', 'history of', or 'family history of'.
getStatus(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getStemmedStr() - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
getStems(String, String, IDictionary) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Get a list of possible stems.
getStn() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
getStopStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following 'stop', 'stopped', or 'discontinue': stopped/li> discontinued
getStr() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getStrength() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for strength - gets
getStrength(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getStrengthBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getStrengthBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for strengthBegin - gets
getStrengthBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getStrengthCombinedMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM: Handles a complex range of strength representations for the discovery of the combined quantity and unit value for this element.
getStrengthElement() - Method in class org.apache.ctakes.drugner.DrugMention
getStrengthElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getStrengthEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getStrengthEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for strengthEnd - gets
getStrengthEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getStrengthMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM: Handles a complex range of strength representations for the discovery of the combined quantity and unit value for this element.
getStrengthMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM: Handles a complex range of strength representations for the discovery of the combined quantity and unit value for this element.
getStrengthMention() - Method in class org.apache.ctakes.drugner.elements.StrengthElement
getStrengthMention() - Method in class org.apache.ctakes.drugner.elements.StrengthUnitElement
getStrengthSlashMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM: Gets a finite state machine that detects the following: 0.5/12.2
getStrengthUnit() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for strengthUnit - gets
getStrengthUnit(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getStrengthUnitBegin() - Method in class org.apache.ctakes.drugner.DrugMention
getStrengthUnitElement() - Method in class org.apache.ctakes.drugner.DrugMention
getStrengthUnitElement() - Method in interface org.apache.ctakes.drugner.DrugModel
getStrengthUnitEnd() - Method in class org.apache.ctakes.drugner.DrugMention
getString(String[], int) - Static method in class org.apache.ctakes.utils.build.BuildPipelinePears
getString(String[], int) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently
getString(String[], int) - Static method in class org.apache.ctakes.utils.build.InstallPipelineFromPears
getStringAsTuis(Collection<String>) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
getStringAttribute(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter: Gets an attribute.
getStringAttribute(String) - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation: Gets an attribute.
getStringAttribute(String) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
getStringAttribute(String) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
getStringCodes(PreparedStatement, Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
getStringParameterValuesMap(String, UimaContext, String) - Static method in class org.apache.ctakes.core.util.ParamUtil
getStringParameterValuesMap(String[], String) - Static method in class org.apache.ctakes.core.util.ParamUtil
getStringParameterValuesSet(String, UimaContext) - Static method in class org.apache.ctakes.core.util.ParamUtil
getStrings() - Method in class org.apache.ctakes.core.resource.LinesFromFileStringsResourceImpl
getStrings() - Method in interface org.apache.ctakes.core.resource.StringsResource
getStt() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getSty() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
getStyleMapFile(AnalysisEngineDescription, String) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
getStyleMapFile(TypeSystemDescription, String) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
getStyleMapFileName(String) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Gets the name of the style map file for the given AE or TypeSystem descriptor filename.
getSubcorpus() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getSuBegin() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for suBegin - gets
getSuBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getSubject(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
getSubject() - Static method in class org.apache.ctakes.core.util.SHARPKnowtatorXMLDefaults
getSubject() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for subject - gets
getSubject(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getSubject() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for subject - gets
getSubject(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getSubSectionAnnotationBodyEnd(Segment, SubSectionIndicator) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Decides where the SubSectionAnnotation should end.
getSubSectionBodyBegin() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: getter for subSectionBodyBegin - gets Sub-section body begin offset.
getSubSectionBodyBegin(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getSubSectionBodyEnd() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: getter for subSectionBodyEnd - gets Sub-section body end offset.
getSubSectionBodyEnd(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getSubSectionHeaderBegin() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: getter for subSectionHeaderBegin - gets Begin offset of subSection header
getSubSectionHeaderBegin(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getSubSectionHeaderEnd() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: getter for subSectionHeaderEnd - gets Ending offset of subsection header
getSubSectionHeaderEnd(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
getSubstanceQuantityMachine() - Method in class org.apache.ctakes.core.fsm.machine.MeasurementFSM: Gets a finite state machine that detects the following: one teaspoon one tsp 1 teaspoon 1 tsp 0.5 tsp 1-5 teaspoons
getSubsumerCount() - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
getSubsumers(ConcRel, Map<String, Set<String>>, short[]) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl: recursively compute the subsumers of a concept
getSubTreeStrings(SimpleTree) - Method in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
getSuEnd() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: getter for suEnd - gets
getSuEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
getSuggestion() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: getter for suggestion - gets
getSuggestion(int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
getSui() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getSumStatusMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM: Gets a finite state machine that detects the following: 'and': and
getSupportVectors() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getSuppress() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getSurroundingTree(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
getSurroundingTreeWithAnnotation(TreebankNode, String) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
getSvmlinDataFileForLabel(File, File) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
getSynonyms(IDictionary, String, String, boolean) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Retrieve a set of synonyms for a word.
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
getSystemAnnotations(JCas, Segment) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
getTableInfos() - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter: Called from initialize()
getTableInfos() - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate: Called from initialize()
getTableName() - Method in interface org.apache.ctakes.core.cc.AbstractJdbcWriter.TableInfo
getTableName() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getTableName() - Method in class org.apache.ctakes.ytex.uima.model.UimaType
getTablePrefix() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getTableSqlInfoMap() - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter
getTag() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
getTag() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
getTargetClassId() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
getTargetClassId() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
getTargetClassIds() - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
getTargetClassName() - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
getTargetType() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getTargetTypeName() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
getTask() - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
getTerm() - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
getTermByConceptId(String) - Method in interface org.apache.ctakes.ytex.web.search.ConceptSearchService
getTermByConceptId(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
getTermFreqVectors(String) - Method in class org.apache.ctakes.utils.wiki.WikiIndex
getTerminals(JCas, Sentence) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
getTerminals() - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: getter for terminals - gets Stores the terminal nodes of the parse tree.
getTerminals(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: indexed getter for terminals - gets an indexed value - Stores the terminal nodes of the parse tree.
getTerminals(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
getTerminals(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
getTest() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getTest() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.TempRelOptions
getTestItems(Evaluation_ImplBase.Options) - Static method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getTestOnCTakes() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getTestPatientSets(File) - Static method in class org.apache.ctakes.temporal.eval.I2B2Data
getTestPatientSets(List<Integer>) - Static method in class org.apache.ctakes.temporal.eval.THYMEData: Deprecated.
Use getPatientSets(patientSets, TEST_REMAINDERS)
getTestRemainders() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getTestTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getText() - Method in class org.apache.ctakes.core.fsm.adapters.TextTokenAdapter
getText() - Method in class org.apache.ctakes.core.fsm.token.adapter.WordTokenAdapter
getText() - Method in interface org.apache.ctakes.core.fsm.token.TextToken
getText() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token
getText() - Method in class org.apache.ctakes.core.sentence.SentenceSpan
getText() - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter: Gets the text.
getText(LookupToken) - Method in class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl.AttributeTextImpl
getText(LookupToken) - Method in class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl.OriginalTextImpl
getText(LookupToken) - Method in interface org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl.TextExtractor
getText() - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation: Gets the text.
getText() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
getText() - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
getText() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
getText() - Method in class org.apache.ctakes.preprocessor.DocumentMetaData
getText() - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
getText() - Method in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter: if this is a word, return the stemmed word, if available - i.e.
getText() - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
getTextBetweenAnnotations(JCas, Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.RelationContextPrinter
getTextBetweenAnnotations(JCas, Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.duration.Utils: Get relation context.
getTextFilesFor(File, Pattern) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getTextMention() - Method in class org.apache.ctakes.drugner.elements.TextMentionElement
getTextSpan() - Method in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
getTextSpan() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
getTextualDateMachine() - Method in class org.apache.ctakes.core.fsm.machine.DateFSM: Gets a finite state machine that detects the following: October 15, 2002 October 15 2002 October 15 October 2002 Oct 15, 2002 Oct 15 2002 Oct 15 Oct 2002 Oct.
getTextURI(JCas) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader: Get the URI that the text in this class was loaded from
getTextURI(JCas) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader: Get the URI that the text in this class was loaded from
getTextURI(JCas) - Method in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
getTextValue(Node) - Static method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: copied from AnnotationViewerDialog.
getTextValue(Node) - Static method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Assumes node has a text field and extracts its value.
getThreeTimesADayMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects three times a day as in the following: t.i.d.
getThresholdFeatures(String, String, String, String, Integer, double, String, double) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getThresholdFeatures(String, String, String, String, Integer, double, String, double) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getTime() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: getter for time - gets
getTime(int) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
getTimeClass() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: getter for timeClass - gets DATE, DURATION, QUANTIFIER, PREPOSTEXP, etc.
getTimeClass(int) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
getTimeModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.EventAndTimeExtractionPipeline.ETOptions
getTimeModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.FullOptions
getTimeModelDirectory() - Method in interface org.apache.ctakes.temporal.pipelines.TimeExtractionPipeline.TimexOptions
getTimeRelationType(String) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType
getTimeRelationType(long, long, long, long) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType
getTimeRelationType(int) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType
getTimeRelationTypeAtoC(TlinkType) - Method in enum org.apache.ctakes.temporal.utils.TlinkType
getTimeUnits(String) - Static method in class org.apache.ctakes.temporal.duration.Utils: Extract time unit(s) from a temporal expression and put in one of the eight bins above.
getTitleMachine() - Method in class org.apache.ctakes.core.fsm.machine.PersonTitleFSM: Gets a finite state machine that detects the following: Dr.
getTlinkType(BinaryTextRelation) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType
getTlinkTypes(BinaryTextRelation) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getTlinkTypes(int, int) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getTlinkTypesAtoC(TlinkTypeSet, TlinkTypeSet) - Static method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
getTn() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getTn() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getTokenCount(String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
getTokenCount() - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
getTokenDistance(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
getTokenIndex() - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: getter for tokenIndex - gets The tokenIndex of a terminal is n, where the terminal is the nth token in a sentence.
getTokenIndex(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
getTokenizedAggregateBuilder() - Static method in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors: Builds the tokenized preprocessing pipeline for ClearNLP
getTokenizedInfPosAggregateBuilder() - Static method in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors: Builds the tokenizedInf preprocessing for ClearNLP
getTokenizedStr() - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
getTokenizedTerm(String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
getTokenNumber() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: getter for tokenNumber - gets
getTokenNumber(int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
getTokenOutputFile() - Method in interface org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.Options
getTokenProcessingPipeline() - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
getTokenRelTreeString(JCas, List<ConllDependencyNode>, Annotation, String) - Static method in class org.apache.ctakes.assertion.util.AssertionDepUtils
getTokenRelTreeString(JCas, List<ConllDependencyNode>, Annotation[], String[]) - Static method in class org.apache.ctakes.assertion.util.AssertionDepUtils
getTokenRelTreeString(JCas, List<ConllDependencyNode>, Annotation[], String[]) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getTokenRelTreeString(JCas, List<ConllDependencyNode>, Annotation[], String[], boolean) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getTokens(String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
getTokenTreeString(JCas, List<ConllDependencyNode>, Annotation) - Static method in class org.apache.ctakes.assertion.util.AssertionDepUtils
getTokenTreeString(JCas, List<ConllDependencyNode>, Annotation, int) - Static method in class org.apache.ctakes.assertion.util.AssertionDepUtils
getTokenTreeString(JCas, List<ConllDependencyNode>, Annotation[], String[], boolean) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getTopFeatures(String, String, String, String, Integer, double, String, Integer) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
getTopFeatures(String, String, String, String, Integer, double, String, Integer) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
getTopicalMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Gets a finite state machine that detects the following medications applied onto the skin, asthma medications, enema, eye or ear drops, decongestants, vaginal creams.
getTopNode(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
getTopNode(List<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
getTp() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
getTp() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getTrainFileToDomain() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
getTrainingClassMap(String, SortedMap<Long, String>, SortedMap<Long, String>, Map<String, Integer>, SortedSet<Long>) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter: pick through the training and test sets, figure out the class id for all instance ids for training.
getTrainItems(Evaluation_ImplBase.Options) - Static method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getTrainPatientSets(File) - Static method in class org.apache.ctakes.temporal.eval.I2B2Data
getTrainPatientSets(List<Integer>) - Static method in class org.apache.ctakes.temporal.eval.THYMEData: Deprecated.
Use getPatientSets(patientSets, TRAIN_REMAINDERS)
getTrainRemainders() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getTrainTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getTransactionManager() - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
getTransactionManager() - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
getTransactionManager() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getTransactionManager() - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
getTransactionManager() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getTransactionManager() - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
getTransactionManager() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getTree() - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: getter for tree - gets
getTree(int) - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
getTree(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String, <any>) - Static method in class org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor
getTreebankDirectory() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getTreebankDirectory() - Method in interface org.apache.ctakes.temporal.utils.RunCorpusDiagnostics.Options
getTreebankParse() - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: getter for treebankParse - gets A bracketed sentence string representing the parse tree.
getTreebankParse(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
getTreeCopy(JCas, TopTreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
getTreeCopy(JCas, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
getTreeMappingInfo() - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
getTs() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getTty() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
getTui() - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
getTui() - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: getter for tui - gets
getTui(int) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
getTui() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
getTuiCode(String) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
getTuiList() - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: list of tuis that corresponds to bitset indices
getTuiList() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
getTuis(Long) - Method in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
getTuiSemanticGroupId(String) - Static method in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil: Sometimes a
getTwiceADayMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects twice a day as in the following: b.i.d.
getTxTemplateNew() - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
getType() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Gets the type of the token.
getType(String) - Static method in class org.apache.ctakes.core.util.JCasUtil
getType(Class<? extends TOP>) - Static method in class org.apache.ctakes.core.util.JCasUtil
getType() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
getType() - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
getType() - Method in class org.apache.ctakes.ytex.kernel.tree.Node
getTypeID() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for typeID - gets The type of named entity (e.g.
getTypeID(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getTypeIndexID() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion
getTypeIndexID() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept
getTypeIndexID() - Method in class org.apache.ctakes.assertion.zoner.types.Heading
getTypeIndexID() - Method in class org.apache.ctakes.assertion.zoner.types.Subzone
getTypeIndexID() - Method in class org.apache.ctakes.assertion.zoner.types.Zone
getTypeIndexID() - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.DemMarkable
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.Markable
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.MarkablePair
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.MarkablePairSet
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.NEMarkable
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.Pair
getTypeIndexID() - Method in class org.apache.ctakes.coreference.type.PronounMarkable
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.DosagesAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.DurationAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.FormAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.FrequencyAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.RouteAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.StrengthAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.sideeffect.type.PSESentence
getTypeIndexID() - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature
getTypeIndexID() - Method in class org.apache.ctakes.sideeffect.type.SESentence
getTypeIndexID() - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification
getTypeIndexID() - Method in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Attribute
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Course
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Date
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Element
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Entity
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Event
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Severity
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.Time
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.Affects
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.Contraindicates
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.DegreeOf
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.Diagnoses
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.Indicates
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.LocationOf
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ManagesTreats
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ManifestationOf
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.Prevents
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.Relation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ResultOf
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.TemporalRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.relation.UMLSRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.ADJP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.ADVP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.CONJP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.ContractionToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.INTJ
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.LST
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.NewlineToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.NP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.O
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.PP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.PRT
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.SBAR
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.SymbolToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.UCP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.VP
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.CourseModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.Markable
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textspan.List
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textspan.Paragraph
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textspan.Segment
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.util.Pair
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.util.Pairs
getTypeIndexID() - Method in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution
getTypeIndexID() - Method in class org.apache.ctakes.ytex.uima.types.Date
getTypeIndexID() - Method in class org.apache.ctakes.ytex.uima.types.DocKey
getTypeIndexID() - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair
getTypesStoreCoveredText() - Method in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
getTypeSystemFromDescriptor(String) - Static method in class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
getTypeSystemFromDescriptor(String) - Static method in class org.apache.ctakes.assertion.medfacts.ConvertXMIAssertionsToi2b2Format
getUimaType() - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
getUimaTypeId() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getUimaTypeID() - Method in class org.apache.ctakes.ytex.uima.model.UimaType
getUimaTypeIdColumnName() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
getUimaTypeName() - Method in class org.apache.ctakes.ytex.uima.model.UimaType
getUmlsConcepts(IdentifiedAnnotation) - Static method in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
getUmlsCuis(IdentifiedAnnotation) - Static method in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
getUmlsDao() - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
getUmlsFirstWordService() - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
getUmlsSemanticType() - Method in interface org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.Options
getUncertainty() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: getter for uncertainty - gets
getUncertainty(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
getUncertainty() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: getter for uncertainty - gets
getUncertainty(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
getUncertainty() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: getter for uncertainty - gets
getUncertainty(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
getUncertaintyTree(JCas, IdentifiedAnnotation, SemanticClasses) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
getUniqueKey(String, String) - Static method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
getUniqueKey() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit: Generates a unique key based on this objects values.
getUnit() - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue: getter for unit - gets
getUnit(int) - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
getUnit() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: getter for unit - gets The periodic unit used, e.g day, month, hour, etc.
getUnit(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
getUnit() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: getter for unit - gets the unit of measurement
getUnit(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
getUpwardPath(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
getUsage() - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
getUsedcTakesSemantics(CollectionMap<Long, Concept, ? extends Collection<Concept>>) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
getUseGoldAttributes() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.TempRelOptions
getUseGoldAttributes() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.TempRelOptions
getUseGoldAttributes() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.TempRelOptions
getUseGoldAttributes() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.TempRelOptions
getUseGoldAttributes() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.TempRelOptions
getUseGoldAttributes() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.TempRelOptions
getUseGoldTrees() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getUseTmp() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.TempRelOptions
getUseTmp() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.TempRelOptions
getUseTmp() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.TempRelOptions
getUseTmp() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.TempRelOptions
getUseTmp() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.TempRelOptions
getUseTmp() - Method in interface org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.TempRelOptions
getValue() - Method in class org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter
getValue() - Method in class org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter
getValue() - Method in class org.apache.ctakes.core.fsm.token.adapter.DecimalTokenAdapter
getValue() - Method in class org.apache.ctakes.core.fsm.token.adapter.IntegerTokenAdapter
getValue() - Method in interface org.apache.ctakes.core.fsm.token.DecimalToken
getValue() - Method in interface org.apache.ctakes.core.fsm.token.IntegerToken
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.Course: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Course_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange: getter for value - gets Indicates the change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.refsem.Severity: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
getValue() - Method in class org.apache.ctakes.typesystem.type.util.Pair: getter for value - gets
getValue(int) - Method in class org.apache.ctakes.typesystem.type.util.Pair_Type
getValue(int) - Method in class org.apache.ctakes.utils.distsem.WordVector
getValue() - Method in class org.apache.ctakes.ytex.kernel.tree.Node
getValueAsDouble() - Method in class org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter
getValueAsDouble() - Method in class org.apache.ctakes.core.fsm.token.adapter.IntegerTokenAdapter
getValueClass() - Method in interface org.apache.ctakes.core.cc.AbstractJdbcWriter.FieldInfo
getValueClass() - Method in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
getValueLong() - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: getter for valueLong - gets
getValueLong(int) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
getValues() - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow
getValues() - Method in class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
getValueString() - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: getter for valueString - gets
getValueString(int) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
getVariant() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
getVcdim() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getVector(String) - Method in class org.apache.ctakes.utils.distsem.WordEmbeddings
getVerbAncestor(ConllDependencyNode) - Static method in class org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor
getViewNames(JCas) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
getViewWithGoldAnnotations(JCas) - Static method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
getWeeklyMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects per week via the following: q.w.k.
getWeeklySuffixMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects the following which indicates 1 per week via the following: /w
getWeight() - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
getWeightParams(File, String) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
getWhitespaceString(int) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
getWindowAnnotations(Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Extracts the list of LookupAnnotation objects representing noun phrases from the context map.
getWindowSpan(JCas, String, int, int, int, boolean, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
getWordIndex(String, String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
getWordTokenLen() - Method in class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
getWriter(String, boolean) - Static method in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
getWriter(String, boolean) - Static method in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline
getWriter(String, boolean) - Static method in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.RelationContextPrinter
getxLeftover() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getxMerge() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getXMIDirectory() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.Options
getXMIDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.PrintFailedTimeNormalizations.Options
getXMIDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.PrintInconsistentAnnotations.Options
getXMIDirectory() - Method in interface org.apache.ctakes.temporal.data.analysis.TimexTreeAlignmentStatistics.Options
getXMIDirectory() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getXMIDirectory() - Method in interface org.apache.ctakes.temporal.utils.RunCorpusDiagnostics.Options
getXMIFile(File, File) - Static method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getXMIFile(File, JCas) - Static method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getXMIReadingPreprocessorAggregateBuilder() - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getXMIWriter(String) - Static method in class org.apache.ctakes.temporal.pipelines.TemporalExtractionPipeline_ImplBase
getXMIWritingPreprocessorAggregateBuilder() - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
getXMLDirectory() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getXMLFormat() - Method in interface org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Options
getxVals() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
getYear() - Method in class org.apache.ctakes.typesystem.type.refsem.Date: getter for year - gets
getYear(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
getYearlySuffixMachine() - Method in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM: Gets a finite state machine that detects the following which indicates 1 per year via the following: /y
getYtexProperties() - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
getYtexProperties() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
getYtexProperties() - Static method in class org.apache.ctakes.ytex.uima.ApplicationContextHolder
getYtexProperties() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
getYtexProperties() - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
getYtexProperties() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
getYtexProperties() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
getYTEXTablePrefix() - Static method in class org.apache.ctakes.ytex.dao.DBUtil
GHC_HIST_SECTIONS - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.relationextractor.eval.SHARPXMI
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.data.analysis.PrintNormalizedTemporalExpressions
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.EventEventDurationStatistics.AnalyseRelationArgumentDuration
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.AnalyseRelationArgumentDuration
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.PreserveCertainEventEventRelationsInGold
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.PreserveCertainEventsInGold
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.PreserveCertainEventTimeRelationsInGold
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.PreserveUMLSEventEventRelationsInGold
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.PreserveUMLSEventTimeRelationsInGold
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
GoldAnnotationAnalysisPipeline - Class in org.apache.ctakes.relationextractor.data: Pipeline for analyzing gold annotations.
GoldAnnotationAnalysisPipeline() - Constructor for class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline
GoldAnnotationAnalysisPipeline.Options - Class in org.apache.ctakes.relationextractor.data
GoldAnnotationAnalysisPipeline.Options() - Constructor for class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline.Options
GoldAnnotationStatsCalculator - Class in org.apache.ctakes.relationextractor.data: Count various stats such as token and relation counts based on the gold standard data.
GoldAnnotationStatsCalculator() - Constructor for class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
GoldEntityAndAttributeReader - Class in org.apache.ctakes.assertion.cr: Read named entity annotations from knowtator xml files into the CAS
GoldEntityAndAttributeReader() - Constructor for class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
GoldEntityAndAttributeReaderPipeline - Class in org.apache.ctakes.assertion.pipelines: A class for testing the reader for the gold standard relation data.
GoldEntityAndAttributeReaderPipeline() - Constructor for class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipeline
GoldEntityAndAttributeReaderPipelineForSeedCorpus - Class in org.apache.ctakes.assertion.pipelines: A class for testing the reader for the gold standard relation data.
GoldEntityAndAttributeReaderPipelineForSeedCorpus() - Constructor for class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
goldEqvCls - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
goldId2AlignId - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
goldRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
goldRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
GoldRelationViewer - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold standard relations and their context.
GoldRelationViewer() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer
GoldRelationViewer - Class in org.apache.ctakes.temporal.data.analysis: Print gold standard relations and their context.
GoldRelationViewer() - Constructor for class org.apache.ctakes.temporal.data.analysis.GoldRelationViewer
GoldRelationViewer.Options - Interface in org.apache.ctakes.relationextractor.data.analysis
GoldRelationViewer.Options - Interface in org.apache.ctakes.temporal.data.analysis
GoldRelationViewer.RelationContextPrinter - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold standard relations and their context.
GoldRelationViewer.RelationContextPrinter() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.RelationContextPrinter
GoldRelationViewer.RelationContextPrinter - Class in org.apache.ctakes.temporal.data.analysis: Print gold standard relations and their context.
GoldRelationViewer.RelationContextPrinter() - Constructor for class org.apache.ctakes.temporal.data.analysis.GoldRelationViewer.RelationContextPrinter
goldSpan2id - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
goldSpans - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
goldStandardDir - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
GoldStandardLabeler - Class in org.apache.ctakes.coreference.util
GoldStandardLabeler(String, String, List<Annotation>) - Constructor for class org.apache.ctakes.coreference.util.GoldStandardLabeler
goldViewDir - Static variable in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
goldViewName - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
goldViewName - Static variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
goldViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveNonUMLSEvents
goldViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveNonUMLSEvents
goldViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveNonUMLSEtEvents
goldViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations
goldViewName - Variable in class org.apache.ctakes.temporal.eval.RemoveTreeAlignedMentions
gotDup - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
gotValidDate - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
goWords - Variable in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
GramMatrixExporter - Interface in org.apache.ctakes.ytex.weka
GramMatrixExporterImpl - Class in org.apache.ctakes.ytex.weka: Deprecated.
don't know if this works ...
GramMatrixExporterImpl() - Constructor for class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
GramMatrixExporterImpl.GramMatrixArffDecorator - Class in org.apache.ctakes.ytex.weka: Deprecated.

add gramIndex attribute to arff file
GramMatrixExporterImpl.GramMatrixArffDecorator(Map<Long, Integer>) - Constructor for class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixArffDecorator: Deprecated.
GramMatrixExporterImpl.GramMatrixType - Enum in org.apache.ctakes.ytex.weka: Deprecated.
GramMatrixExporterImpl.GramMatrixType() - Constructor for enum org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixType: Deprecated.
GT_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
GT_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
GTEQ_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
GTEQ_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl

H

handledRanges - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
handlePossibleRedirect(ScoreDoc) - Method in class org.apache.ctakes.utils.wiki.WikiIndex: Return the document to which the input document redirects.
hasAncestor(ConcRel, ConcRel, HashSet<Integer>) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: check cycle.
hasAncestor(String) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel: is the specified concept an ancestor of this concept?
hasAnnotation(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Checks whether this XCAS file has an annotation with the specified id.
hasAnnotation(XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Checks whether this XCAS file has the specified XcasAnnotation.
hascTakesSemantic(Integer, Iterable<Concept>) - Static method in class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
hasEntityType(int) - Static method in class org.apache.ctakes.temporal.ae.EventAnnotator
hashCode() - Method in class org.apache.ctakes.assertion.cr.RelationInfo
hashCode() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact.Span
hashCode() - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
hashCode() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CuePhrase
hashCode() - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
hashCode() - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation
hashCode() - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation.Span
hashCode() - Method in class org.apache.ctakes.coreference.eval.helpers.Span
hashCode() - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit
hashCode() - Method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey
hashCode() - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupHitKey
hashCode() - Method in class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl: Deprecated.
hashCode() - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm: Override default equals method.
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
hashCode() - Method in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
hashCode() - Method in class org.apache.ctakes.relationextractor.eval.ParameterSettings
hashCode() - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
hashCode() - Method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
hashCode() - Method in class org.apache.ctakes.relationextractor.knowtator.Span
hashCode(Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
hashCode(Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
hashCode() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
hashCode() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
hashCode() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
hashCode() - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
hashCode() - Method in class org.apache.ctakes.ytex.kernel.OrderedPair
hashCode() - Method in class org.apache.ctakes.ytex.kernel.Pair
hashCode() - Method in class org.apache.ctakes.ytex.kernel.tree.Node
hashCode() - Method in class org.apache.ctakes.ytex.kernel.tree.NodeKey
hashCode() - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
hashCode() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
hashCode() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
hashCode() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
hashCode() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
hashCode() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
hashCode() - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
hashCode() - Method in class org.apache.ctakes.ytex.uima.model.UimaType
hashCode() - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
hashCode() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
hashCode() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
HashSetMap<K,V> - Class in org.apache.ctakes.dictionary.lookup2.util.collection: Author: SPF Affiliation: CHIP-NLP Date: 6/24/14
HashSetMap() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
HashSetMap(int) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
hashToFeatureList(HashMap<String, Boolean>) - Static method in class org.apache.ctakes.assertion.attributes.features.GenericFeaturesExtractor
hashToFeatureList(HashMap<String, Boolean>) - Static method in class org.apache.ctakes.assertion.attributes.features.HistoryFeaturesExtractor
hashToFeatureList(HashMap<String, Boolean>) - Static method in class org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor
hasMultipleDrugsInSpan(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Return true if exists more than one drug and reason within the span, otherwise return false
hasMultipleElementsInSpan(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Return true if exists more than one drug and reason within the span, otherwise return false
hasNext() - Method in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
hasNext() - Method in class org.apache.ctakes.assertion.cr.NegExCorpusReader
hasNext() - Method in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
hasNext() - Method in class org.apache.ctakes.assertion.eval.XMIReader
hasNext() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Similar to 'org.apache.uima.collection.CollectionReader' method hasNext() except interations represents the actual number of documents to be processed, so if the total number of documents in a queue is more than the 'Iterations' value then only the iteration amount will be processed.
hasNext() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
hasNext() - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader
hasNext() - Method in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
hasNext() - Method in class org.apache.ctakes.core.cr.TextReader
hasNext() - Method in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
hasNext() - Method in class org.apache.ctakes.core.cr.XMIReader
hasNext() - Method in class org.apache.ctakes.core.util.FSListIterator
hasNext() - Method in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
hasNext() - Method in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
hasNext() - Method in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
hasNext() - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
hasNext() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
hasOverlap(Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
hasOverlap(Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations
hasOverlapNNs(JCas, EventMention, EventMention) - Static method in class org.apache.ctakes.temporal.ae.TemporalRelationRuleAnnotator: Method for checking if two arguments share some common NNs ob VBs.
hasOverlappingSpan(EventMention, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.ae.feature.NumberOfEventsInTheSameSentenceExtractor
hasPatternOfDiscontDrugBecausePse(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if discontVerb...DRUG+...because|after...PSE+
hasPatternOfDrugCausePse(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if Drug+***causeVerb...Pse+ -- allow other than drug NE between Drug and causeVerb (eg: Paxil was started for anxiety but caused a rash and was discontinued.)
hasPatternOfDrugDiscontBecausePse(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if DRUG+***discontVerb...because|after...PSE+
hasPatternOfDrugDueToPse(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if drug+...DueToWord...pse+
hasPatternOfDrugMadePse(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if Drug+***madeVerb him/her Pse+ -- allow other than drug NE between Drug and madeVerb (eg: Paxil was started for anxiety but made him a rash.)
hasPatternOfNotePseWithDrug(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if noteVerb...PSE+...with...Drug+
hasPatternOfPseAfterDrug(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if pse+...after taking/after starting...drug+ but if the pse sentence contains certain word, return false
hasPatternOfPseDueToDrug(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if pse+...DueToWord...drug+ - drug must NOT be negated - only consecutive drug(s) are permitted for multiple causing drugs
hasSideEffectAsPse(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if pse is sideEffectWord and there is no other pse(s) in the pse.sentence but if the pse sentence contains certain word, return false - this is a naive rule - sideEffectWord must not be negated
hasTlinkType(int, int, TlinkType) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
hasValidExtension(File) - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
hasWordOfSideEffect(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if pse is NOT sideEffectWord and the pse.sentence contains sideEffectWord - this is a naive rule - sideEffectWord must not be negated
hbe - Variable in class org.apache.ctakes.coreference.util.AttributeCalculator
hbs - Variable in class org.apache.ctakes.coreference.util.AttributeCalculator
headerPatt - Static variable in class org.apache.ctakes.temporal.ae.THYMETreebankReader
Heading - Class in org.apache.ctakes.assertion.zoner.types: a section heading Updated by JCasGen Wed Sep 30 11:06:06 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-assertion-zoner/target/jcasgen/typesystem.xml
Heading() - Constructor for class org.apache.ctakes.assertion.zoner.types.Heading: Never called.
Heading(int, TOP_Type) - Constructor for class org.apache.ctakes.assertion.zoner.types.Heading: Internal - constructor used by generator
Heading(JCas) - Constructor for class org.apache.ctakes.assertion.zoner.types.Heading
Heading(JCas, int, int) - Constructor for class org.apache.ctakes.assertion.zoner.types.Heading
Heading_Type - Class in org.apache.ctakes.assertion.zoner.types: a section heading Updated by JCasGen Wed Sep 30 11:06:06 EDT 2015
Heading_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.zoner.types.Heading_Type: initialize variables to correspond with Cas Type and Features
HELP_MESSAGE - Static variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
HIDDEN_TEXT - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
HISTORY_STATUS - Static variable in class org.apache.ctakes.core.fsm.output.StatusIndicator
HISTORY_STATUS - Static variable in class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
HistoryAttributeClassifier - Class in org.apache.ctakes.assertion.attributes.history
HistoryAttributeClassifier() - Constructor for class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
HistoryAttributeClassifier.AnnotLocationComparator - Class in org.apache.ctakes.assertion.attributes.history
HistoryAttributeClassifier.AnnotLocationComparator() - Constructor for class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier.AnnotLocationComparator
HistoryCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
HistoryCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
HistoryFeaturesExtractor - Class in org.apache.ctakes.assertion.attributes.features: HistoryFeaturesExtractor Ports the features and classification decisions of the first version (logic) of the subject tool
HistoryFeaturesExtractor() - Constructor for class org.apache.ctakes.assertion.attributes.features.HistoryFeaturesExtractor
HistoryOfModifier - Class in org.apache.ctakes.typesystem.type.textsem: An indication of explicit mentioning of a past history.
HistoryOfModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier: Never called.
HistoryOfModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier: Internal - constructor used by generator
HistoryOfModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier
HistoryOfModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier
HistoryOfModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: An indication of explicit mentioning of a past history.
HistoryOfModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type: initialize variables to correspond with Cas Type and Features
HobbsTreeNavigator - Class in org.apache.ctakes.coreference.util
HobbsTreeNavigator() - Constructor for class org.apache.ctakes.coreference.util.HobbsTreeNavigator
holdLargestPeriod - Variable in class org.apache.ctakes.drugner.DrugMention
HOURLY - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
HourMinuteCondition - Class in org.apache.ctakes.core.fsm.condition: Handles case where 2:00 is a single WordToken.
HourMinuteCondition(int, int, int, int) - Constructor for class org.apache.ctakes.core.fsm.condition.HourMinuteCondition
hsql - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
HSQL_DB_EXT - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
HSQL_FILE_PREFIX - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
htmlRB - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
htmlRB - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
HtmlTableCasConsumer - Class in org.apache.ctakes.core.cc: Outputs an HTML table that visualizes the specified Annotation objects over the document text.
HtmlTableCasConsumer() - Constructor for class org.apache.ctakes.core.cc.HtmlTableCasConsumer
HtmlTableCasConsumer.AnnotationLengthComparator - Class in org.apache.ctakes.core.cc: Comparator for comparing two Annotation objects based on span length.
HtmlTableCasConsumer.AnnotationLengthComparator() - Constructor for class org.apache.ctakes.core.cc.HtmlTableCasConsumer.AnnotationLengthComparator
HtmlTableCasConsumer.AnnotationPositionComparator - Class in org.apache.ctakes.core.cc: Comparator for comparing two Annotation objects based on offset position.
HtmlTableCasConsumer.AnnotationPositionComparator() - Constructor for class org.apache.ctakes.core.cc.HtmlTableCasConsumer.AnnotationPositionComparator
HYPH_FREQ_TABLE_RESRC_KEY - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
HYPHEN_OR_MINUS_SIGN - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
HyphenatedDrugFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect hyphenated drug information adjoined to dosage data in the given input of tokens.
HyphenatedDrugFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.HyphenatedDrugFSM: Constructor
HyphenatedDrugToken - Class in org.apache.ctakes.drugner.fsm.output.util
HyphenatedDrugToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.HyphenatedDrugToken
hyphenatedPrefixes - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
hyphenatedPrefixesLookup - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
HyphenatedPTB - Class in org.apache.ctakes.core.nlp.tokenizer
HyphenatedPTB() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
hyphenatedSuffixes - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
hyphenatedSuffixesLookup - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
hyphenatedWords - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
hyphenatedWordsLookup - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
hyphenfilepath - Variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
HyphenTextModifierImpl - Class in org.apache.ctakes.core.ci
HyphenTextModifierImpl(String, int) - Constructor for class org.apache.ctakes.core.ci.HyphenTextModifierImpl
HyphenTextModifierImpl(InputStream, int) - Constructor for class org.apache.ctakes.core.ci.HyphenTextModifierImpl: Default constructor takes a name of the file containing hyphenated phrases, with their frequency.

I

i - Static variable in class org.apache.ctakes.assertion.cr.NegExCorpusReader
i - Variable in class org.apache.ctakes.core.util.CtakesFileNamer
i - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
I2B2_2010_CORPUS - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
I2B2_2010_TEST_CORPUS - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
I2B2_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
I2B2_MIPACQ_NEGEX_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
I2B2_MIPACQ_NEGEX_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
I2B2_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
I2B2_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
I2B2_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
I2B2_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
I2B2_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
I2B2Challenge2010CollectionReader - Class in org.apache.ctakes.assertion.cr
I2B2Challenge2010CollectionReader() - Constructor for class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
I2B2Data - Class in org.apache.ctakes.temporal.eval
I2B2Data() - Constructor for class org.apache.ctakes.temporal.eval.I2B2Data
i2b2Output - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
I2B2TemporalXMLReader - Class in org.apache.ctakes.temporal.ae
I2B2TemporalXMLReader() - Constructor for class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
iAnnotationType - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iAnnotationType - Variable in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
iBoundaryAnnType - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
ICD10_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
ICD9_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
iCurrentCtr - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
id - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The unique identifier assigned to this annotation by Knowtator
id - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.IdAndSlot
ID - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
id - Variable in class org.apache.ctakes.preprocessor.SegmentMetaData
ID - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
id1 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
id1 - Variable in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
id1 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
id2 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
id2 - Variable in class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
id2 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
idCount - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
IdentifiedAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Any span of text that has been discovered or flagged for some reason, such as a Named Entity.
IdentifiedAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: Never called.
IdentifiedAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: Internal - constructor used by generator
IdentifiedAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
IdentifiedAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
IdentifiedAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Any span of text that has been discovered or flagged for some reason, such as a Named Entity.
IdentifiedAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type: initialize variables to correspond with Cas Type and Features
IdentifiedAnnotationExpander - Class in org.apache.ctakes.relationextractor.ae
IdentifiedAnnotationExpander() - Constructor for class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
IdentifiedAnnotationFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature: Given a token, check if this token is inside any identified annotation if so check if the identifiled annotion is a known event.
IdentifiedAnnotationFeatureExtractor(String, Map<String, double[]>) - Constructor for class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor
IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor - Class in org.apache.ctakes.temporal.ae.feature
IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor() - Constructor for class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor
identifiedAnnotationId - Variable in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
IdentifiedAnnotationUtil - Class in org.apache.ctakes.core.util
IdentifiedAnnotationUtil() - Constructor for class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
identifier - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
idf(long, long) - Method in class org.apache.ctakes.utils.wiki.ApproximateSimilarity
idfMap - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: for tf-idf, term-document count map
ifDependent(JCas, EventMention, EventMention) - Static method in class org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator
ignoreAnatomicalSites - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
ignoreConditional - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
ignoredSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
ignoreGeneric - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
ignoreHistory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
ignoreImpossibleGoldRelations - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
ignorePolarity - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
ignoreSubject - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
ignoreUncertainty - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
ImmutableCollectionMap<K,V,T extends java.util.Collection<V>> - Class in org.apache.ctakes.dictionary.lookup2.util.collection: Author: SPF Affiliation: CHIP-NLP Date: 9/5/2014
ImmutableCollectionMap(CollectionMap<K, V, T>) - Constructor for class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
IMPLANT - Static variable in class org.apache.ctakes.drugner.elements.FormElement
IMPLEMENTATION_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Each RareWordDictionary, ConceptFactory, and TermConsumer must have a java implementation.
importClassifierEvaluation(String, Integer, String, String, String, String, BufferedReader) - Method in interface org.apache.ctakes.ytex.weka.WekaResultsImporter
importClassifierEvaluation(String, Integer, String, String, String, String, BufferedReader) - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
importDirectory(CommandLine) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter: Expect directory with subdirectories for each evaluation.
importDirectory(File, ClassifierEvaluationParser) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter: recursively import directory.
importDirectory(CommandLine) - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults: Expect directory with subdirectories for each evaluation.
importDocumentResults(String, BufferedReader) - Method in interface org.apache.ctakes.ytex.weka.WekaResultsImporter: load results into document class table.
importDocumentResults(String, BufferedReader) - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl: Delegate to importResults
importInstanceResult(Integer, List<String>, String, int, int, List<Double>) - Method in class org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter
importInstanceResult(Integer, List<String>, String, int, int, List<Double>) - Method in interface org.apache.ctakes.ytex.weka.WekaResultInstanceImporter
importInstanceResult(Integer, List<String>, String, int, int, List<Double>) - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl.ClassifierEvaluationInstanceImporter
importPred(CommandLine) - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults
importResults(WekaResultInstanceImporter, String, BufferedReader) - Method in interface org.apache.ctakes.ytex.weka.WekaResultsImporter: Parse weka output file, pass results to the specified importer to save results
importResults(WekaResultInstanceImporter, String, BufferedReader) - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl: Parse results, pass them off to WekaResultInstanceImporter
ImportWekaResults - Class in org.apache.ctakes.ytex.weka: Runs org.apache.ctakes.ytex.weka.WekaResultsImporter for the specified task and result file.
ImportWekaResults() - Constructor for class org.apache.ctakes.ytex.weka.ImportWekaResults
ImputedFeatureEvaluator - Interface in org.apache.ctakes.ytex.kernel
ImputedFeatureEvaluator.MeasureType - Enum in org.apache.ctakes.ytex.kernel
ImputedFeatureEvaluator.MeasureType(String) - Constructor for enum org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator.MeasureType
ImputedFeatureEvaluatorImpl - Class in org.apache.ctakes.ytex.kernel: Calculate the mutual information of each concept of a corpus wrt a concept graph and classification task (label) and possibly a fold.
ImputedFeatureEvaluatorImpl() - Constructor for class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
ImputedFeatureEvaluatorImpl.ConceptInstanceMapExtractor - Class in org.apache.ctakes.ytex.kernel: fill in map of Concept Id - bin - instance ids
ImputedFeatureEvaluatorImpl.ConceptInstanceMapExtractor(Map<String, Map<String, Set<Long>>>, ConceptGraph) - Constructor for class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.ConceptInstanceMapExtractor
ImputedFeatureEvaluatorImpl.JointDistribution - Class in org.apache.ctakes.ytex.kernel: joint distribution of concept (x) and class (y).
ImputedFeatureEvaluatorImpl.JointDistribution(Set<String>, Set<String>) - Constructor for class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: set up the joint distribution table.
ImputedFeatureEvaluatorImpl.JointDistribution(Set<String>, Set<String>, Map<String, Set<Long>>, Map<String, Set<Long>>, String) - Constructor for class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution
ImputedFeatureEvaluatorImpl.Parameters - Class in org.apache.ctakes.ytex.kernel: We are passing around quite a few parameters.
ImputedFeatureEvaluatorImpl.Parameters() - Constructor for class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
ImputedFeatureEvaluatorImpl.Parameters(Properties) - Constructor for class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
imputeWeight - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
IN_HIST_SECTION - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
INCLUDE_HEADER - Static variable in interface org.apache.ctakes.ytex.sparsematrix.InstanceDataExporter
INCLUDE_REL - Static variable in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
includeSectionMarkers - Variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
inCourseSection(EventMention, List<Segment>) - Static method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
INCREASE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
INCREASE_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
INCREASEFROM - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
IndentStartState - Class in org.apache.ctakes.drugner.fsm.states.util
IndentStartState(String) - Constructor for class org.apache.ctakes.drugner.fsm.states.util.IndentStartState
index - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
index - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
INDEX_NAME - Static variable in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixArffDecorator: Deprecated.
INDEX_NAME_NOMINAL - Static variable in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixArffDecorator: Deprecated.
indexOfRegex(String, Pattern) - Static method in class org.apache.ctakes.drugner.DrugMention: Scan a string for the first occurrence of some regex Pattern.
indexOfTokenToInclude - Variable in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster
indexPath - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
indexReader - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
indexSearcher - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
Indicates - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
Indicates() - Constructor for class org.apache.ctakes.typesystem.type.relation.Indicates: Never called.
Indicates(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Indicates: Internal - constructor used by generator
Indicates(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Indicates
Indicates_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
Indicates_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Indicates_Type: initialize variables to correspond with Cas Type and Features
IndicatesTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
IndicatesTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation: Never called.
IndicatesTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation: Internal - constructor used by generator
IndicatesTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation
IndicatesTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
IndicatesTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation_Type: initialize variables to correspond with Cas Type and Features
inferForIndex(int) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
inferTlinkTypesForAnnotationAtoBwithCandD(int, int, int, TlinkType) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
inferTlinkTypesForIndexAtoBtoC(int, int, int, TlinkTypeSet, TlinkTypeSet) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
inFile - Variable in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
INFOCONTENT - Static variable in interface org.apache.ctakes.ytex.kernel.InfoContentEvaluator
infoContentEvaluator - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
InfoContentEvaluator - Interface in org.apache.ctakes.ytex.kernel
InfoContentEvaluatorImpl - Class in org.apache.ctakes.ytex.kernel: Calculate the information content of each concept in a corpus wrt the specified concept graph.
InfoContentEvaluatorImpl() - Constructor for class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
INHALANT - Static variable in class org.apache.ctakes.drugner.elements.FormElement
init() - Static method in class org.apache.ctakes.utils.xcas_comparison.Const
init() - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
init() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
init() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
InitableJdbcConnectionResourceImpl - Class in org.apache.ctakes.ytex.uima.resource: copied from mayo JdbcConnectionResourceImpl.
InitableJdbcConnectionResourceImpl() - Constructor for class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl
initalizeRuleList() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
initBoundaryData() - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
initBoundaryData() - Method in class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer
initBoundaryData() - Method in class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer
initClassifierEval(String, String, String, String, String) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser
initClassifierEval(String, String, String, String, String, ClassifierEvaluation) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser
initClassifierEvaluation(String, ClassifierEvaluation) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
initClassifierEvaluationFromProperties(Properties, ClassifierEvaluation) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
initCountPrepStmt(String) - Method in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
initCuiMainSuiMap() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel: init the cui -> 'main sui' map.
initCuiTuiMapFromCorpus() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl: load cui-tui for the specified corpus from the MRSTY table
initDB(String, String) - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
initDocKeyMapping() - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
initEntityWikiSim() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
initExclusionSet() - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord: initialize lvg exclusion set
initFeatureEval(ImputedFeatureEvaluatorImpl.Parameters, String, int, String) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
initializationComplete() - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
initializationComplete() - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the initialization is completed.
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.attributes.GenericAttributeAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.attributes.SubjectAttributeAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
initialize() - Method in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
initialize() - Method in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.eval.XMIReader
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
initialize() - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
initialize() - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
initialize(UimaContext) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: Performs initialization logic.
initialize(UimaContext) - Method in interface org.apache.ctakes.chunker.ae.ChunkCreator
initialize(UimaContext) - Method in class org.apache.ctakes.chunker.ae.Chunker
initialize(UimaContext) - Method in class org.apache.ctakes.chunker.ae.DefaultChunkCreator
initialize(UimaContext) - Method in class org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator
initialize(UimaContext) - Method in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator: Method invoked by UIMA framework to initialize this annotator
initialize(UimaContext) - Method in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
initialize(org.apache.uima.UimaContext) - Method in class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
initialize() - Method in class org.apache.ctakes.constituency.parser.uima.co.ParserTreeWriterConsumer
initialize(UimaContext) - Method in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.CDASegmentAnnotator: Init and load the sections mapping file and precompile the regex matches into a hashmap
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.CopyAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.FilterAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.SectionSegmentAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.SentenceDetector
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.SimpleSegmentWithTagsAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
initialize() - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter
initialize() - Method in class org.apache.ctakes.core.cc.CasConsumer: Read in configuration parameters
initialize() - Method in class org.apache.ctakes.core.cc.FilesInDirectoryCasConsumer
initialize() - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
initialize() - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate
initialize() - Method in class org.apache.ctakes.core.cc.NormalizedFilesInDirectoryCasConsumer
initialize() - Method in class org.apache.ctakes.core.cc.SentenceTokensPrinter: Checks for parameter OutputDirectory.
initialize() - Method in class org.apache.ctakes.core.cc.TokenFreqCasConsumer: This method opens/creates the file specified by "TokenFreqFile" and initializes the data structure that will keep track of frequency counts.
initialize() - Method in class org.apache.ctakes.core.cc.TokenOffsetsCasConsumer
initialize(UimaContext) - Method in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
initialize() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
initialize() - Method in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
initialize() - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader
initialize() - Method in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
initialize(UimaContext) - Method in class org.apache.ctakes.core.cr.TextReader
initialize() - Method in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
initialize(UimaContext) - Method in class org.apache.ctakes.core.cr.XMIReader
initialize(UimaContext) - Method in class org.apache.ctakes.core.util.CtakesFileNamer
initialize(UimaContext) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
initialize(UimaContext) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
initialize(UimaContext) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
initialize(UimaContext) - Method in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
initialize(UimaContext) - Method in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.SerializeDocumentToXMI
initialize(UimaContext) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
initialize(UimaContext) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
initialize(UimaContext) - Method in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
initialize() - Method in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
initialize() - Method in class org.apache.ctakes.dependency.parser.DependencyNodeWriter: Read in configuration parameters
initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator: Set the number of consecutive and total tokens that can be skipped (optional).
initialize(UimaContext) - Method in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
initialize() - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
initialize(UimaContext) - Method in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator: Performs initialization logic.
initialize(UimaContext) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Performs initialization logic.
initialize(UimaContext) - Method in interface org.apache.ctakes.necontexts.ContextAnalyzer: This will be called by the ContextAnnotator during its initialize method
initialize(UimaContext) - Method in class org.apache.ctakes.necontexts.ContextAnalyzerAdapter
initialize(UimaContext) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer
initialize(UimaContext) - Method in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
initialize() - Method in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
initialize(UimaContext) - Method in class org.apache.ctakes.postagger.POSTagger
initialize(UimaContext) - Method in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
initialize() - Method in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
initialize(UimaContext) - Method in class org.apache.ctakes.sideeffect.ae.PSESentenceAnnotator
initialize(AnnotatorContext) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceClassifierAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
initialize() - Method in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
initialize() - Method in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
initialize(UimaContext) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
initialize(UimaContext) - Method in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
initialize(UimaContext) - Method in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster: Performs initialization logic.
initialize() - Method in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
initialize(UimaContext) - Method in class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer
initialize(UimaContext) - Method in class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.EventAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.TimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
initialize(UimaContext) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIWriter
initialize() - Method in class org.apache.ctakes.utils.wiki.WikiIndex
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.DBConsumer: read config parameters
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator: Load the regex-segment map from the database using the segmentRegexDao.
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
initialize() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
initialize_generic_extractor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
initialize_history_extractor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
initialize_subject_extractor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
initializeAttributes(SparseData, SortedSet<String>) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter: initialize attributes
initializeConceptFilter() - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
initializeConceptGraph(ConceptGraph) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: replace cui strings in concrel with references to other nodes.
initialized - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
initializeDomainAdaptation() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
initializeExport(InstanceData, Properties, SparseData) - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: get needed properties out of outdir.
initializeExport(InstanceData, Properties, SparseData) - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: initialize export - called once
initializeExport(InstanceData, Properties, SparseData) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter
initializeExport(InstanceData, Properties, SparseData) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter: write distance up to 6 digit precision.
initializeExport(InstanceData, Properties, SparseData) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
initializeExport(InstanceData, Properties, SparseData) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter: add the "0" class for transductive learning
initializeExport(InstanceData, Properties, SparseData) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
initializeFeatureEvaluation(String, String, String, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: initialize data structures for the fold that will be exported.
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory.SVMLinDataFormatter
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter: write a file with the attribute names corresponding to the indices in the libsvm data file
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter
initializeFold(SparseData, String, Integer, Integer, SortedMap<Boolean, SortedMap<Long, String>>) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
initializeFrags(String) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
initializeFrags() - Static method in class org.apache.ctakes.relationextractor.ae.features.TreeFragmentFeatureExtractor
initializeInstanceIndices(String, Map<Long, String>, Map<Long, Integer>) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
initializeInstances(String, BagOfWordsData, BagOfWordsDecorator) - Method in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl: initialize the weka Instances
initializeInstances(SparseData, SortedMap<Long, String>, boolean, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter: initialize the weka Instances
initializeLabel(String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>, Properties, SparseData) - Method in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter
initializeLabel(String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>, Properties, SparseData) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter
initializeLabel(String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>, Properties, SparseData) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
initializeLabel(String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>, Properties, SparseData) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
initializeLabel(String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>, Properties, SparseData) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter: initialize attributes on a per-label basis even if the data is the same across all labels.
initializePreLoad() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
initializeQueue(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.coreference.util.HobbsTreeNavigator
initializeRules() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
initInfoContent() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl: initialize information content caches TODO replace strings with concept ids from conceptGraph to save memory
initLCSes(String, String, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric: compute the lcses and min path distance for the concept pair, if this hasn't been done already
initLcsIC(Map<String, Double>, SimilarityInfo, boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric: get the best lcs and its information content if this hasn't been done already.
initLcsIC(String, String, Map<String, Double>, SimilarityInfo, boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric: call initLCSes and initLcsIC
initLvg() - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord: initialize lvgCmd
initMapArgs(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
initMapInfo(FeatureStructure) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: load mapping info
initMetaDataPrepStmt(String) - Method in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
initMetrics() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
initNGrams(HashMap<String, Integer>, String, int) - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
initOptions() - Static method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
initOptions() - Static method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
initOptions() - Static method in class org.apache.ctakes.ytex.KernelLauncher
initOptions() - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults
initRegexes() - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
initRegexMap(List<NamedEntityRegex>) - Method in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
initRegexMap(List<SegmentRegex>) - Method in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
initSimilarityMetricMap() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl: initialize the metrics
initTerminalNodes(TopTreebankNode, JCas) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
initTokenizer() - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord: initialize the tokenizer.
initTruthData() - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
initWikiSim() - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
initWordSets() - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
INJECTION - Static variable in class org.apache.ctakes.drugner.elements.FormElement
innerEvaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
innerEvaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.ProductKernel
innerEvaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel: return the product of all the similarity metrics
innerEvaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel: concepts have overlapping semantic types? yes return 1, else return 0
innerEvaluate(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SumKernel
iNonSmokerCtr - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
input - Variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
input - Variable in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
input - Variable in class org.apache.ctakes.sideeffect.util.PatternMatch
INPUT_FORMAT_PARAM - Static variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader: "InputFormat" is a optional, single, boolean parameter that determines whether or not the features associated with each word will be loaded into the CAS or not.
inputDir - Variable in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances.Options
inputDir - Variable in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
inputDirectory - Static variable in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
inputDirectory - Variable in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls
inputDirectory - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline.Options
inputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.Options
inputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline.Options
inputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.Options
inputDirectory - Variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.Options
inputDirPath - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
inputFile - Variable in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
inputFile - Static variable in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
inputFilename - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
inputFormat - Variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
insdObject - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
insertAnnotationContainmentLinks(int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: insert annotation containment links.
insertAnnotationNode(JCas, TopTreebankNode, Annotation, String) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
insertAttribute(String, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Inserts an (attribute, value) pair to this XcasAnnotation.
insertAuiFirstWord(List<UmlsAuiFirstWord>) - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao
insertAuiFirstWord(List<UmlsAuiFirstWord>) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
insertChild(int, SimpleTree) - Method in class org.apache.ctakes.utils.tree.SimpleTree
insertFolds(List<Set<Long>>, String, String, String, int) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl: insert the folds into the database
insertIntReference(String, int[]) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
insertReference(String, XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
installationDir - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
installationDir - Variable in class org.apache.ctakes.utils.build.InstallPearSilently.RunInstallation
installPear(File, File) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently: Method that installs the given PEAR file to the given installation directory.
InstallPearSilently - Class in org.apache.ctakes.utils.build: This class is used to install a pear file locally in a directory chosen by the user and then run the installed AE in CVD.
InstallPearSilently() - Constructor for class org.apache.ctakes.utils.build.InstallPearSilently
InstallPearSilently.RunInstallation - Class in org.apache.ctakes.utils.build: The RunInstallation class implements a thread that is used to run the installation.
InstallPearSilently.RunInstallation(File, File) - Constructor for class org.apache.ctakes.utils.build.InstallPearSilently.RunInstallation: Constructor that sets a given input PEAR file and a given installation directory.
InstallPipelineFromPears - Class in org.apache.ctakes.utils.build: This class is used to install a pear file locally in a directory chosen by the user and then run the installed AE in CVD.
InstallPipelineFromPears() - Constructor for class org.apache.ctakes.utils.build.InstallPipelineFromPears
INSTANCE_ID - Static variable in class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
INSTANCE_ID - Static variable in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
InstanceData - Class in org.apache.ctakes.ytex.kernel: data structure to store instance ids, their classes, folds, runs, and labels.
InstanceData() - Constructor for class org.apache.ctakes.ytex.kernel.InstanceData
instanceDataExporter - Variable in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
InstanceDataExporter - Interface in org.apache.ctakes.ytex.sparsematrix
instanceDataExporter - Variable in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
instanceDataExporter - Variable in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
InstanceDataExporterImpl - Class in org.apache.ctakes.ytex.sparsematrix: output the instance data
InstanceDataExporterImpl() - Constructor for class org.apache.ctakes.ytex.sparsematrix.InstanceDataExporterImpl
instanceFeatureCount - Variable in class org.apache.ctakes.temporal.utils.SMOTEplus
instanceGatheringOutputDir - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
instanceId - Variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
instanceId - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
instanceId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
instanceId - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
instanceID - Variable in class org.apache.ctakes.ytex.uima.model.Document: external document id
instanceId1 - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
instanceId2 - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
instanceIDField - Variable in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
instanceIDMap - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.SliceEvaluator
instanceIDQuery - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
instanceIds - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
instanceIds - Variable in class org.apache.ctakes.ytex.kernel.SparseData: the instance ids in this sparse data set
instanceIdToIndexMap - Variable in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixArffDecorator: Deprecated.
instanceKernel - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
instanceKey - Variable in class org.apache.ctakes.ytex.uima.model.Document
instanceLabel - Variable in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
instanceLabel - Variable in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
instanceLabel - Variable in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
instanceNominalWords - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: instance nominal attribute values
instanceNominalWords - Variable in class org.apache.ctakes.ytex.kernel.SparseData: instance nominal attribute values
instanceNumericWords - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: map if instance id to map of attribute name - value pairs
instanceNumericWords - Variable in class org.apache.ctakes.ytex.kernel.SparseData: map if instance id to map of attribute name - value pairs
instanceQueryMappingInfo - Variable in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
instanceTreeBuilder - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
InstanceTreeBuilder - Interface in org.apache.ctakes.ytex.kernel.tree
InstanceTreeBuilderImpl - Class in org.apache.ctakes.ytex.kernel.tree
InstanceTreeBuilderImpl() - Constructor for class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
INTEGER_TYPE - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
IntegerCondition - Class in org.apache.ctakes.core.fsm.condition
IntegerCondition() - Constructor for class org.apache.ctakes.core.fsm.condition.IntegerCondition
IntegerRange - Class in org.apache.ctakes.preprocessor: Defines a range of integers.
IntegerRange() - Constructor for class org.apache.ctakes.preprocessor.IntegerRange
IntegerRangeCondition - Class in org.apache.ctakes.core.fsm.condition
IntegerRangeCondition(int, int) - Constructor for class org.apache.ctakes.core.fsm.condition.IntegerRangeCondition
IntegerToken - Interface in org.apache.ctakes.core.fsm.token
IntegerTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
IntegerTokenAdapter(NumToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter
IntegerTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter
IntegerTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.IntegerTokenAdapter
IntegerValueCondition - Class in org.apache.ctakes.core.fsm.condition
IntegerValueCondition(int) - Constructor for class org.apache.ctakes.core.fsm.condition.IntegerValueCondition
interact(JCas, IdentifiedAnnotation, JudgeAttributeInstances.Selector) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
interInstanceDistance - Variable in class org.apache.ctakes.temporal.utils.SMOTEplus
intermediateTypesToRemove - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
intersects(int, int, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Returns true if one span intersects with the other
INTJ - Class in org.apache.ctakes.typesystem.type.syntax: An interjection Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.INTJ Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
INTJ() - Constructor for class org.apache.ctakes.typesystem.type.syntax.INTJ: Never called.
INTJ(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.INTJ: Internal - constructor used by generator
INTJ(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.INTJ
INTJ(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.INTJ
INTJ_Type - Class in org.apache.ctakes.typesystem.type.syntax: An interjection Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.INTJ Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
INTJ_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.INTJ_Type: initialize variables to correspond with Cas Type and Features
INTRAARTERIAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
INTRAARTERIAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
INTRACARDIAC - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
INTRACARDIAC - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
INTRAMUSCULAR - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
INTRAMUSCULAR - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
INTRAPERITONEAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
INTRAPERITONEAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
INTRATHECAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
INTRATHECAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
INTRAVENOUS - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
INTRAVENOUS - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
INTRINSIC_INFOCONTENT - Static variable in interface org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluator
intrinsicIC - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
intrinsicIC - Variable in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum
intrinsicIC - Variable in class org.apache.ctakes.ytex.kernel.metric.LinMetric
intrinsicICMax - Variable in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
intrinsicInfoContent - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel
intrinsicInfoContentEvaluator - Variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
IntrinsicInfoContentEvaluator - Interface in org.apache.ctakes.ytex.kernel
IntrinsicInfoContentEvaluatorImpl - Class in org.apache.ctakes.ytex.kernel
IntrinsicInfoContentEvaluatorImpl() - Constructor for class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo - Class in org.apache.ctakes.ytex.kernel
IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo(ConcRel) - Constructor for class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
IntrinsicLCHMetric - Class in org.apache.ctakes.ytex.kernel.metric: compute intrinsic LCH as in eqn 28 from http://dx.doi.org/10.1016/j.jbi.2011.03.013 Scale to unit interval
IntrinsicLCHMetric(ConceptSimilarityService, Double) - Constructor for class org.apache.ctakes.ytex.kernel.metric.IntrinsicLCHMetric
intrinsicLcs - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
intrinsicLcsIC - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
intrinsicLcsTerm - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
IntrinsicPathMetric - Class in org.apache.ctakes.ytex.kernel.metric: compute Intrinsic path distance.
IntrinsicPathMetric(ConceptSimilarityService, Double) - Constructor for class org.apache.ctakes.ytex.kernel.metric.IntrinsicPathMetric
IntrinsicRadaMetric - Class in org.apache.ctakes.ytex.kernel.metric: compute Intrinsic rada distance as in eqn 23 from http://dx.doi.org/10.1016/j.jbi.2011.03.013.
IntrinsicRadaMetric(ConceptSimilarityService, Double) - Constructor for class org.apache.ctakes.ytex.kernel.metric.IntrinsicRadaMetric
invoke(MethodInvocation) - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
iPastSmokerCtr - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
irClass - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
irClassId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
IRMetrics - Class in org.apache.ctakes.ytex.kernel
IRMetrics() - Constructor for class org.apache.ctakes.ytex.kernel.IRMetrics
IRMetrics(int, int, int, int) - Constructor for class org.apache.ctakes.ytex.kernel.IRMetrics
isAcceptableBreak(String, int, int) - Method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Allows subclasses to check an overzealous (read: poorly trained) model from flagging obvious non-breaks as breaks based on some boolean determination of a break's acceptability.
isAdmission(EventMention) - Static method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
isAlias() - Method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
isAlphabetLetter(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
isAlphabetLetterOrDigit(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
isAnnotationPresentInSpan(JCas, int, int, int) - Static method in class org.apache.ctakes.core.util.FSUtil: returns a true if the annotation type is present in the span
isAutoCommit() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection
isBe(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
isBefore(IdentifiedAnnotation, IdentifiedAnnotation) - Static method in class org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor
isBoundary(Annotation, int) - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
isBoundary(Annotation, int) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
isBoundary(Annotation, int) - Method in interface org.apache.ctakes.necontexts.ContextAnalyzer: This method is called by the ContextAnnotator.
isBoundary(Annotation, int) - Method in class org.apache.ctakes.necontexts.ContextAnalyzerAdapter
isBoundary(Annotation, int) - Method in class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer
isBoundary(Annotation, int) - Method in class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer
isCacheNorm() - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
isCommonNode(ConllDependencyNode) - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
isConnected() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection
isConstrained(String, String) - Method in interface org.apache.ctakes.dictionary.lookup.strtable.FieldConstraint
isConstrained(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
isContained(String) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl: Helper method
isContraction(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
isContractionThatStartsWithApostrophe(int, String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
isContractionThatStartsWithApostrophe(int, String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
isCorpusIC() - Method in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum: is this measure based on corpus IC?
isDefinite(String) - Static method in class org.apache.ctakes.coreference.util.AttributeCalculator
isDemonstrative(String) - Static method in class org.apache.ctakes.coreference.util.AttributeCalculator
isDigit(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
isDischarge(EventMention) - Static method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
isDiscussionContext(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
isDiscussionContext(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
isDistantBetween(int, int) - Method in class org.apache.ctakes.sideeffect.util.PatternMatch: Return true if exist other than "and" "or" "," (ignoring DRUG and PSE) in input.substring(begin, end)
isDonorTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
isDonorTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
isDonorTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
isDrugBetween(int, int) - Method in class org.apache.ctakes.sideeffect.util.PatternMatch: Return true if finds "DRUG" in input.substring(begin, end)
isDrugBetween(int, int, int[]) - Method in class org.apache.ctakes.sideeffect.util.PatternMatch: Return true if finds "DRUG" in input.substring(begin, end) and assign offsets of DRUG to span
isDrugBetween(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return true if a drug is between begin and end
isDuplicate(LookupHit) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator: Checks to see whether this hit is a duplicate.
isDuplicate(LookupHit) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator: Checks to see whether this hit is a duplicate.
isDuplicate(Object[], int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
isEllipsis(int, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
isEmpty() - Method in class org.apache.ctakes.dictionary.lookup2.concept.Concept
isEmpty() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
isEmpty() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
isEmpty() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
isEmpty() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
isEmpty() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
isEmpty() - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
isEnclosed(RelationExtractorAnnotator.IdentifiedAnnotationPair, TreebankNode) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Is this pair of entities enclosed inside a noun phrase?
isEndOfLine(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
isEqual(String, String) - Method in class org.apache.ctakes.core.fsm.condition.TextValueCondition
isEqual(String, String) - Method in class org.apache.ctakes.core.fsm.condition.WordValueCondition
isFamilyTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
isFilteredByPreLookup(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Helper method that applies Pre-lookup filtering to the input text.
isGoldPair(Annotation, Annotation) - Method in class org.apache.ctakes.coreference.util.GoldStandardLabeler
isInAllergySection(JCas, SideEffectAnnotator.PotentialSideEffect) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: This rule is customized in the local document.
isIndexOk(int) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
IsIndicatedFor - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
IsIndicatedFor() - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor: Never called.
IsIndicatedFor(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor: Internal - constructor used by generator
IsIndicatedFor(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor
IsIndicatedFor_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
IsIndicatedFor_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor_Type: initialize variables to correspond with Cas Type and Features
IsIndicatedForTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
IsIndicatedForTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation: Never called.
IsIndicatedForTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation: Internal - constructor used by generator
IsIndicatedForTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation
IsIndicatedForTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
IsIndicatedForTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation_Type: initialize variables to correspond with Cas Type and Features
isInDictionary(JCas, SideEffectAnnotator.PotentialSideEffect) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Return true if pse belongs to side effects in the side-effect dictionary
isInHistSection(Sentence) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
isInParenthesis(JCas, SideEffectAnnotator.PotentialSideEffect, String) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: This rule is customized in the local document.
isInstanceOfOneOfClassesToCopy(Annotation) - Static method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
isInteger() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token
isInteger(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Given that the token text is a number, this method will determine if the number is an integer or not.
isIntrinsicIC() - Method in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum: is this measure based on intrinsic IC?
isIntrinsicIC() - Method in class org.apache.ctakes.ytex.kernel.metric.LinMetric
isInUpperCaseStringLine(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return true if the given NE belongs to the line consisting of a upper-cased string without " - "
isKeyNameToLowerCase() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
isLeaf() - Method in class org.apache.ctakes.utils.tree.SimpleTree
isLeaf() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
isLimitToRegex() - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
isMedicationPattern(JCas, EventMention) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor: Return true of this is a medication pattern.
iSmokerCtr - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
isMutable() - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
isMutable() - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
isNegated(JCas, EventMention) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor: Return true if sign/symptom is negated.
isNormalizedLaplacian() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
isNumber(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Applies number rules to the given token.
isNumericChar(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: ",.0123456789"
ISO8601Converter - Class in org.apache.ctakes.ytex.uima.mapper: convert ISO8601 formatted date to Date/Timestamp object
ISO8601Converter() - Constructor for class org.apache.ctakes.ytex.uima.mapper.ISO8601Converter
isOtherTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
isPleonastic(TerminalTreebankNode, HashSet<String>, HashSet<String>, HashSet<String>) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
isPossibleFinalPunctuation(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
ispref - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
isPrefix(String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
isPreload() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
isPronominal(Markable) - Static method in class org.apache.ctakes.coreference.util.AttributeCalculator
isPronoun(Markable) - Static method in class org.apache.ctakes.coreference.util.AttributeCalculator
isProperSubstring(ArrayList<String>, ArrayList<String>) - Static method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
isPseBetween(int, int) - Method in class org.apache.ctakes.sideeffect.util.PatternMatch: Return true if finds "PSE" in input.substring(begin, end)
isPseBetween(int, int, int[]) - Method in class org.apache.ctakes.sideeffect.util.PatternMatch: Return true if finds "PSE" in input.substring(begin, end) and assign offsets of PSE to span
isPSEBetween(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return true if a sign/symptom or disease/disorder is between begin and end
isPunctuation(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
isPunctuation(char) - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
isRarableToken(String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
isRelationArgument(String) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
isRomanNumeral(String) - Method in class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM.RomanNumeralCondition: Validates whether the given string is a roman numeral.
isRoot() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
isRXNORMCui(String) - Method in interface org.apache.ctakes.ytex.umls.dao.UMLSDao
isRXNORMCui(String) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
isSmokingStatusKnown(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: determines of value set by KUClassifier
isSoftLabel() - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
isSpanInSameLine(JCas, int, int) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil: Return true if the given offsets are in the same line
isSuffix(String, int) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
isTagExcluded(String) - Method in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
isTagExcluded(String) - Method in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
istance - Static variable in class org.apache.ctakes.jdl.common.Singleton
isTaxonomy() - Method in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum: is this measure taxonomy based?
isTelephoneNumberChar(char) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: "0123456789-"
isTermMatch(RareWordTerm, List<FastLookupToken>, int, int) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TokenMatchUtil: Hopefully the jit will inline this method
isTfIdf() - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
isTokenMatch(char[], int, char[]) - Static method in class org.apache.ctakes.dictionary.lookup2.util.TokenMatchUtil: Check the rare word term to see if a given token is at a given index within that term Hopefully the jit will inline this method
isTrain() - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
isTrain() - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
isTrained - Variable in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
isTrained - Variable in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
isUpperCaseString(String) - Static method in class org.apache.ctakes.sideeffect.util.SEUtil
isValid(Annotation) - Method in class org.apache.ctakes.core.ae.FilterAnnotator
isValid(String, String) - Method in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
isValid(String, String) - Method in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
isValidNE(int, int[]) - Static method in class org.apache.ctakes.core.util.FSUtil
isValidUMLSUser(String, String, String, String) - Static method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
isValidUMLSUser(String, String, String, String) - Static method in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
isValidUMLSUser(UimaContext, Properties) - Method in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover: validate the UMLS license / user
isValidUMLSUser(String, String, String, String) - Method in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover: validate the UMLS license / user
isWindowOk(Annotation) - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: Skip windows that are section headers/footers.
isWindowOk(Annotation) - Method in interface org.apache.ctakes.dictionary.lookup2.ae.WindowProcessor: Some windows should be skipped entirely, such as "[section *]"
items - Variable in class org.apache.ctakes.temporal.eval.CommandLine.IntegerRanges
iter - Variable in class org.apache.ctakes.core.util.ListIterable
iterator() - Method in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.Option
iterator() - Method in class org.apache.ctakes.core.util.ListIterable
iterator() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
iterator() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
iterator() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
iterator() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
iterator() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
iterator() - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
iUnknownCtr - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_aAnnotType - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator
iv_action - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator
iv_allowedClassifications - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_annot - Variable in class org.apache.ctakes.core.fsm.adapters.BaseTokenAdapter
iv_annot - Variable in class org.apache.ctakes.core.fsm.adapters.TextTokenAdapter
iv_annotTypeArr - Variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_annotTypeArr - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_annotVer - Variable in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator
iv_annotVer - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
iv_annotVerPropKey - Variable in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator
iv_annotVerPropKey - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
iv_appendWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM
iv_attrMap - Variable in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
iv_attrMap - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
iv_bAnnotType - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator
iv_begin - Variable in class org.apache.ctakes.smokingstatus.util.ClassifiableEntry
iv_beginSrc - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
iv_bw - Variable in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
iv_bw - Variable in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
iv_bw - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: The buffered writer used to write the document classification
iv_caps - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_changeStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_changeWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_char - Variable in class org.apache.ctakes.core.fsm.adapters.CharacterTokenAdapter
iv_char - Variable in class org.apache.ctakes.core.fsm.token.adapter.CharacterTokenAdapter
iv_classifiableIdx - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_classification - Variable in class org.apache.ctakes.smokingstatus.util.ClassifiableEntry
iv_classification - Variable in class org.apache.ctakes.smokingstatus.util.TruthValue
iv_cntPrepStmt - Variable in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
iv_combinedSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM
iv_condition1 - Variable in class org.apache.ctakes.core.fsm.condition.CombineCondition
iv_condition1 - Variable in class org.apache.ctakes.core.fsm.condition.DisjoinCondition
iv_condition2 - Variable in class org.apache.ctakes.core.fsm.condition.CombineCondition
iv_condition2 - Variable in class org.apache.ctakes.core.fsm.condition.DisjoinCondition
iv_confirmedSubBeginSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_confirmedSubNextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_conn - Variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl
iv_conn - Variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl
iv_context - Variable in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
iv_contiguousTextBuffer - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_copulaSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_count - Variable in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
iv_currentIndex - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_currentIndex - Variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
iv_DailyMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_DailySuffixMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_dailySuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_dailyWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_dateFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_dayNightSet - Variable in class org.apache.ctakes.core.fsm.machine.TimeFSM
iv_dbConn - Variable in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
iv_decimalFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_decreaseFromStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_decreaseStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_delimeter - Variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
iv_delimiter - Variable in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
iv_delimiter - Variable in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
iv_delimiter - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
iv_destContr - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
iv_destContr - Variable in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
iv_dictEngine - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl
iv_dictEngine - Variable in class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl
iv_docMetaData - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_docMetaDataMap - Variable in class org.apache.ctakes.preprocessor.DocumentMetaData
iv_dosagesFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_double - Variable in class org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter
iv_double - Variable in class org.apache.ctakes.core.fsm.token.adapter.IntegerTokenAdapter
iv_dupMap - Variable in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
iv_durationFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_eightTimesPerDayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_encoding - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_end - Variable in class org.apache.ctakes.smokingstatus.util.ClassifiableEntry
iv_endOffset - Variable in class org.apache.ctakes.core.fsm.output.BaseTokenImpl
iv_endOffset - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_endOffset - Variable in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
iv_endOffset - Variable in class org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl
iv_endSrc - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
iv_entryIndexMap - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_EveryOtherDayMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_everyOtherDayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_EveryOtherHourMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_everyOtherHourWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_examComponentTableDataCnt - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_examComponentText - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_excludeMatches - Variable in class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl
iv_excludeMatches - Variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl
iv_excludeMatches - Variable in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
iv_exclusionTagSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_exclusionTagSet - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_exclusionTagSet - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_extensions - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_familyHistoryMachine - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_familyHistoryMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_familyHistorySet - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_familyHistorySet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_fieldMap - Variable in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow
iv_fieldName - Variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
iv_fieldValue - Variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
iv_fieldValueClass - Variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
iv_file - Variable in class org.apache.ctakes.core.resource.FileResourceImpl
iv_fileForInput - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
iv_files - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_firstDecreaseDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_firstIncreaseDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_firstMaxDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_firstNoChangeDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_firstStartDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_firstStopDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_firstTokenDictEngine - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
iv_FiveTimesADayMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_fiveTimesPerDayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_formFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_foundProvider1 - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_FourTimesADayMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_fourTimesPerDayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_fractionFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_fractionFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_freqCutoff - Variable in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
iv_frequencyFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_frequencySet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM
iv_frequencySet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_frequencyUnitFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_fullTextSet - Variable in class org.apache.ctakes.core.fsm.machine.MeasurementFSM
iv_fullTextSet - Variable in class org.apache.ctakes.core.fsm.machine.PersonTitleFSM
iv_fullTextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FormFSM
iv_fullTextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM
iv_GastricMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_getSetMap - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
iv_getSetMap - Variable in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
iv_getterMethMap - Variable in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
iv_headerList - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_highNum - Variable in class org.apache.ctakes.core.fsm.condition.DecimalRangeCondition
iv_highNum - Variable in class org.apache.ctakes.core.fsm.condition.IntegerRangeCondition
iv_histCollocSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_histColPartSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_historyMachine - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_historyMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_historySet - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_historySet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_historySubBeginSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_historySubMidSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_historySubNextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_HourlyMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_HourlySuffixMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_hourlySuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_hyphenatedSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM
iv_hyphenatedSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_hyphenatedSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM
iv_hyphenatedSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_hyphenDrugSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.HyphenatedDrugFSM
iv_hyphMap - Variable in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
iv_includeSectionMarkers - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_increaseFromStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_increaseStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_indexReader - Variable in class org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl
iv_InjectMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_insideAdminData - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideCaption - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideExamComponent - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideHeader - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideKnownBy - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideLegalAuth - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insidePatient - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insidePatientEncounter - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideProvider - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideSection - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideServiceLoc - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideTable - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideTableData - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideTableHeader - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideTableRow - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_insideTranscriptionist - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_inSrc - Variable in class org.apache.ctakes.preprocessor.DTDloader
iv_isCaseSensitive - Variable in class org.apache.ctakes.core.fsm.condition.TextSetCondition
iv_isCaseSensitive - Variable in class org.apache.ctakes.core.fsm.condition.TextValueCondition
iv_isCaseSensitive - Variable in class org.apache.ctakes.core.fsm.condition.WordSetCondition
iv_isCaseSensitive - Variable in class org.apache.ctakes.core.fsm.condition.WordValueCondition
iv_isCaseSensitive - Variable in class org.apache.ctakes.drugner.fsm.elements.conditions.ContainsSetTextValueCondition
iv_isHospitalSummary - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_isInteger - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_isPositive - Variable in class org.apache.ctakes.core.fsm.adapters.NumberTokenAdapter
iv_isPositive - Variable in class org.apache.ctakes.core.fsm.token.adapter.NumberTokenAdapter
iv_iteration - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
iv_jcasAnnotObj - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
iv_language - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_language - Variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
iv_linesFromFile - Variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
iv_logger - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_logger - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator
iv_logger - Variable in class org.apache.ctakes.core.cc.CasConsumer
iv_logger - Variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
iv_logger - Variable in class org.apache.ctakes.core.resource.FileResourceImpl
iv_logger - Variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl
iv_logger - Variable in class org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl
iv_logger - Variable in class org.apache.ctakes.core.resource.StringIntegerMapResourceImpl
iv_logger - Variable in class org.apache.ctakes.core.resource.StringMapResourceImpl
iv_logger - Variable in class org.apache.ctakes.dependency.parser.DependencyNodeWriter
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.DebugConsumerImpl
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.DirectLookupInitializerImpl
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
iv_logger - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl
iv_logger - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_logger - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
iv_logger - Variable in class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer
iv_logger - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_logger - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_logger - Variable in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
iv_logger - Variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
iv_logger - Variable in class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer
iv_logger - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_logger - Variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl
iv_lookupFieldName - Variable in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
iv_lookupFieldName - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl
iv_lookupFieldName - Variable in class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl
iv_lookupSpecSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
iv_lowNum - Variable in class org.apache.ctakes.core.fsm.condition.DecimalRangeCondition
iv_lowNum - Variable in class org.apache.ctakes.core.fsm.condition.IntegerRangeCondition
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.FractionFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.MeasurementFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.PersonTitleFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.RangeFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_machineSet - Variable in class org.apache.ctakes.core.fsm.machine.TimeFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DecimalStrengthFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FormFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.HyphenatedDrugFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_machineSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM
iv_machineSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_map - Variable in class org.apache.ctakes.core.resource.StringIntegerMapResourceImpl
iv_map - Variable in class org.apache.ctakes.core.resource.StringMapResourceImpl
iv_maxHits - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
iv_maxHits - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl
iv_maxHour - Variable in class org.apache.ctakes.core.fsm.condition.HourMinuteCondition
iv_maxListSize - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
iv_maxMinute - Variable in class org.apache.ctakes.core.fsm.condition.HourMinuteCondition
iv_maxPermutationLevel - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
iv_maxSize - Static variable in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
iv_maxStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_mdh - Variable in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
iv_mdhComparator - Variable in class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl
iv_mdhCount - Variable in class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl
iv_mdPrepStmt - Variable in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
iv_measurementFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_medicalSections - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
iv_medicationRelatedSections - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_metaFieldName - Variable in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
iv_metaFieldName - Variable in class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator
iv_metaFieldNames - Variable in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl: Deprecated.
iv_metaFieldNames - Variable in class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl
iv_metaFieldOp - Variable in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
iv_metaFieldType - Variable in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
iv_metaMap - Variable in class org.apache.ctakes.necontexts.ContextHit
iv_middleNumericTermSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM
iv_middleTermSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM
iv_middleTermSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_middleTermSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_middleWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_minHour - Variable in class org.apache.ctakes.core.fsm.condition.HourMinuteCondition
iv_minMinute - Variable in class org.apache.ctakes.core.fsm.condition.HourMinuteCondition
iv_modalVerbsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_modalVerbsSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_modalVerbsSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_modalVerbsSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_monthFullNameSet - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
iv_MonthlySuffixMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_monthlySuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_monthShortNameSet - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
iv_multiThenWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_nameMap - Variable in class org.apache.ctakes.dictionary.lookup.strtable.StringTable
iv_negAdjectivesSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negAdjectivesSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negAdjectivesSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negAdjectivesSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_negCol1of3PartSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negCol2of3PartSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negColAnyOf3PartSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negCollocSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negCollocSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negCollocSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negCollocSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_negColPartSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negColPartSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negColPartSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negColPartSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_negDeterminersSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negDeterminersSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negDeterminersSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negDeterminersSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM
iv_negDeterminersSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_negDetPlusPrepSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negIndicatorFSM - Variable in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
iv_negInitialDetermineMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negInitialDetermineMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM
iv_negInitialDeterminersSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negInitialDeterminersSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM
iv_negParticlesSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negParticlesSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negParticlesSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negParticlesSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_negPrepositionsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negPrepositionsSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negPrepositionsSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negPrepositionsSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_negVerbsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_negVerbsSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_negVerbsSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_negVerbsSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_nestedAnnTypeArr - Variable in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
iv_newEndOffset - Variable in class org.apache.ctakes.core.ci.TextModification
iv_newStartOffset - Variable in class org.apache.ctakes.core.ci.TextModification
iv_newText - Variable in class org.apache.ctakes.core.ci.TextModification
iv_noChangeStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_noChangeWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_num - Variable in class org.apache.ctakes.core.fsm.condition.DecimalValueCondition
iv_num - Variable in class org.apache.ctakes.core.fsm.condition.IntegerValueCondition
iv_numberTextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM
iv_numPosition - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_offsetComp - Variable in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
iv_oneOfTwoTextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM
iv_op - Variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
iv_OralMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_origEndOffset - Variable in class org.apache.ctakes.core.ci.TextModification
iv_originalCondition - Variable in class org.apache.ctakes.core.fsm.condition.NegateCondition
iv_origStartOffset - Variable in class org.apache.ctakes.core.ci.TextModification
iv_outputDir - Variable in class org.apache.ctakes.core.cc.CasConsumer
iv_outputDir - Variable in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
iv_outputDir - Variable in class org.apache.ctakes.dependency.parser.DependencyNodeWriter
iv_outputDirectory - Variable in class org.apache.ctakes.core.cc.FilesInDirectoryCasConsumer
iv_outputDirectory - Variable in class org.apache.ctakes.core.cc.NormalizedFilesInDirectoryCasConsumer
iv_outputDirectory - Variable in class org.apache.ctakes.core.cc.TokenOffsetsCasConsumer
iv_outputDirectory - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
iv_outputFormat - Variable in class org.apache.ctakes.dependency.parser.DependencyNodeWriter
iv_PatchesMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_patient_level_file - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
iv_perDayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_periodSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM
iv_periodSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyFSM
iv_periodSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_periodSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_periodSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_permCacheMap - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
iv_personTitleFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_perWeekWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_phrBuilder - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl
iv_phrBuilder - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
iv_plfArr - Variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl
iv_postEightWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_postFourWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_postPatientLvlProcess - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
iv_postSixWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_previousElement - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_PrnMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_prnWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_probableCollocSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_probableColPartSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_probableMachine - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_probableMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_probableMachineNoTerm - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_probableSet - Variable in class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM
iv_probableSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM
iv_probableSubBeginSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_probableSubEndSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_probableSubNextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_procCount - Variable in class org.apache.ctakes.core.cc.CasConsumer
iv_procCount - Variable in class org.apache.ctakes.dependency.parser.DependencyNodeWriter
iv_procEntryList - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_props - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
iv_props - Variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_props - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl
iv_props - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl
iv_props - Variable in class org.apache.ctakes.smokingstatus.lookup.ae.UnknownSmokerNamedEntityLookupConsumerImpl
iv_props - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
iv_punctChar - Variable in class org.apache.ctakes.core.fsm.condition.PunctuationValueCondition
iv_quantity - Variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
iv_rangeFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_rangeFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_rangeSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM
iv_recordID - Variable in class org.apache.ctakes.smokingstatus.util.ClassifiableEntry
iv_RectalMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_recurse - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_regNounsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_regNounsSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_regNounsSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_regNounsSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_regPrepositionsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_regPrepositionsSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_regPrepositionsSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_regPrepositionsSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_regVerbsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
iv_regVerbsSet - Variable in class org.apache.ctakes.core.fsm.machine.NegationFSM
iv_regVerbsSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM
iv_regVerbsSet - Variable in class org.apache.ctakes.smokingstatus.machine.NegationFSM
iv_relation - Variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl
iv_romanNumeralFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_rootPath - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
iv_routeFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_sb - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: buffer used to compile results of a given doc
iv_scAnnotationList - Variable in class org.apache.ctakes.preprocessor.DocumentMetaData
iv_searcher - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
iv_searcher - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl
iv_secondDualFromWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_secondDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_secondMaxDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_secondOffDualWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_sectionIdentifier - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_sectionNestingLevel - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_sectionStartOffset - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_sectionText - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_segList - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_segmentType - Variable in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
iv_segMetaDataHash - Variable in class org.apache.ctakes.preprocessor.DocumentMetaData
iv_selector - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator.DeleteActionImpl
iv_selector - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
iv_sentenceList - Variable in class org.apache.ctakes.smokingstatus.util.TruthValue
iv_shortTextSet - Variable in class org.apache.ctakes.core.fsm.machine.MeasurementFSM
iv_shouldbeHyphenMap - Variable in class org.apache.ctakes.core.ci.HyphenTextModifierImpl
iv_singleChangeWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleDecreaseWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleIncreaseWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleInjectWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_singleMaxWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleNoChangeWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleOralWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_singleRectalWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_singleStartWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleStopWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleSumWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_singleTopicalWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_singleWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_singleWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_SixTimesADayMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_sixTimesPerDayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_skipSegmentsSet - Variable in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
iv_soloTextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM
iv_sortAscending - Variable in class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator
iv_specifiedGastricWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_specifiedInjectWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_specifiedOralWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_specifiedPatchesWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_specifiedWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DurationFSM
iv_specifiedWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_srcType - Variable in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
iv_startOffset - Variable in class org.apache.ctakes.core.fsm.output.BaseTokenImpl
iv_startOffset - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_startOffset - Variable in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
iv_startOffset - Variable in class org.apache.ctakes.drugner.fsm.output.elements.BaseTokenImpl
iv_startStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_status - Variable in class org.apache.ctakes.core.fsm.output.StatusIndicator
iv_status - Variable in class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
iv_statusFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_stopStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_strengthCombinedMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM
iv_strengthFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_strengthMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM
iv_strengthMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM
iv_strengthUnitFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_strTable - Variable in class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl
iv_subMedSectionFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_subSectionIDConfirmMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_subSectionIDHistoryMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_subSectionIDProbableMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM
iv_suffixFSM - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iv_sumStatusMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DrugChangeStatusFSM
iv_symbolChar - Variable in class org.apache.ctakes.core.fsm.condition.SymbolValueCondition
iv_tableHeaderKeyID - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_tableName - Variable in class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
iv_tableSpanType - Variable in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
iv_tdCounter - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_tdStartOffset - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_tdStyleArr - Variable in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
iv_text - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_text - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_text - Variable in class org.apache.ctakes.preprocessor.DocumentMetaData
iv_text - Variable in class org.apache.ctakes.smokingstatus.util.ClassifiableEntry
iv_textDenominatorSet - Variable in class org.apache.ctakes.core.fsm.machine.FractionFSM
iv_textDenominatorSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM
iv_textExtractorList - Variable in class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl
iv_textMetaFieldNames - Variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl
iv_textNumberSet - Variable in class org.apache.ctakes.core.fsm.machine.MeasurementFSM
iv_textNumberSet - Variable in class org.apache.ctakes.core.fsm.machine.RangeFSM
iv_textNumberSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.DosagesFSM
iv_textNumberSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM
iv_textNumeratorSet - Variable in class org.apache.ctakes.core.fsm.machine.FractionFSM
iv_textNumeratorSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FractionStrengthFSM
iv_textPrefixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_textPrefixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_textSet - Variable in class org.apache.ctakes.core.fsm.condition.TextSetCondition
iv_TextSet - Variable in class org.apache.ctakes.drugner.fsm.elements.conditions.ContainsSetTextValueCondition
iv_textSuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_textSuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM
iv_textSuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM
iv_ThreeTimesADayMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_threeTimesADayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_timeFSM - Variable in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
iv_tok - Variable in class org.apache.ctakes.core.fsm.token.adapter.BaseTokenAdapter
iv_tok - Variable in class org.apache.ctakes.core.fsm.token.adapter.WordTokenAdapter
iv_tok - Variable in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
iv_tokenizer - Variable in class org.apache.ctakes.core.ci.HyphenTextModifierImpl
iv_TopicalMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM
iv_truthMap - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
iv_TwiceADayMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_twiceADayWordSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_twoOfTwoTextSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM
iv_type - Variable in class org.apache.ctakes.core.nlp.tokenizer.Token
iv_type - Variable in class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator
iv_type - Variable in class org.apache.ctakes.preprocessor.Annotation
iv_typesOfOverlapToProcess - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator
iv_useCDAProcess - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
iv_useCurrentMedsSectionOnly - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
iv_val - Variable in class org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter
iv_val - Variable in class org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter
iv_val - Variable in class org.apache.ctakes.core.fsm.token.adapter.DecimalTokenAdapter
iv_val - Variable in class org.apache.ctakes.core.fsm.token.adapter.IntegerTokenAdapter
iv_value - Variable in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
iv_varAttrName - Variable in class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl.AttributeTextImpl
iv_WeeklyMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_WeeklySuffixMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_weeklySuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_windowSize - Variable in class org.apache.ctakes.core.ci.HyphenTextModifierImpl
iv_word - Variable in class org.apache.ctakes.core.fsm.condition.TextValueCondition
iv_word - Variable in class org.apache.ctakes.core.fsm.condition.WordValueCondition
iv_wordSet - Variable in class org.apache.ctakes.core.fsm.condition.WordSetCondition
iv_wta - Variable in class org.apache.ctakes.core.fsm.adapters.WordTokenAdapter
iv_xmlParser - Variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
iv_YearlySuffixMachine - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iv_yearlySuffixSet - Variable in class org.apache.ctakes.drugner.fsm.machines.elements.FrequencyUnitFSM
iWindowSize - Variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
iwriter - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

J

JaccardMetric - Class in org.apache.ctakes.ytex.kernel.metric: Jaccard metric as in eqn 13 from http://dx.doi.org/10.1016/j.jbi.2011.03.013
JaccardMetric(ConceptSimilarityService) - Constructor for class org.apache.ctakes.ytex.kernel.metric.JaccardMetric
javaViewerRB - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
javaViewerRB - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
javaViewerUCRB - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
javaViewerUCRB - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
jcas - Variable in class org.apache.ctakes.assertion.medfacts.CasIndexer
jcas - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
jcas - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
jcas - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
jcas - Variable in class org.apache.ctakes.coreference.util.AttributeCalculator
jcas_local - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
JCasTermAnnotator - Interface in org.apache.ctakes.dictionary.lookup2.ae: An annotator that looks up dictionary terms in text using RareWordDictionary s and adds them as entities to the Cas using a TermConsumer Author: SPF Affiliation: CHIP-NLP Date: 2/24/14
JCasUtil - Class in org.apache.ctakes.core.util
JCasUtil() - Constructor for class org.apache.ctakes.core.util.JCasUtil
JDBC_DRIVER - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
JDBC_DRIVER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
JDBC_PASS - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
JDBC_PASS - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
JDBC_URL - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
JDBC_URL - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
JDBC_USER - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
JDBC_USER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
JdbcCollectionReader - Class in org.apache.ctakes.core.cr: Collection Reader that pulls documents to be processed from a database.
JdbcCollectionReader() - Constructor for class org.apache.ctakes.core.cr.JdbcCollectionReader
JdbcConceptFactory - Class in org.apache.ctakes.dictionary.lookup2.concept: Author: SPF Affiliation: CHIP-NLP Date: 11/20/13
JdbcConceptFactory(String, UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
JdbcConceptFactory(String, String, String, String, String, String, String, String, String, String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
JdbcConnectionFactory - Enum in org.apache.ctakes.dictionary.lookup2.util: Some JDBC Connections can be reused, for instance by a Dictionary and Concept Factory.
JdbcConnectionFactory() - Constructor for enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
JdbcConnectionFactory.DotPlotter - Class in org.apache.ctakes.dictionary.lookup2.util
JdbcConnectionFactory.DotPlotter() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.DotPlotter
JdbcConnectionResource - Interface in org.apache.ctakes.core.resource: Resource for obtaining a JDBC database connection.
JdbcConnectionResourceImpl - Class in org.apache.ctakes.core.resource: Implementation of JdbcConnectionResource.
JdbcConnectionResourceImpl() - Constructor for class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl
JdbcDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup.jdbc
JdbcDictionaryImpl(Connection, String, String) - Constructor for class org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl
jdbcProperties - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: properties loaded from ytex.properties file
JdbcRareWordDictionary - Class in org.apache.ctakes.dictionary.lookup2.dictionary: Preferred dictionary to use for large collections of terms.
JdbcRareWordDictionary(String, UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
JdbcRareWordDictionary(String, String, String, String, String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
JdbcRareWordDictionary.FIELD_INDEX - Enum in org.apache.ctakes.dictionary.lookup2.dictionary: Column (field) indices in the database.
JdbcRareWordDictionary.FIELD_INDEX(int) - Constructor for enum org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.FIELD_INDEX
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
jdbcTemplate - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
jdbcTemplate - Variable in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
JdbcWriterTemplate - Class in org.apache.ctakes.core.cc: Template Cas Consumer to write a table to a sql database using jdbc
JdbcWriterTemplate() - Constructor for class org.apache.ctakes.core.cc.JdbcWriterTemplate
JdbcWriterTemplate.I2b2Concept - Class in org.apache.ctakes.core.cc: A more useful representation of umls concept for our purposes - we don't want repeat cuis for multiple tuis
JdbcWriterTemplate.I2b2Concept(String) - Constructor for class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
JdbcWriterTemplate.I2b2Concept(String, String) - Constructor for class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
JdbcWriterTemplate.I2b2FieldInfo - Enum in org.apache.ctakes.core.cc
JdbcWriterTemplate.I2b2FieldInfo(int, String, Class<?>) - Constructor for enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
JdlConnection - Class in org.apache.ctakes.jdl.data.base: Connection with db.
JdlConnection(JdbcType) - Constructor for class org.apache.ctakes.jdl.data.base.JdlConnection
jointDistroTable - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: A y*x table where the cells hold the instance ids.
JudgeAttributeInstances - Class in org.apache.ctakes.assertion.cc: A simple CAS consumer that generates XCAS (XML representation of the CAS) files in the filesystem.
JudgeAttributeInstances() - Constructor for class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
JudgeAttributeInstances.Selector - Enum in org.apache.ctakes.assertion.cc
JudgeAttributeInstances.Selector() - Constructor for enum org.apache.ctakes.assertion.cc.JudgeAttributeInstances.Selector
judgeAttributes(JCas) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
JustJudgeStep - Class in org.apache.ctakes.assertion.train
JustJudgeStep() - Constructor for class org.apache.ctakes.assertion.train.JustJudgeStep
jxpath - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo

K

KAlphaType - Enum in org.apache.ctakes.coreference.eval.helpers
KAlphaType() - Constructor for enum org.apache.ctakes.coreference.eval.helpers.KAlphaType
keepTrackOfDupBegin - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
keepTrackOfDupEnd - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
kernel - Variable in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
Kernel - Class in org.apache.ctakes.utils.kernel
Kernel() - Constructor for class org.apache.ctakes.utils.kernel.Kernel
Kernel - Interface in org.apache.ctakes.ytex.kernel.evaluator
kernel - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
kernelApplicationContext - Static variable in class org.apache.ctakes.ytex.kernel.KernelContextHolder
kernelApplicationContext - Static variable in class org.apache.ctakes.ytex.kernel.SimSvcContextHolder
KernelContextHolder - Class in org.apache.ctakes.ytex.kernel
KernelContextHolder() - Constructor for class org.apache.ctakes.ytex.kernel.KernelContextHolder
KernelEvaluation - Class in org.apache.ctakes.ytex.kernel.model
KernelEvaluation() - Constructor for class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
KernelEvaluationDao - Interface in org.apache.ctakes.ytex.kernel.dao
kernelEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
kernelEvaluationDao - Variable in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
kernelEvaluationDao - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
kernelEvaluationDao - Variable in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
kernelEvaluationDao - Variable in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
KernelEvaluationDaoImpl - Class in org.apache.ctakes.ytex.kernel.dao
KernelEvaluationDaoImpl() - Constructor for class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
kernelEvaluationId - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
kernelEvaluationId - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
KernelEvaluationInstance - Class in org.apache.ctakes.ytex.kernel.model: Although there is a many-to-one relationship the KernelEvaluation, we don't model that here - we just use the id so we can batch insert the kernelEvaluations.
KernelEvaluationInstance() - Constructor for class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
KernelEvaluationInstance(int, long, long, double) - Constructor for class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
KernelLauncher - Class in org.apache.ctakes.ytex
KernelLauncher() - Constructor for class org.apache.ctakes.ytex.KernelLauncher
KernelMatrixCompositor - Class in org.apache.ctakes.coreference.treekernel.training
KernelMatrixCompositor() - Constructor for class org.apache.ctakes.coreference.treekernel.training.KernelMatrixCompositor
kernelParams - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
kernelParams - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
kernelUtil - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter
kernelUtil - Variable in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
kernelUtil - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
KernelUtil - Interface in org.apache.ctakes.ytex.kernel
kernelUtil - Variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
kernelUtil - Variable in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory
kernelUtil - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory
kernelUtil - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
kernelUtil - Variable in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
kernelUtil - Variable in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory
kernelUtil - Variable in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
kernelUtil - Variable in class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory
kernelUtil - Variable in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory
kernelUtil - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
kernelUtil - Variable in class org.apache.ctakes.ytex.weka.WekaFormatterFactory
KernelUtilImpl - Class in org.apache.ctakes.ytex.kernel
KernelUtilImpl() - Constructor for class org.apache.ctakes.ytex.kernel.KernelUtilImpl
keyDrugMap - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
keyNameToLowerCase - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
keySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
keySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
keySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
keySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
keySet() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
keySet() - Method in class org.apache.ctakes.utils.struct.CounterTreeMap
keyTypeName - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader: the key type.
KeyValuePair - Class in org.apache.ctakes.ytex.uima.types: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
KeyValuePair() - Constructor for class org.apache.ctakes.ytex.uima.types.KeyValuePair: Never called.
KeyValuePair(int, TOP_Type) - Constructor for class org.apache.ctakes.ytex.uima.types.KeyValuePair: Internal - constructor used by generator
KeyValuePair(JCas) - Constructor for class org.apache.ctakes.ytex.uima.types.KeyValuePair
KeyValuePair_Type - Class in org.apache.ctakes.ytex.uima.types: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
KeyValuePair_Type(JCas, Type) - Constructor for class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type: initialize variables to correspond with Cas Type and Features
keywords - Variable in class org.apache.ctakes.sideeffect.util.PatternMatch
keywords - Variable in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData
KnowtatorAnnotation - Class in org.apache.ctakes.core.knowtator: Represents a Knowtator annotation.
KnowtatorAnnotation() - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: Construct a new KnowtatorAnnotation.
KnowtatorAnnotation.Span - Class in org.apache.ctakes.core.knowtator: Represents the character offsets of a Knowtator annotation.
KnowtatorAnnotation.Span(int, int) - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorAnnotation.Span: Construct a new Span.
knowtatorXMLDirectory - Variable in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
KnowtatorXMLParser - Class in org.apache.ctakes.core.knowtator
KnowtatorXMLParser(String...) - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
KnowtatorXMLParser(Set<String>) - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
KnowtatorXMLParser.IdAndSlot<T> - Class in org.apache.ctakes.core.knowtator
KnowtatorXMLParser.IdAndSlot(String, KnowtatorXMLParser.Slot<T>) - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.IdAndSlot
KnowtatorXMLParser.Option<T> - Class in org.apache.ctakes.core.knowtator
KnowtatorXMLParser.Option(T) - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.Option
KnowtatorXMLParser.Slot<T> - Class in org.apache.ctakes.core.knowtator
KnowtatorXMLParser.Slot(String, T) - Constructor for class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.Slot
KuRuleBasedClassifierAnnotator - Class in org.apache.ctakes.smokingstatus.ae
KuRuleBasedClassifierAnnotator() - Constructor for class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator

L

L_POS_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
L_POS_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
L_POS_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
L_REL_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
L_REL_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
L_REL_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
L_TOK_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
L_TOK_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
L_TOK_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
Lab - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Laboratory Procedures.
Lab() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Lab: Never called.
Lab(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Lab: Internal - constructor used by generator
Lab(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Lab
Lab_Type - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Laboratory Procedures.
Lab_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Lab_Type: initialize variables to correspond with Cas Type and Features
LabDeltaFlag - Class in org.apache.ctakes.typesystem.type.refsem: An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
LabDeltaFlag() - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag: Never called.
LabDeltaFlag(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag: Internal - constructor used by generator
LabDeltaFlag(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag
LabDeltaFlag_Type - Class in org.apache.ctakes.typesystem.type.refsem: An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
LabDeltaFlag_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type: initialize variables to correspond with Cas Type and Features
LabDeltaFlagModifier - Class in org.apache.ctakes.typesystem.type.textsem: An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
LabDeltaFlagModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier: Never called.
LabDeltaFlagModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier: Internal - constructor used by generator
LabDeltaFlagModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier
LabDeltaFlagModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier
LabDeltaFlagModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
LabDeltaFlagModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type: initialize variables to correspond with Cas Type and Features
label - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
label - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
label - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
label - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
label - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
label - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
labeler - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
labelQuery - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
labelsPattern - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser
labelToClassIndexMap - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: map of label - [class name - class index]
labelToClassMap - Variable in class org.apache.ctakes.ytex.kernel.InstanceData: labels - class
labelToInstanceMap - Variable in class org.apache.ctakes.ytex.kernel.InstanceData: map of labels - runs - folds - train/test - instances - class for test instances
LabEstimatedModifier - Class in org.apache.ctakes.typesystem.type.textsem: Signals that the lab value was estimated, e.g., "GFR (estimated): 81".
LabEstimatedModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier: Never called.
LabEstimatedModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier: Internal - constructor used by generator
LabEstimatedModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier
LabEstimatedModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier
LabEstimatedModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Signals that the lab value was estimated, e.g., "GFR (estimated): 81".
LabEstimatedModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type: initialize variables to correspond with Cas Type and Features
LabInterpretationModifier - Class in org.apache.ctakes.typesystem.type.textsem: Test result interpretations organized in a valued list e.g., "rare cells seen" or "few cells seen" in urinalysis, now combined with very_abnormal and abnormal.
LabInterpretationModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier: Never called.
LabInterpretationModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier: Internal - constructor used by generator
LabInterpretationModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier
LabInterpretationModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier
LabInterpretationModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Test result interpretations organized in a valued list e.g., "rare cells seen" or "few cells seen" in urinalysis, now combined with very_abnormal and abnormal.
LabInterpretationModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type: initialize variables to correspond with Cas Type and Features
LabMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (Lab) Event.
LabMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabMention: Never called.
LabMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabMention: Internal - constructor used by generator
LabMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabMention
LabMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabMention
LabMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (Lab) Event.
LabMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabMention_Type: initialize variables to correspond with Cas Type and Features
LabReferenceRange - Class in org.apache.ctakes.typesystem.type.refsem: Holds a narrative (i.e.
LabReferenceRange() - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange: Never called.
LabReferenceRange(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange: Internal - constructor used by generator
LabReferenceRange(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange
LabReferenceRange_Type - Class in org.apache.ctakes.typesystem.type.refsem: Holds a narrative (i.e.
LabReferenceRange_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type: initialize variables to correspond with Cas Type and Features
LabReferenceRangeModifier - Class in org.apache.ctakes.typesystem.type.textsem: Holds a narrative (i.e.
LabReferenceRangeModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier: Never called.
LabReferenceRangeModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier: Internal - constructor used by generator
LabReferenceRangeModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier
LabReferenceRangeModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier
LabReferenceRangeModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Holds a narrative (i.e.
LabReferenceRangeModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type: initialize variables to correspond with Cas Type and Features
LabValue - Class in org.apache.ctakes.typesystem.type.refsem: Quantitative results of a laboratory, with number and unit.
LabValue() - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabValue: Never called.
LabValue(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabValue: Internal - constructor used by generator
LabValue(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabValue
LabValue_Type - Class in org.apache.ctakes.typesystem.type.refsem: Quantitative results of a laboratory, with number and unit.
LabValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.LabValue_Type: initialize variables to correspond with Cas Type and Features
LabValueModifier - Class in org.apache.ctakes.typesystem.type.textsem: Quantitative results of a laboratory, with number and unit.
LabValueModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabValueModifier: Never called.
LabValueModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabValueModifier: Internal - constructor used by generator
LabValueModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabValueModifier
LabValueModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabValueModifier
LabValueModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Quantitative results of a laboratory, with number and unit.
LabValueModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type: initialize variables to correspond with Cas Type and Features
lambda - Static variable in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
lambda - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
lambda - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
lambdaSquared - Static variable in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
language - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
language - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
language - Variable in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
lastInPattern(JCas, int, int, int, int[][]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
lastLabel - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
lastQuery - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
lat - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
launchThatViewer(String, TypeSystem, String[], boolean, boolean, boolean, File, File) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: copied from AnnotationViewerDialog.
launchThatViewer(String, String, TypeSystem, String[], boolean, boolean, boolean, File, File) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
lca - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
LCHMetric - Class in org.apache.ctakes.ytex.kernel.metric
LCHMetric(ConceptSimilarityService, Integer) - Constructor for class org.apache.ctakes.ytex.kernel.metric.LCHMetric
lcs(String, String, List<LCSPath>) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService
lcs(String, String, List<LCSPath>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
lcs - Variable in class org.apache.ctakes.ytex.kernel.metric.LCSPath
lcsCache - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl: cache to hold lcs's
lcsDist - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
lcses - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
lcsImputedType - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
LCSPath - Class in org.apache.ctakes.ytex.kernel.metric
LCSPath() - Constructor for class org.apache.ctakes.ytex.kernel.metric.LCSPath
lcsPathMap - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
lcsPaths - Variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
leafCount - Variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
LEFT_SCOPE - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator
leftScopeSize - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
Lemma - Class in org.apache.ctakes.typesystem.type.syntax: Stores a lemma (canonical form of a token).
Lemma() - Constructor for class org.apache.ctakes.typesystem.type.syntax.Lemma: Never called.
Lemma(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Lemma: Internal - constructor used by generator
Lemma(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Lemma
Lemma_Type - Class in org.apache.ctakes.typesystem.type.syntax: Stores a lemma (canonical form of a token).
Lemma_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.Lemma_Type: initialize variables to correspond with Cas Type and Features
lemmaCacheFileLocation - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
lemmaCacheFileLocation - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
lemmaCacheFreqCutoff - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
lemmaCacheFreqCutoff - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
lemmaCacheMap - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
lemmaCacheMap - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
lemmatize(String, String) - Static method in class org.apache.ctakes.temporal.duration.Utils: Lemmatize word using ClearNLP lemmatizer.
lemmatizer - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
lemmatizerDataFile - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
length - Variable in class org.apache.ctakes.coreference.eval.helpers.Span
length() - Method in class org.apache.ctakes.coreference.eval.helpers.Span
length - Variable in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor.StringToDoublesProcessor
length - Variable in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor
lenIfHyphenatedSuffix(String, int) - Static method in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
lenIfIsAbbreviation(int, String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: Assumes no white space between currentPosition and endOfInputToConsider If last of a sentence is a period, then don't include the period with the abbreviation, count it as punctuation.
lenIfIsEmailAddress(int, String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: Assumes no white space between currentPosition and endOfInputToConsider
lenIfIsNumberContainingComma(int, String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: such as -4,012.67 or 5 or 5.5 or 4,000,153
lenIfIsPostalCode(int, String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
lenIfIsTelephoneNumber(int, String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
lenIfIsUrl(int, String, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
lenIncludingHyphensToKeep(String, int, int, int, int) - Static method in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
lenOfFirstTokenInContraction(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
lenOfFirstTokenInContraction(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
lenOfSecondTokenInContraction(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
lenOfThirdTokenInContraction(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
lettersAfterApostropheForMiddleOfContraction - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
lettersAfterApostropheForMiddleOfContraction - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
LF - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
LF - Static variable in class org.apache.ctakes.core.sentence.SentenceSpan
LF - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
LibSVMFormatterFactory - Class in org.apache.ctakes.ytex.libsvm
LibSVMFormatterFactory() - Constructor for class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory
LibSVMFormatterFactory.LibSVMFormatter - Class in org.apache.ctakes.ytex.libsvm
LibSVMFormatterFactory.LibSVMFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter
LibSVMGramMatrixExporter - Interface in org.apache.ctakes.ytex.libsvm
LibSVMGramMatrixExporterImpl - Class in org.apache.ctakes.ytex.libsvm: export gram matrix for libsvm.
LibSVMGramMatrixExporterImpl() - Constructor for class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
LibSVMParser - Class in org.apache.ctakes.ytex.libsvm
LibSVMParser() - Constructor for class org.apache.ctakes.ytex.libsvm.LibSVMParser
libsvmUtil - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
LibSVMUtil - Interface in org.apache.ctakes.ytex.libsvm
LibSVMUtilImpl - Class in org.apache.ctakes.ytex.libsvm
LibSVMUtilImpl() - Constructor for class org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl
limitToRegex - Variable in class org.apache.ctakes.ytex.uima.model.SegmentRegex
line - Variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
line - Variable in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
LinearKernel - Class in org.apache.ctakes.utils.kernel
LinearKernel() - Constructor for class org.apache.ctakes.utils.kernel.LinearKernel
LinearKernel(boolean) - Constructor for class org.apache.ctakes.utils.kernel.LinearKernel
LinearKernelMatrixWriter - Class in org.apache.ctakes.coreference.treekernel.training
LinearKernelMatrixWriter(String, String) - Constructor for class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
lineNum - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
lineNumber - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation: Each line consist of following fields line number Condition (from within sentence) sentence negation_status (Negated, Affirmed) also handles if possible)
linePatt - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.BrownClusterFeatureFunction
linePatt - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
lines - Variable in class org.apache.ctakes.core.resource.LinesFromFileStringsResourceImpl
LinesFromFileCollectionReader - Class in org.apache.ctakes.core.cr: The original code was copied from org.apache.uima.examples.cpe.FileSystemCollectionReader and modified for Mayo use.
LinesFromFileCollectionReader() - Constructor for class org.apache.ctakes.core.cr.LinesFromFileCollectionReader
LinesFromFileStringsResourceImpl - Class in org.apache.ctakes.core.resource: Reads in an array of Strings from a file - each line in the file is a string.
LinesFromFileStringsResourceImpl() - Constructor for class org.apache.ctakes.core.resource.LinesFromFileStringsResourceImpl
LinKernel - Class in org.apache.ctakes.ytex.kernel.evaluator
LinKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.LinKernel
LinMetric - Class in org.apache.ctakes.ytex.kernel.metric: compute corpus-ic or intrinsic-ic based lin measure.
LinMetric(ConceptSimilarityService, boolean) - Constructor for class org.apache.ctakes.ytex.kernel.metric.LinMetric
LIQUID - Static variable in class org.apache.ctakes.drugner.elements.FormElement
list - Static variable in class org.apache.ctakes.assertion.cr.NegExCorpusReader
list - Variable in class org.apache.ctakes.core.util.FSListIterator
List - Class in org.apache.ctakes.typesystem.type.textspan: A semi-structured text span, containing other Annotations (typically Sentences, other Lists, etc).
List() - Constructor for class org.apache.ctakes.typesystem.type.textspan.List: Never called.
List(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.List: Internal - constructor used by generator
List(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textspan.List
List(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textspan.List
List_Type - Class in org.apache.ctakes.typesystem.type.textspan: A semi-structured text span, containing other Annotations (typically Sentences, other Lists, etc).
List_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.List_Type: initialize variables to correspond with Cas Type and Features
listDocumentIds - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
ListFactory - Class in org.apache.ctakes.core.util: Factory to build List of built-in CAS types such as FloatList, IntegerList, StringList, and FSList.
ListFactory() - Constructor for class org.apache.ctakes.core.util.ListFactory
ListFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
ListFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.ListFeaturesExtractor
ListIterable<T> - Class in org.apache.ctakes.core.util
ListIterable(FSList) - Constructor for class org.apache.ctakes.core.util.ListIterable
listNegexRules - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
listToDoubleArray(ArrayList<Integer>) - Method in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
listToString(List<String>) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil: convert list of strings to comma-delimited string;
load(URI) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
load(URI) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
load(DataResource) - Method in class org.apache.ctakes.core.resource.FileResourceImpl
load(DataResource) - Method in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl
load(DataResource) - Method in class org.apache.ctakes.core.resource.LinesFromFileStringsResourceImpl
load(DataResource) - Method in class org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl: Loads a Lucene index for reading.
load(DataResource) - Method in class org.apache.ctakes.core.resource.StringIntegerMapResourceImpl: Loads data from a file.
load(DataResource) - Method in class org.apache.ctakes.core.resource.StringMapResourceImpl: Loads data from a file.
load(String) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile: Loads text from a file.
load(String) - Static method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel: Loads text from a file.
load(DataResource) - Method in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
load(String) - Static method in class org.apache.ctakes.preprocessor.test.TestDriver: Loads text from a file.
load(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
load(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
load(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
load(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
load(DataResource) - Method in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl
LOAD_WORDS_ONLY_PARAM - Static variable in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader: "LoadWordsOnly" is a optional, single, boolean parameter that determines whether or not the part-of-speech tags associated with each word will be loaded into the CAS or not.
loadClassIdMap(File, String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
loadClassInfo(File, String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
loadClassLabels(String, Set<String>) - Method in interface org.apache.ctakes.ytex.libsvm.LibSVMUtil
loadClassLabels(String, Set<String>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl
loadCmdCacheFile(String) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator: Helper method that loads a Norm cache file.
loadCmdCacheFile(String) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Helper method that loads a Norm cache file.
loadConceptFilter(String, int, Map<String, Double>) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: For the given label and cutoff, get the corresponding concepts whose propagated ig meets the threshold.
loadConceptFilter(String, int, Map<String, Double>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl: For the given label and cutoff, get the corresponding concepts whose propagated ig meets the threshold.
loadConceptInstanceMap(String, ConceptGraph, String) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: load the map of concept - instances
loadData(BagOfWordsData, String, String, BagOfWordsDecorator) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
loadData(InstanceData, String, String, String, String, BagOfWordsDecorator, String, Integer, Integer) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
loadDescription(String) - Static method in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors: Simple method to load xml description and return an AnalysisEngineDescription object
loadDocument() - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
loadDocument() - Method in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
loadDocumentCas(String, TypeSystem) - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: load document from db
loadDocumentIds(List<Long>, List<Long>, String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl: load the document ids from the instanceIDQuery
loadDocumentIds() - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
loader - Variable in class org.apache.ctakes.jdl.data.loader.CsvLoader
Loader - Class in org.apache.ctakes.jdl.data.loader: Abstract Loader.
Loader() - Constructor for class org.apache.ctakes.jdl.data.loader.Loader
loader - Variable in class org.apache.ctakes.jdl.data.loader.XmlLoader
loadFeatures(int[], String) - Static method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
loadGoldStandard() - Method in class org.apache.ctakes.coreference.util.GoldStandardLabeler
loadGramMatrix(SortedSet<Long>, String, String, String, String, int, int, double, String) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil
loadGramMatrix(SortedSet<Long>, String, String, String, String, int, int, double, String) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
loadGramMatrix(String, String, double, String, String, String, int, int, InstanceData, SortedSet<Long>, Map<Long, Integer>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
loadHyphMap(String) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile: Loads hyphenated words and a frequency value for each, from a file.
loadInputStream(String) - Method in class org.apache.ctakes.jdl.common.PropertiesFile: External.
loadInstanceClassInfo(File, String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
loadInstances(String) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil: read query
loadInstances(String) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl: this can be very large - avoid loading the entire jdbc ResultSet into memory
loadInstanceTrees(TreeMappingInfo) - Method in interface org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilder: Generate trees from the results of a sorted query
loadInstanceTrees(String) - Method in interface org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilder
loadInstanceTrees(String) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
loadInstanceTrees(TreeMappingInfo) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
loadInstanceTrees(String, QueryMappingInfo, Map<NodeKey, Node>) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
loadJDBCProperties() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
loadLemmaCacheFile(String) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator: Helper method that loads a Lemma cache file.
loadLemmaCacheFile(String) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Helper method that loads a Lemma cache file.
loadList(String) - Static method in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl: Load a comma delimited list
loadProperties(String, Properties) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
loadProperties(String, boolean) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil
loadProperties(String, Properties) - Method in interface org.apache.ctakes.ytex.kernel.KernelUtil
loadProperties(String, Properties) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
loadProps(File) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser: load properties from outputDir/options.properties.
loadRawText(int) - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
loadResourceAsStream(String) - Method in class org.apache.ctakes.jdl.common.PropertiesFile: Internal.
loadSystemPairs(List<Annotation>) - Method in class org.apache.ctakes.coreference.util.GoldStandardLabeler
loadTruthData(File, String) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Parses the TRUTH file in delimited format.
loadValueFile(File) - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader: Loads the prepared statement value file.
loadWordsOnly - Variable in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
loc - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
localTearFile - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
locateFile(String) - Static method in class org.apache.ctakes.core.resource.FileLocator: Where a Stream is usable, use FileLocator.getAsStream(String) .
locateOnClasspath(String) - Static method in class org.apache.ctakes.core.resource.FileLocator: Check the java classpath for the presence of a file pointed to by relativePath
LocationOf - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
LocationOf() - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOf: Never called.
LocationOf(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOf: Internal - constructor used by generator
LocationOf(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOf
LocationOf_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
LocationOf_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOf_Type: initialize variables to correspond with Cas Type and Features
LocationOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies Location_Of relations between EventMentions and AnatomicalSiteMentions.
LocationOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
LocationOfTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
LocationOfTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation: Never called.
LocationOfTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation: Internal - constructor used by generator
LocationOfTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
LocationOfTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
LocationOfTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation_Type: initialize variables to correspond with Cas Type and Features
log - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
log - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
log - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
LOG - Variable in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
log - Static variable in class org.apache.ctakes.jdl.AppJdl
log - Static variable in class org.apache.ctakes.jdl.data.loader.CsvLoader
log(String, Object...) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
log(<any>) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
log(<any>) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
log - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
log - Static variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
log - Static variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
log - Static variable in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
log - Static variable in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
log - Static variable in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
log - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
log - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.ProductKernel
log - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
log - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
log - Static variable in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.metric.LinMetric
log - Static variable in class org.apache.ctakes.ytex.kernel.model.ConcRel
log - Static variable in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
log - Static variable in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser
log - Static variable in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory.SVMLinDataFormatter
log - Static variable in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
log - Static variable in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
log - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
log - Static variable in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
log - Static variable in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
log - Static variable in class org.apache.ctakes.ytex.uima.ApplicationContextHolder
log - Static variable in class org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl
log - Static variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
log - Static variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
log - Static variable in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
log - Static variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
log - Static variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
log - Static variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
log - Static variable in class org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter
log - Static variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
log - Static variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
log2adjust - Static variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
logClassificationErrors(File, String) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
logClassificationErrors(File, String) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
logdm - Variable in class org.apache.ctakes.ytex.kernel.metric.LCHMetric: log(max depth * 2)
logger - Variable in class org.apache.ctakes.assertion.attributes.GenericAttributeAnalysisEngine
logger - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
logger - Variable in class org.apache.ctakes.assertion.attributes.SubjectAttributeAnalysisEngine
logger - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
LOGGER - Static variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
LOGGER - Static variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
LOGGER - Static variable in class org.apache.ctakes.assertion.cr.NegExCorpusReader
logger - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
LOGGER - Static variable in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
logger - Static variable in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
logger - Variable in class org.apache.ctakes.assertion.medfacts.CasIndexer
logger - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
logger - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest
logger - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest2
logger - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
logger - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
logger - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
logger - Static variable in class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
logger - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
logger - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
logger - Static variable in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
logger - Variable in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster
logger - Variable in class org.apache.ctakes.chunker.ae.Chunker
logger - Variable in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
logger - Variable in class org.apache.ctakes.constituency.parser.MaxentParserWrapper
logger - Variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
logger - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
logger - Variable in class org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine
logger - Variable in class org.apache.ctakes.core.ae.SectionSegmentAnnotator
logger - Variable in class org.apache.ctakes.core.ae.SentenceDetector
LOGGER - Static variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
logger - Variable in class org.apache.ctakes.core.ae.SimpleSegmentWithTagsAnnotator
logger - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
logger - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
LOGGER - Static variable in class org.apache.ctakes.core.cc.AbstractJdbcWriter
LOGGER - Static variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate
LOGGER - Static variable in class org.apache.ctakes.core.cc.SentenceTokensPrinter
logger - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
LOGGER - Static variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
LOGGER - Static variable in class org.apache.ctakes.core.resource.FileLocator
LOGGER - Static variable in class org.apache.ctakes.core.util.IdentifiedAnnotationUtil
LOGGER - Static variable in class org.apache.ctakes.core.util.SourceMetadataUtil
logger - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
logger - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
logger - Variable in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
logger - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
logger - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
logger - Static variable in class org.apache.ctakes.dependency.parser.util.AnnotationDepUtils
logger - Variable in class org.apache.ctakes.dependency.parser.util.ClearDependencyUtility
logger - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyUtility
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
LOGGER - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
LOGGER - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory
LOGGER - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
logger - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
logger - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
logger - Variable in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
logger - Variable in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
logger - Variable in class org.apache.ctakes.postagger.POSTagger
logger - Variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
logger - Variable in class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
logger - Static variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
logger - Variable in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor.StringToDoublesProcessor
logger - Variable in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor
LOGGER - Static variable in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
logger - Static variable in class org.apache.ctakes.temporal.ae.THYMETreebankReader
LOGGER - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
logger - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
logger - Static variable in class org.apache.ctakes.temporal.eval.RemoveTreeAlignedMentions
logger - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
loggers - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
loggers - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
logHeader(<any>) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
logMaxIC2 - Variable in class org.apache.ctakes.ytex.kernel.metric.IntrinsicLCHMetric
logs - Static variable in class org.apache.ctakes.utils.wiki.ApproximateMath
lookForAlpha - Static variable in class org.apache.ctakes.drugner.DrugMention: regex pattern to look for, in this case alpha upper and lower characters
lookForPercent - Static variable in class org.apache.ctakes.drugner.DrugMention: regex pattern to look for, in this case alpha upper and lower characters
lookup(List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.DirectPassThroughImpl: Lookup the given text specified via LookupToken objects.
lookup(List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Lookup the given text specified via LookupToken objects.
lookup(List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in interface org.apache.ctakes.dictionary.lookup.algorithms.LookupAlgorithm: Lookup the given text specified via LookupToken objects.
LOOKUP_PATH - Static variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
LOOKUP_PATH - Static variable in class org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor
LOOKUP_PATH - Static variable in class org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor
LOOKUP_TOKEN_ADAPTER - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
LookupAlgorithm - Interface in org.apache.ctakes.dictionary.lookup.algorithms: Generic interface to specific lookup algorithm implementations.
LookupAnnotation - Interface in org.apache.ctakes.dictionary.lookup.vo: Value object that models a text annotation.
LookupAnnotationToJCasAdapter - Class in org.apache.ctakes.dictionary.lookup.ae
LookupAnnotationToJCasAdapter(Annotation) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter
LookupAnnotationToTokAdapter - Class in org.apache.ctakes.dictionary.lookup.vo
LookupAnnotationToTokAdapter(Token) - Constructor for class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter
lookupByAddress(int) - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
lookupConceptType(FSArray) - Static method in class org.apache.ctakes.assertion.medfacts.ConceptLookup
LookupConsumer - Interface in org.apache.ctakes.dictionary.lookup.ae: Defines how to consume the lookup hits produced by the LookupAnnotator.
LookupHit - Class in org.apache.ctakes.dictionary.lookup.vo: Represents a single hit found by a lookup algorithm.
LookupHit(MetaDataHit, int, int) - Constructor for class org.apache.ctakes.dictionary.lookup.vo.LookupHit
LookupInitializer - Interface in org.apache.ctakes.dictionary.lookup.ae: Defines how to initialize the LookupAnnotator.
LookupParseUtilities - Class in org.apache.ctakes.dictionary.lookup.ae
LookupParseUtilities() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
LookupParseUtilitiesRefactor - Class in org.apache.ctakes.dictionary.lookup.ae
LookupParseUtilitiesRefactor() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
LookupSpec - Class in org.apache.ctakes.dictionary.lookup.ae: A container for three related classes used to lookup terms in a dictionary and process hits found.
LookupSpec(LookupAlgorithm, LookupInitializer, LookupConsumer) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
LookupToken - Interface in org.apache.ctakes.dictionary.lookup.vo: This object represents the SMALLEST span of text that could potentially be a lookup hit.
lookupTokenAdapterCtor - Variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
LookupTokenComparator - Enum in org.apache.ctakes.dictionary.lookup.vo: Comparator that sorts LookupToken objects by their start and end offsets.
LookupTokenComparator() - Constructor for enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator
LookupUtil - Class in org.apache.ctakes.dictionary.lookup2.util: Author: SPF Affiliation: CHIP-NLP Date: 12/16/13
LookupUtil() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.LookupUtil
LookupWindowAnnotation - Class in org.apache.ctakes.typesystem.type.textspan: Defines a window within which dictionary terms may match.
LookupWindowAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation: Never called.
LookupWindowAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation: Internal - constructor used by generator
LookupWindowAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
LookupWindowAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
LookupWindowAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textspan: Defines a window within which dictionary terms may match.
LookupWindowAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type: initialize variables to correspond with Cas Type and Features
LOTION - Static variable in class org.apache.ctakes.drugner.elements.FormElement
lowercaseWords(SimpleTree) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
LOZENGE - Static variable in class org.apache.ctakes.drugner.elements.FormElement
LST - Class in org.apache.ctakes.typesystem.type.syntax: A list item, usually intra-sentential Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.LST Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
LST() - Constructor for class org.apache.ctakes.typesystem.type.syntax.LST: Never called.
LST(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.LST: Internal - constructor used by generator
LST(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.LST
LST(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.LST
LST_Type - Class in org.apache.ctakes.typesystem.type.syntax: A list item, usually intra-sentential Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.LST Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
LST_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.LST_Type: initialize variables to correspond with Cas Type and Features
LT_KEY_USE_FOR_LOOKUP - Static variable in class org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl: Key value for LookupToken attribute.
LT_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
LT_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
LTEQ_OP - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
LTEQ_OP - Static variable in class org.apache.ctakes.dictionary.lookup.strtable.FieldConstraintImpl
LUCENE_FILTER_RESRC_KEY_PRP_KEY - Variable in class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl
LUCENE_FILTER_RESRC_KEY_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
LuceneDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup.lucene
LuceneDictionaryImpl(IndexSearcher, String) - Constructor for class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl: Constructor
LuceneDictionaryImpl(IndexSearcher, String, int) - Constructor for class org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl: Constructor
LuceneDocumentMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup.lucene
LuceneDocumentMetaDataHitImpl(Document) - Constructor for class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
LuceneIndexReaderResource - Interface in org.apache.ctakes.core.resource
LuceneIndexReaderResourceImpl - Class in org.apache.ctakes.core.resource: Oct 2010 - convert to lucene 3.0.2
LuceneIndexReaderResourceImpl() - Constructor for class org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl
lui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
lvg - Variable in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
LVG_BASE_TOKEN_ANNOTATOR_PATH - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
LvgAnnotator - Class in org.apache.ctakes.lvg.ae: UIMA annotator that uses the UMLS LVG package to find the canonical form of WordTokens.
LvgAnnotator() - Constructor for class org.apache.ctakes.lvg.ae.LvgAnnotator
LvgAnnotator.LemmaLocalClass - Class in org.apache.ctakes.lvg.ae: Basic class to group a lemma word with its various parts of speech.
LvgAnnotator.LemmaLocalClass() - Constructor for class org.apache.ctakes.lvg.ae.LvgAnnotator.LemmaLocalClass
LvgBaseTokenAnnotator - Class in org.apache.ctakes.lvg.ae: UIMA annotator that uses the UMLS LVG package to find the canonical form of BaseTokens.
LvgBaseTokenAnnotator() - Constructor for class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
LvgBaseTokenAnnotator.LemmaLocalClass - Class in org.apache.ctakes.lvg.ae: Basic class to group a lemma word with its various parts of speech.
LvgBaseTokenAnnotator.LemmaLocalClass() - Constructor for class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator.LemmaLocalClass
lvgCmd - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
lvgCmd - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
lvgCmd - Variable in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
LVGCMDAPI_RESRC_KEY - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
LvgCmdApiResource - Interface in org.apache.ctakes.lvg.resource
LvgCmdApiResourceImpl - Class in org.apache.ctakes.lvg.resource: Loads NLM Lvg and Norm, reading configuration information from a config (properties) file Since the value of the LVG_DIR property in the lvg properties file must be either a hard coded absolute pathname or the value AUTO_MODE, and we want to support installing this project in a directory of the user's choice, we avoid using a hardcoded pathname and choose to use LVG_DIR=AUTO_MODE in the properties file.
LvgCmdApiResourceImpl() - Constructor for class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
lvgLexItem - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
lvgLexItem - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
lvgLexItem - Variable in class org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl
lvgResource - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator

M

m - Variable in class org.apache.ctakes.coreference.ae.MarkableProb
m - Variable in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
m1 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
m2 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
madeVerb - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
main(String[]) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
main(String[]) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
main(String[]) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
main(String[]) - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader: This main method is only for testing purposes.
main(String[]) - Static method in class org.apache.ctakes.assertion.cr.NegExAnnotation: test a single line
main(String[]) - Static method in class org.apache.ctakes.assertion.cr.NegExCorpusReader: This main method is only for testing purposes.
main(String[]) - Static method in class org.apache.ctakes.assertion.cr.RelationInfo
main(String[]) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
main(String[]) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionSampleFeatureGenerator
main(String[]) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
main(String[]) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest
main(String[]) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.CueWordTest2
main(String[]) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
main(String[]) - Static method in class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
main(String[]) - Static method in class org.apache.ctakes.assertion.medfacts.ConvertXMIAssertionsToi2b2Format
main(String[]) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
main(String[]) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
main(String[]) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipeline
main(String[]) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
main(String[]) - Static method in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances
main(String[]) - Static method in class org.apache.ctakes.assertion.train.CrossValidateAttributeModels
main(String[]) - Static method in class org.apache.ctakes.assertion.train.CrossValidateChi2GridSearch
main(String[]) - Static method in class org.apache.ctakes.assertion.train.JustJudgeStep
main(String[]) - Static method in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
main(String[]) - Static method in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
main(String[]) - Static method in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
main(String[]) - Static method in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
main(String[]) - Static method in class org.apache.ctakes.assertion.train.ReadAndPreprocessForAttributeModels
main(String[]) - Static method in class org.apache.ctakes.assertion.train.ReadPreprocessTrainTestJudge
main(String[]) - Static method in class org.apache.ctakes.assertion.train.TestAttributeModels
main(String[]) - Static method in class org.apache.ctakes.assertion.train.TrainAttributeModels
main(String...) - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
main(String[]) - Static method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls
main(String[]) - Static method in class org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator
main(String[]) - Static method in class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
main(String[]) - Static method in class org.apache.ctakes.constituency.parser.util.CommandLineParserUtil
main(String[]) - Static method in class org.apache.ctakes.core.ae.SentenceDetector: Train a new sentence detector from the training data in the first file and write the model to the second file.
The training data file is expected to have one sentence per line.
main(String[]) - Static method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader: This main method is only for testing purposes.
main(String[]) - Static method in class org.apache.ctakes.core.cc.CASConsumerTestDriver
main(String[]) - Static method in class org.apache.ctakes.core.ci.HyphenTextModifierImpl: Simple tests of TextModification
Output expected:
UNSUPPORTED: TextModification with offset changes.
UNSUPPORTED: TextModification with offset changes.
UNSUPPORTED: TextModification with offset changes.
Orig: Non Hodgkin's the x ray without any non small cell complications.
New: (new text not generated, see previous messages) Non-Hodgkin Orig: 0-12 New: 0-11
x-ray Orig: 19-25 New: 18-23
non-small-cell Orig: 38-53 New: 36-50
Orig: Non Hodgkin's the x ray without any non small cell complications.
New: Non-Hodgkin's the x-ray without any non-small-cell complications.
Non-Hodgkin Orig: 0-11 New: 0-11
x-ray Orig: 18-23 New: 18-23
non-small-cell Orig: 36-50 New: 36-50
Note the case of the words doesn't matter.
main(String[]) - Static method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner
main(String[]) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
main(String[]) - Static method in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
main(String[]) - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
main(String[]) - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
main(String[]) - Static method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Trains a new sentence detection model.
main(String[]) - Static method in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
main(String[]) - Static method in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi
main(String[]) - Static method in class org.apache.ctakes.coreference.eval.helpers.Test
main(String[]) - Static method in class org.apache.ctakes.coreference.treekernel.training.KernelMatrixCompositor
main(String[]) - Static method in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
main(String[]) - Static method in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
main(String[]) - Static method in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
main(String[]) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
main(String[]) - Static method in class org.apache.ctakes.examples.pipelines.ExampleAggregatePipeline
main(String[]) - Static method in class org.apache.ctakes.jdl.App
main(String[]) - Static method in class org.apache.ctakes.jdl.AppMain
main(String[]) - Static method in class org.apache.ctakes.postagger.TagDictionaryCreator: Read a file containing POS-tagged tokens in OpenNLP format, and output a tagDictionary (OpenNLP format)
Example input:
winning_JJ body_NN
winning_VBG
Example output:
body NN
winning JJ VBG
main(String[]) - Static method in class org.apache.ctakes.preprocessor.test.TestDriver
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.analysis.Utils
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.Splitter
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.Stats
main(String[]) - Static method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
main(String[]) - Static method in class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics
main(String[]) - Static method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
main(String[]) - Static method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipelineSingleCas
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
main(String[]) - Static method in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData: keywordsFile and stopwordsFile must point to the files in the resources dataFile is your own sentence-level data in the format (class_label: C, P, S): sentence|class_label sentence|class_label ...
main(String[]) - Static method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
main(String[]) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
main(String[]) - Static method in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader: Just runs reader over files.
main(String[]) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.GoldRelationViewer
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.PrintFailedTimeNormalizations
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.PrintInconsistentAnnotations
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.data.analysis.TimexTreeAlignmentStatistics
main(String[]) - Static method in class org.apache.ctakes.temporal.duration.EventDurationDistribution
main(String[]) - Static method in class org.apache.ctakes.temporal.duration.EventEventDurationStatistics
main(String[]) - Static method in class org.apache.ctakes.temporal.duration.EventTimeDurationStatistics
main(String[]) - Static method in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation
main(String[]) - Static method in class org.apache.ctakes.temporal.duration.Utils
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
main(String[]) - Static method in class org.apache.ctakes.temporal.eval.PrintRelations
main(String[]) - Static method in class org.apache.ctakes.temporal.pipelines.EventAndTimeExtractionPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.pipelines.EventExtractionPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.pipelines.EventPrintingPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.pipelines.TimeExtractionPipeline
main(String[]) - Static method in class org.apache.ctakes.temporal.utils.CheckKnowtatorAnnotations
main(String[]) - Static method in class org.apache.ctakes.temporal.utils.RunCorpusDiagnostics
main(String[]) - Static method in class org.apache.ctakes.utils.build.BuildPear
main(String[]) - Static method in class org.apache.ctakes.utils.build.BuildPipelinePears
main(String[]) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently: Starts the application.
main(String[]) - Static method in class org.apache.ctakes.utils.build.InstallPipelineFromPears
main(String[]) - Static method in class org.apache.ctakes.utils.distsem.DistanceMetrics
main(String[]) - Static method in class org.apache.ctakes.utils.tree.SimpleTree
main(String[]) - Static method in class org.apache.ctakes.utils.wiki.TestCosineSimilarity
main(String[]) - Static method in class org.apache.ctakes.utils.xcas_comparison.Compare
main(String[]) - Static method in class org.apache.ctakes.utils.xcas_comparison.ConvertAndCompare
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: create a concept graph.
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.evaluator.TreePrinter
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.RRFtoWideTab
main(String[]) - Static method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.KernelLauncher
main(String[]) - Static method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
main(String[]) - Static method in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
main(String[]) - Static method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
main(String[]) - Static method in class org.apache.ctakes.ytex.tools.DBPing
main(String[]) - Static method in class org.apache.ctakes.ytex.tools.ExportCAS
main(String[]) - Static method in class org.apache.ctakes.ytex.tools.RunCPE: main class.
main(String[]) - Static method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
main(String[]) - Static method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: Train a new sentence detector from the training data in the first file and write the model to the second file.
The training data file is expected to have one sentence per line.
main(String[]) - Static method in class org.apache.ctakes.ytex.weka.ExportBagOfWords
main(String[]) - Static method in class org.apache.ctakes.ytex.weka.ExportGramMatrix
main(String[]) - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults
main(String[]) - Static method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
mainComponentId - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
mainComponentRootPath - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
MAINSUI - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
mainSuiCheck(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
makeFeatures(String) - Method in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData: set "features" - list of features.
makeTfIdfVector(ArrayList<Terms>) - Method in class org.apache.ctakes.utils.wiki.WikiIndex: Return a hash table that maps terms to their tfidf values.
ManagesTreats - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ManagesTreats() - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreats: Never called.
ManagesTreats(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreats: Internal - constructor used by generator
ManagesTreats(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreats
ManagesTreats_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ManagesTreats_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreats_Type: initialize variables to correspond with Cas Type and Features
ManagesTreatsRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies manages/treats relation.
ManagesTreatsRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
ManagesTreatsTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ManagesTreatsTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation: Never called.
ManagesTreatsTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation: Internal - constructor used by generator
ManagesTreatsTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation
ManagesTreatsTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ManagesTreatsTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation_Type: initialize variables to correspond with Cas Type and Features
ManifestationOf - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
ManifestationOf() - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOf: Never called.
ManifestationOf(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOf: Internal - constructor used by generator
ManifestationOf(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOf
ManifestationOf_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
ManifestationOf_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOf_Type: initialize variables to correspond with Cas Type and Features
ManifestationOfTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ManifestationOfTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation: Never called.
ManifestationOfTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation: Internal - constructor used by generator
ManifestationOfTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
ManifestationOfTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ManifestationOfTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation_Type: initialize variables to correspond with Cas Type and Features
map - Static variable in class org.apache.ctakes.assertion.pipelines.SharpCorpusSplit
map - Variable in class org.apache.ctakes.utils.struct.CounterTreeMap
MAP_PREP_STMT_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
mapAnnoMappingInfo - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
mapByAddress - Variable in class org.apache.ctakes.assertion.medfacts.CasIndexer
mapField - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
mapI2B2AssertionValueToCtakes(String, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
mapIndexWeight - Variable in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
Mapper - Class in org.apache.ctakes.core.util: Map various category names to their ctakes integer id.
Mapper() - Constructor for class org.apache.ctakes.core.util.Mapper
MapperConfig - Class in org.apache.ctakes.ytex.uima.mapper: semi-ugly hack to communicate options from the MapperService to the individual Mappers.
MapperConfig(Set<String>, int) - Constructor for class org.apache.ctakes.ytex.uima.mapper.MapperConfig
mapRow(ResultSet, int) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.InstanceIDRowMapper
mapRow(ResultSet, int) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl.ConceptFirstWordRowMapper
mapRow(ResultSet, int) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl.DocumentSearchResultMapper
mapThyme - Variable in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
Markable - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
Markable() - Constructor for class org.apache.ctakes.coreference.type.Markable: Never called.
Markable(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.Markable: Internal - constructor used by generator
Markable(JCas) - Constructor for class org.apache.ctakes.coreference.type.Markable
Markable(JCas, int, int) - Constructor for class org.apache.ctakes.coreference.type.Markable
Markable - Class in org.apache.ctakes.typesystem.type.textsem: A type for representing text spans that can potentially be linked together via coreference.
Markable() - Constructor for class org.apache.ctakes.typesystem.type.textsem.Markable: Never called.
Markable(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Markable: Internal - constructor used by generator
Markable(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Markable
Markable(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Markable
Markable_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
Markable_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.Markable_Type: initialize variables to correspond with Cas Type and Features
Markable_Type - Class in org.apache.ctakes.typesystem.type.textsem: A type for representing text spans that can potentially be linked together via coreference.
Markable_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Markable_Type: initialize variables to correspond with Cas Type and Features
MarkableDepUtils - Class in org.apache.ctakes.coreference.util
MarkableDepUtils() - Constructor for class org.apache.ctakes.coreference.util.MarkableDepUtils
markableNode(JCas, int, int, TreebankNode) - Static method in class org.apache.ctakes.coreference.util.MarkableDepUtils
markableNode(JCas, int, int) - Static method in class org.apache.ctakes.coreference.util.MarkableTreeUtils
MarkablePair - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
MarkablePair() - Constructor for class org.apache.ctakes.coreference.type.MarkablePair: Never called.
MarkablePair(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.MarkablePair: Internal - constructor used by generator
MarkablePair(JCas) - Constructor for class org.apache.ctakes.coreference.type.MarkablePair
MarkablePair_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
MarkablePair_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.MarkablePair_Type: initialize variables to correspond with Cas Type and Features
MarkablePairSet - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
MarkablePairSet() - Constructor for class org.apache.ctakes.coreference.type.MarkablePairSet: Never called.
MarkablePairSet(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.MarkablePairSet: Internal - constructor used by generator
MarkablePairSet(JCas) - Constructor for class org.apache.ctakes.coreference.type.MarkablePairSet
MarkablePairSet(JCas, int, int) - Constructor for class org.apache.ctakes.coreference.type.MarkablePairSet
MarkablePairSet_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
MarkablePairSet_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.MarkablePairSet_Type: initialize variables to correspond with Cas Type and Features
MarkableProb - Class in org.apache.ctakes.coreference.ae
MarkableProb(Markable, Double) - Constructor for class org.apache.ctakes.coreference.ae.MarkableProb
MarkableTreeUtils - Class in org.apache.ctakes.coreference.util
MarkableTreeUtils() - Constructor for class org.apache.ctakes.coreference.util.MarkableTreeUtils
mat - Variable in class org.apache.ctakes.sideeffect.util.PatternMatch
match - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
matcher(CharSequence) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
matches(String) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
matchesList - Variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
matchesList - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
matchingType(CEAFType) - Static method in enum org.apache.ctakes.coreference.eval.helpers.MatType
matchSpan(Annotation, Annotation) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
MatType - Enum in org.apache.ctakes.coreference.eval.helpers
MatType() - Constructor for enum org.apache.ctakes.coreference.eval.helpers.MatType
MAX - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
MAX_BATCH_SIZE - Static variable in class org.apache.ctakes.core.cc.AbstractJdbcWriter
MAX_DAY - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
MAX_HOUR - Variable in class org.apache.ctakes.core.fsm.machine.TimeFSM
MAX_LEFT_SCOPE_SIZE_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "MaxLeftScopeSize" is a required, single, integer parameter that specifies the maximum size of the left scope.
MAX_LIST_SIZE - Static variable in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
MAX_LIST_SIZE - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
MAX_MINUTE - Variable in class org.apache.ctakes.core.fsm.machine.TimeFSM
MAX_MONTH - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
MAX_P_LEVEL_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
MAX_P_LEVEL_PRP_KEY - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
MAX_RIGHT_SCOPE_SIZE_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "MaxRightScopeSize" is a required, single, integer parameter that specifies the maximum size of the right scope.
MAX_YEAR - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
maxAttributeIndex - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: 1-based attribute index
MAXDISTANCE - Static variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
MaxentParserWrapper - Class in org.apache.ctakes.constituency.parser
MaxentParserWrapper(InputStream) - Constructor for class org.apache.ctakes.constituency.parser.MaxentParserWrapper
maxHits - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
maxIC - Variable in class org.apache.ctakes.ytex.kernel.metric.IntrinsicPathMetric
maxIC - Variable in class org.apache.ctakes.ytex.kernel.metric.IntrinsicRadaMetric
MAXIMUM_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
maxSizeList - Static variable in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
maxSpanID - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
mcDefault - Static variable in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
mCPE - Variable in class org.apache.ctakes.ytex.tools.RunCPE: The CPE instance.
mCurrentIndex - Variable in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
mCurrentIndex - Variable in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
MD_KEY_ADMIT_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_CUSTOMER_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_DISCHARGE_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_DOC_CONFIDENTIAL_IND - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_DOC_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_DOC_LINK_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_DOC_REVISION_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_DOC_STATUS_CODE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_EVENT_TYPE_CODE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_FACILITY_CODE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_HISTORY_SECTION - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_LOCATION - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_MINUTES_COUNSELING - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_NOTE_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PATIENT_CITY - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PATIENT_CNT - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PATIENT_STATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PATIENT_STREET_ADDR - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PATIENT_ZIP - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PROVIDER2_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PROVIDER_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_BILLING_CODE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_BIRTH_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_BMI - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_BSA - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_GENDER - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_HEAD_CIRCUMFERENCE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_HEIGHT - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_RESPIRATORY_RATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_TEMPERATURE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_PT_WEIGHT - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_REV_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_SERVICE_CODE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_SIGNATURE_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_SIGNATURE_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_SITE_CODE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_TOTAL_TIME - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_TRANSCRIBER_ID - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
MD_KEY_TRANSCRIPTION_DATE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
mDocNum - Variable in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
meanValues - Variable in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor
meanValues - Variable in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor
measure - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
MeasurementAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
MeasurementAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation: Never called.
MeasurementAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation: Internal - constructor used by generator
MeasurementAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
MeasurementAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
MeasurementAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
MeasurementAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type: initialize variables to correspond with Cas Type and Features
MeasurementFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect measurements in the given input of tokens.
MeasurementFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.MeasurementFSM: Constructor
MeasurementToken - Class in org.apache.ctakes.core.fsm.output
MeasurementToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.MeasurementToken
med1 - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
MED_STATUS_CHANGE_DECREASE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_DECREASEFROM - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_INCREASE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_INCREASEFROM - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_MAX - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_NOCHANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_START - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_STOP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MED_STATUS_CHANGE_SUM - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
Medication - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Chemicals and Drugs, pruned by RxNORM source.
Medication() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Medication: Never called.
Medication(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Medication: Internal - constructor used by generator
Medication(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Medication
MEDICATION_TUIS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
Medication_Type - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Chemicals and Drugs, pruned by RxNORM source.
Medication_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Medication_Type: initialize variables to correspond with Cas Type and Features
medicationAbrs - Static variable in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
MedicationAllergyModifier - Class in org.apache.ctakes.typesystem.type.textsem: Indication of whether the medication is mentioned in the context of Allergies.
MedicationAllergyModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier: Never called.
MedicationAllergyModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier: Internal - constructor used by generator
MedicationAllergyModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier
MedicationAllergyModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier
MedicationAllergyModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Indication of whether the medication is mentioned in the context of Allergies.
MedicationAllergyModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationDosage - Class in org.apache.ctakes.typesystem.type.refsem: Dosage indicates how much of a prescribed drug should be taken.
MedicationDosage() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDosage: Never called.
MedicationDosage(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDosage: Internal - constructor used by generator
MedicationDosage(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDosage
MedicationDosage_Type - Class in org.apache.ctakes.typesystem.type.refsem: Dosage indicates how much of a prescribed drug should be taken.
MedicationDosage_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type: initialize variables to correspond with Cas Type and Features
MedicationDosageModifier - Class in org.apache.ctakes.typesystem.type.textsem: Dosage indicates how much of a prescribed drug should be taken.
MedicationDosageModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier: Never called.
MedicationDosageModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier: Internal - constructor used by generator
MedicationDosageModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier
MedicationDosageModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier
MedicationDosageModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Dosage indicates how much of a prescribed drug should be taken.
MedicationDosageModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationDuration - Class in org.apache.ctakes.typesystem.type.refsem: The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks" Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
MedicationDuration() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDuration: Never called.
MedicationDuration(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDuration: Internal - constructor used by generator
MedicationDuration(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDuration
MedicationDuration_Type - Class in org.apache.ctakes.typesystem.type.refsem: The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks" Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
MedicationDuration_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type: initialize variables to correspond with Cas Type and Features
MedicationDurationModifier - Class in org.apache.ctakes.typesystem.type.textsem: The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks" Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
MedicationDurationModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier: Never called.
MedicationDurationModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier: Internal - constructor used by generator
MedicationDurationModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier
MedicationDurationModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier
MedicationDurationModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks" Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
MedicationDurationModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationEventMention - Class in org.apache.ctakes.typesystem.type.textsem: As of cTAKEs 3.1, see org.apache.ctakes.typesystem.type.textsem.MedicationMention.
MedicationEventMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: Never called.
MedicationEventMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: Internal - constructor used by generator
MedicationEventMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention
MedicationEventMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention
MedicationEventMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: As of cTAKEs 3.1, see org.apache.ctakes.typesystem.type.textsem.MedicationMention.
MedicationEventMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type: initialize variables to correspond with Cas Type and Features
MedicationForm - Class in org.apache.ctakes.typesystem.type.refsem: Form of this medication.
MedicationForm() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationForm: Never called.
MedicationForm(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationForm: Internal - constructor used by generator
MedicationForm(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationForm
MedicationForm_Type - Class in org.apache.ctakes.typesystem.type.refsem: Form of this medication.
MedicationForm_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type: initialize variables to correspond with Cas Type and Features
MedicationFormModifier - Class in org.apache.ctakes.typesystem.type.textsem: Form of this medication.
MedicationFormModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier: Never called.
MedicationFormModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier: Internal - constructor used by generator
MedicationFormModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier
MedicationFormModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier
MedicationFormModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Form of this medication.
MedicationFormModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationFrequency - Class in org.apache.ctakes.typesystem.type.refsem: How often a medication should be used.
MedicationFrequency() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: Never called.
MedicationFrequency(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: Internal - constructor used by generator
MedicationFrequency(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency
MedicationFrequency_Type - Class in org.apache.ctakes.typesystem.type.refsem: How often a medication should be used.
MedicationFrequency_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type: initialize variables to correspond with Cas Type and Features
MedicationFrequencyModifier - Class in org.apache.ctakes.typesystem.type.textsem: How often a medication should be used.
MedicationFrequencyModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier: Never called.
MedicationFrequencyModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier: Internal - constructor used by generator
MedicationFrequencyModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier
MedicationFrequencyModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier
MedicationFrequencyModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: How often a medication should be used.
MedicationFrequencyModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (Medication) Event.
MedicationMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationMention: Never called.
MedicationMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationMention: Internal - constructor used by generator
MedicationMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationMention
MedicationMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationMention
MedicationMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (Medication) Event.
MedicationMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type: initialize variables to correspond with Cas Type and Features
MedicationRoute - Class in org.apache.ctakes.typesystem.type.refsem: Means by which the medication was taken or administered.
MedicationRoute() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationRoute: Never called.
MedicationRoute(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationRoute: Internal - constructor used by generator
MedicationRoute(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationRoute
MedicationRoute_Type - Class in org.apache.ctakes.typesystem.type.refsem: Means by which the medication was taken or administered.
MedicationRoute_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type: initialize variables to correspond with Cas Type and Features
MedicationRouteModifier - Class in org.apache.ctakes.typesystem.type.textsem: Means by which the medication was taken or administered.
MedicationRouteModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier: Never called.
MedicationRouteModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier: Internal - constructor used by generator
MedicationRouteModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier
MedicationRouteModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier
MedicationRouteModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Means by which the medication was taken or administered.
MedicationRouteModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationStatusChange - Class in org.apache.ctakes.typesystem.type.refsem: Status refers to the whether the medication is currently being taken or not.
MedicationStatusChange() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange: Never called.
MedicationStatusChange(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange: Internal - constructor used by generator
MedicationStatusChange(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange
MedicationStatusChange_Type - Class in org.apache.ctakes.typesystem.type.refsem: Status refers to the whether the medication is currently being taken or not.
MedicationStatusChange_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type: initialize variables to correspond with Cas Type and Features
MedicationStatusChangeModifier - Class in org.apache.ctakes.typesystem.type.textsem: Status refers to the whether the medication is currently being taken or not.
MedicationStatusChangeModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier: Never called.
MedicationStatusChangeModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier: Internal - constructor used by generator
MedicationStatusChangeModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier
MedicationStatusChangeModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier
MedicationStatusChangeModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Status refers to the whether the medication is currently being taken or not.
MedicationStatusChangeModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier_Type: initialize variables to correspond with Cas Type and Features
MedicationStrength - Class in org.apache.ctakes.typesystem.type.refsem: Strength indicates the strength number and unit of the prescribed drug.
MedicationStrength() - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: Never called.
MedicationStrength(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: Internal - constructor used by generator
MedicationStrength(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStrength
MedicationStrength_Type - Class in org.apache.ctakes.typesystem.type.refsem: Strength indicates the strength number and unit of the prescribed drug.
MedicationStrength_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type: initialize variables to correspond with Cas Type and Features
MedicationStrengthModifier - Class in org.apache.ctakes.typesystem.type.textsem: Strength indicates the strength number and unit of the prescribed drug.
MedicationStrengthModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier: Never called.
MedicationStrengthModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier: Internal - constructor used by generator
MedicationStrengthModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier
MedicationStrengthModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier
MedicationStrengthModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Strength indicates the strength number and unit of the prescribed drug.
MedicationStrengthModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type: initialize variables to correspond with Cas Type and Features
MemConceptFactory - Class in org.apache.ctakes.dictionary.lookup2.concept: Author: SPF Affiliation: CHIP-NLP Date: 9/9/2014
MemConceptFactory(String, Map<Long, Concept>) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.MemConceptFactory
MemRareWordDictionary - Class in org.apache.ctakes.dictionary.lookup2.dictionary: A RareWordDictionary that uses a HashMap of Rare Words and Terms for lookup
Author: SPF Affiliation: CHIP-NLP Date: 1/9/14
MemRareWordDictionary(String, CollectionMap<String, RareWordTerm, ? extends Collection<RareWordTerm>>) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.MemRareWordDictionary
mEncoding - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
MENTION - Static variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
mention1ContextFeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor
mention1CoveredFeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor: All extractors for mention 1, with features named to distinguish them from mention 2
mention1FeaturesExtractor - Variable in class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor: All extractors for mention 1, with features named to distinguish them from mention 2
mention1FeaturesExtractor - Variable in class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor: All extractors for mention 1, with features named to distinguish them from mention 2
mention1FeaturesExtractor - Variable in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor: All extractors for mention 1, with features named to distinguish them from mention 2
mention1FeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor: All extractors for mention 1, with features named to distinguish them from mention 2
mention1FeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor: All extractors for mention 1, with features named to distinguish them from mention 2
mention2ContextFeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor
mention2CoveredFeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor: All extractors for mention 2, with features named to distinguish them from mention 1
mention2FeaturesExtractor - Variable in class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor: All extractors for mention 2, with features named to distinguish them from mention 1
mention2FeaturesExtractor - Variable in class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor: All extractors for mention 2, with features named to distinguish them from mention 1
mention2FeaturesExtractor - Variable in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor: All extractors for mention 2, with features named to distinguish them from mention 1
mention2FeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor: All extractors for mention 2, with features named to distinguish them from mention 1
mention2FeaturesExtractor - Variable in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor: All extractors for mention 2, with features named to distinguish them from mention 1
merge(List<ImputedFeatureEvaluatorImpl.JointDistribution>, Map<String, Set<Long>>, String) - Static method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: merge joint distributions into a single distribution.
MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas - Class in org.apache.ctakes.assertion.eval: Read in gold annotations from XMI and create a view within the current CAS, and copy the gold annotations into the new view within the current CAS.
MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas() - Constructor for class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
mergeNP(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
message - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
Metadata - Class in org.apache.ctakes.typesystem.type.structured: Structured data that captures information about the document, patient, or context of the clinical text.
Metadata() - Constructor for class org.apache.ctakes.typesystem.type.structured.Metadata: Never called.
Metadata(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.Metadata: Internal - constructor used by generator
Metadata(JCas) - Constructor for class org.apache.ctakes.typesystem.type.structured.Metadata
Metadata_Type - Class in org.apache.ctakes.typesystem.type.structured: Structured data that captures information about the document, patient, or context of the clinical text.
Metadata_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.Metadata_Type: initialize variables to correspond with Cas Type and Features
MetaDataHit - Interface in org.apache.ctakes.dictionary.lookup
MetaDataHitComparator - Class in org.apache.ctakes.dictionary.lookup: Allows two MetaDataHit objects to be compared based on a specific metadata value that they both contain.
MetaDataHitComparator(String, int, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.MetaDataHitComparator: Constructor
MetaDataHitConst - Interface in org.apache.ctakes.dictionary.lookup
MetaDataPostLookupFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter
MetaDataPostLookupFilterImpl(DictionaryEngine, String[], boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.MetaDataPostLookupFilterImpl
metaKey - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator
metaKeywords - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator
metaLookup(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine: Gets a collection of MetaDataHits from the Dictionary based on the input text.
MetaMapToCTakesAnnotator - Class in org.apache.ctakes.ytex.uima.annotators: Convert metamap concepts to ctakes named entities.
MetaMapToCTakesAnnotator() - Constructor for class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
MetaMapToCTakesAnnotator.NegSpan - Class in org.apache.ctakes.ytex.uima.annotators
MetaMapToCTakesAnnotator.NegSpan(int, int) - Constructor for class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
MetaMapToCTakesAnnotator.NegSpan(Annotation) - Constructor for class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
metaReplace(String) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
MetaTimeAnnotator - Class in org.apache.ctakes.temporal.ae
MetaTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
MethodCachingInterceptor - Class in org.apache.ctakes.ytex.kernel.evaluator: simple caching interceptor.
MethodCachingInterceptor() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
methodMapArray - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
methodName - Variable in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
metric - Variable in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
metricArrayToList(String[]) - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
metricNames - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
metrics - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
metrics - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
metricSelectCorpusIC - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
metricSelectIntrinsicIC - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
metricSelectTaxonomy - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
mFailOnUnknownType - Variable in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
mFailOnUnknownType - Variable in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
mFiles - Variable in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
mFiles - Variable in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
MIDDLE_SCOPE - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: Provides context annotations that are "inside" the focus annotation.
milliDay - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
milliWeek - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
MIN_DAY - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
MIN_HOUR - Variable in class org.apache.ctakes.core.fsm.machine.TimeFSM
MIN_MINUTE - Variable in class org.apache.ctakes.core.fsm.machine.TimeFSM
MIN_MONTH - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
MIN_YEAR - Variable in class org.apache.ctakes.core.fsm.machine.DateFSM
minInfo - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
mInitCompleteTime - Variable in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener: Start time of the processing
mInitCompleteTime - Variable in class org.apache.ctakes.ytex.tools.RunCPE: Start time of the processing
minorityInsts - Variable in class org.apache.ctakes.temporal.utils.SMOTEplus
MINUS_OR_HYPHEN - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
mipacDevXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
MiPACQ_CORPUS - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
MIPACQ_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
MIPACQ_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
MIPACQ_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
MIPACQ_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
MIPACQ_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
MIPACQ_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
mipacqAllXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
MiPACQKnowtatorXMLReader - Class in org.apache.ctakes.assertion.cr: assumes knowtator xml files are in "exported-xml" subdirectory w/ train/dev/test subsubdirs and the original plaintext files are in "text" subdirectory w/ train/dev/test subsubdirs
MiPACQKnowtatorXMLReader() - Constructor for class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
MiPACQKnowtatorXMLReader.DelayedFeature - Class in org.apache.ctakes.assertion.cr
MiPACQKnowtatorXMLReader.DelayedFeature(Annotation, String, KnowtatorAnnotation) - Constructor for class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
MiPACQKnowtatorXMLReader.DelayedFeatureFromFeature - Class in org.apache.ctakes.assertion.cr
MiPACQKnowtatorXMLReader.DelayedFeatureFromFeature(Annotation, String, KnowtatorAnnotation) - Constructor for class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeatureFromFeature
MiPACQKnowtatorXMLReader.DelayedRelationFeature - Class in org.apache.ctakes.assertion.cr
MiPACQKnowtatorXMLReader.DelayedRelationFeature(Annotation, String, KnowtatorAnnotation, Class<? extends BinaryTextRelation>, Annotation, Class<? extends Annotation>, Annotation, Class<? extends Annotation>) - Constructor for class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
MipacqMarkableCreator - Class in org.apache.ctakes.coreference.ae
MipacqMarkableCreator() - Constructor for class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
MipacqMarkableExpander - Class in org.apache.ctakes.coreference.ae
MipacqMarkableExpander() - Constructor for class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
MipacqMarkablePairGenerator - Class in org.apache.ctakes.coreference.ae
MipacqMarkablePairGenerator() - Constructor for class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
MipacqSvmChainCreator - Class in org.apache.ctakes.coreference.ae
MipacqSvmChainCreator() - Constructor for class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
mipacqTestXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
mipacqTrainXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
mod_coref - Variable in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
modalAdj - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
mode - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
model - Variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests.TestPair
model - Variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests.TestPair
model - Variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: The maximum entropy model to use to evaluate contexts.
model - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceClassifierAnnotator
model - Variable in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
model - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
modelDirectory - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
modelFile - Variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors.Options
modelFilename - Variable in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
modelOutputDirectory - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
modelsDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
Modifier - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to an Attribute.
Modifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.Modifier: Never called.
Modifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Modifier: Internal - constructor used by generator
Modifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Modifier
Modifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Modifier
Modifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to an Attribute.
Modifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Modifier_Type: initialize variables to correspond with Cas Type and Features
MODIFIER_TYPE_ID_COURSE_CLASS - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MODIFIER_TYPE_ID_SEVERITY_CLASS - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
MODIFIER_TYPE_ID_UNKNOWN - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ModifierExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae
ModifierExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
ModifierExtractorEvaluation - Class in org.apache.ctakes.relationextractor.eval
ModifierExtractorEvaluation(File, ParameterSettings) - Constructor for class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
ModifierExtractorEvaluation.OnlyGoldModifiers - Class in org.apache.ctakes.relationextractor.eval: Class that copies the manual Modifier annotations to the default CAS.
ModifierExtractorEvaluation.OnlyGoldModifiers() - Constructor for class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation.OnlyGoldModifiers
modify(String) - Method in class org.apache.ctakes.core.ci.HyphenTextModifierImpl
modify(String) - Method in interface org.apache.ctakes.core.ci.TextModifier: Generates modifications for the specified text.
modifyBegin(Annotation, Annotation, Annotation) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
modifyEnd(Annotation, Annotation, Annotation) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
monthFullNames - Static variable in class org.apache.ctakes.core.util.DateParser
MONTHLY - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
monthShortNames - Static variable in class org.apache.ctakes.core.util.DateParser
mOutputDir - Variable in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
moveTimexDownToNP(SimpleTree) - Static method in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
moveTimexDownToNP(SimpleTree) - Static method in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor
MRCONSO - Class in org.apache.ctakes.ytex.umls.model
MRCONSO() - Constructor for class org.apache.ctakes.ytex.umls.model.MRCONSO
MRREL - Class in org.apache.ctakes.ytex.umls.model: mapped to umls MRREL table
MRREL() - Constructor for class org.apache.ctakes.ytex.umls.model.MRREL
MRSTY - Class in org.apache.ctakes.ytex.umls.model
MRSTY() - Constructor for class org.apache.ctakes.ytex.umls.model.MRSTY
ms1 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
ms2 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator
msg - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
mssql - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
mStartTime - Variable in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener: Start time of CPE initialization
mStartTime - Variable in class org.apache.ctakes.ytex.tools.RunCPE: Start time of CPE initialization
mu - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
multipleDrugsInSpan(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Return true if exists more than one drug and reason within the span, otherwise return false
multipleElementsInSpan(JCas, int, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Return true if exists more than one drug and reason within the span, otherwise return false
MultiTextSpan - Class in org.apache.ctakes.dictionary.lookup2.textspan: A useful key for hash collections based upon start and end indices and missing internal spans.
MultiTextSpan(int, int, Collection<TextSpan>) - Constructor for class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan: Given span indices should be ordered start < end, but it is not an absolute requirement.
MultiTokenFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature: for every UMLS entities covering the annotation, extracted related token features
MultiTokenFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor
MultiTokenWordLenToken1 - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
MultiTokenWordLenToken1 - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
MultiTokenWordLenToken2 - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
MultiTokenWordLenToken2 - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
MultiTokenWordLenToken3 - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
MultiTokenWords - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
MultiTokenWords - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
MultiTokenWordsLookup - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
MultiTokenWordsLookup - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
mutualInformation(String, OUTCOME_T) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
mutualInformation(String, OUTCOME_T) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
MutualInformationFeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.assertion.attributes.features.selection: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
MutualInformationFeatureSelection(String) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
MutualInformationFeatureSelection(String, int) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
MutualInformationFeatureSelection(String, MutualInformationFeatureSelection.CombineScoreMethod, double, int) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
MutualInformationFeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
MutualInformationFeatureSelection(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
MutualInformationFeatureSelection(String, int) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
MutualInformationFeatureSelection(String, MutualInformationFeatureSelection.CombineScoreMethod, double, int) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
MutualInformationFeatureSelection.CombineScoreMethod - Enum in org.apache.ctakes.assertion.attributes.features.selection: Specifies how scores for each outcome should be combined/aggregated into a single score
MutualInformationFeatureSelection.CombineScoreMethod() - Constructor for enum org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.CombineScoreMethod
MutualInformationFeatureSelection.CombineScoreMethod - Enum in org.apache.ctakes.temporal.ae.feature.selection: Specifies how scores for each outcome should be combined/aggregated into a single score
MutualInformationFeatureSelection.CombineScoreMethod() - Constructor for enum org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.CombineScoreMethod
MutualInformationFeatureSelection.MutualInformationStats<OUTCOME_T> - Class in org.apache.ctakes.assertion.attributes.features.selection: Helper class for aggregating and computing mutual information statistics
MutualInformationFeatureSelection.MutualInformationStats(double) - Constructor for class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
MutualInformationFeatureSelection.MutualInformationStats<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Helper class for aggregating and computing mutual information statistics
MutualInformationFeatureSelection.MutualInformationStats(double) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
mutualInfoStats - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
mutualInfoStats - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
mysql - Static variable in class org.apache.ctakes.ytex.dao.DBUtil

N

n1 - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
n2 - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
name - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.Slot
name - Variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
name - Variable in class org.apache.ctakes.temporal.ae.feature.ChunkingExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.ClosestVerbExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.DateAndMeasurementExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.DeterminerRelationFeaturesExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.EventPositionFeatureExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.EventPropertyExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseXExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.SectionHeaderExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.TimeXExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.TimeXPropertyRelationFeaturesExtractor
name - Variable in class org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor
name - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
name - Variable in enum org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator.MeasureType
name - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
NAME_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Each dictionary, concept factory, pairing and term consumer should have a unique name
NamedEntityContextAnalyzer - Class in org.apache.ctakes.necontexts: This context analyzer provides code that is shared by the StatusContextAnalyzer and NegationContextAnalyzer which are both analyzers that examine the contexts surrounding named entity annotations.
NamedEntityContextAnalyzer() - Constructor for class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer
NamedEntityContextAnalyzer - Class in org.apache.ctakes.smokingstatus.context: This context analyzer provides code that is shared by the StatusContextAnalyzer and NegationContextAnalyzer which are both analyzers that examine the contexts surrounding named entity annotations.
NamedEntityContextAnalyzer() - Constructor for class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer
NamedEntityContextHitConsumer - Class in org.apache.ctakes.necontexts
NamedEntityContextHitConsumer() - Constructor for class org.apache.ctakes.necontexts.NamedEntityContextHitConsumer
NamedEntityFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
NamedEntityFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor
NamedEntityLookupConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae
NamedEntityLookupConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
NamedEntityLookupConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
NamedEntityNegationKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: Evaluate negation status and certainty of named entities.
NamedEntityNegationKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.NamedEntityNegationKernel
NamedEntityRegex - Class in org.apache.ctakes.ytex.uima.model: Mapped to ref_named_entity_regex.
NamedEntityRegex() - Constructor for class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
NamedEntityRegexAnnotator - Class in org.apache.ctakes.ytex.uima.annotators: Create NamedEntity annotations.
NamedEntityRegexAnnotator() - Constructor for class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
NamedEntityRegexDao - Interface in org.apache.ctakes.ytex.uima.dao: Dao to access NamedEntity Regular Expressions used by the NamedEntityRegexAnnotator
NamedEntityRegexDaoImpl - Class in org.apache.ctakes.ytex.uima.dao
NamedEntityRegexDaoImpl() - Constructor for class org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDaoImpl
namedEntityRegexID - Variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
namedEntityType - Variable in class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor
namedJdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
namedJdbcTemplate - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
namedParamJdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
NamedState - Class in org.apache.ctakes.core.fsm.state: Used mainly for aiding the debugging process.
NamedState(String) - Constructor for class org.apache.ctakes.core.fsm.state.NamedState
nameFile(JCas) - Method in class org.apache.ctakes.core.util.CtakesFileNamer
NAMESPACE_PREFIXES_FEATURE_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Namespace prefixes feature id (http://xml.org/sax/features/namespace-prefixes).
NAMESPACES_FEATURE_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Namespaces feature id (http://xml.org/sax/features/namespaces).
nameStartingWithApostrophe - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
nameToFormatterMap - Variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
nameToParserMap - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
NE - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
ne - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.PotentialSideEffect
NE_CERTAINTY_NEGATED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_CERTAINTY_POSITIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_CONDITIONAL_FALSE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_CONDITIONAL_TRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
ne_coref_feats - Static variable in class org.apache.ctakes.coreference.util.FeatureVector
NE_DIAG_STATUS_CONFIRMED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_DIAG_STATUS_FAM_HISTORY_OF - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_DIAG_STATUS_HISTORY_OF - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_DIAG_STATUS_PROBABLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_DISCOVERY_TECH_DICT_LOOKUP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_DISCOVERY_TECH_GOLD_ANNOTATION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_GENERIC_FALSE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_GENERIC_TRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_HISTORY_OF_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_HISTORY_OF_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_POLARITY_NEGATION_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_POLARITY_NEGATION_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_ANATOMICAL_SITE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_CLINICAL_ATTRIBUTE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_DEVICE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_DISORDER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_DRUG - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_FINDING - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_LAB - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_PHENOMENA - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_PROCEDURE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_TYPE_ID_UNKNOWN - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_UNCERTAINTY_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NE_UNCERTAINTY_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
NearbyVerbTenseRelationExtractor - Class in org.apache.ctakes.temporal.ae.feature
NearbyVerbTenseRelationExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor
NearbyVerbTenseXExtractor - Class in org.apache.ctakes.temporal.ae.feature
NearbyVerbTenseXExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseXExtractor
NearestFlagFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
NearestFlagFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.NearestFlagFeatureExtractor
NEDIST - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
negAnaphInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
negateAnnotations(JCas, AnnotationIndex, AnnotationIndex, NegexAnnotator.TargetAnnoFilter) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
NegateCondition - Class in org.apache.ctakes.core.fsm.condition
NegateCondition(Condition) - Constructor for class org.apache.ctakes.core.fsm.condition.NegateCondition
NEGATED - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
negatePossibilities - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
negation - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
NEGATION_IND_FSM_CLASS - Static variable in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl: Specifies the NegationIndicatorFSMClass that needs to be used
NegationContextAnalyzer - Class in org.apache.ctakes.necontexts.negation
NegationContextAnalyzer() - Constructor for class org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
NegationContextAnalyzer - Class in org.apache.ctakes.smokingstatus.context.negation
NegationContextAnalyzer() - Constructor for class org.apache.ctakes.smokingstatus.context.negation.NegationContextAnalyzer
NegationContextHitConsumer - Class in org.apache.ctakes.necontexts.negation
NegationContextHitConsumer() - Constructor for class org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
NegationDependencyFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
NegationDependencyFeatureExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.NegationDependencyFeatureExtractor
NegationDepRegex - Class in org.apache.ctakes.assertion.util
NegationDepRegex() - Constructor for class org.apache.ctakes.assertion.util.NegationDepRegex: Constructor
NegationFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect dates in the given input of tokens.
NegationFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.NegationFSM: Constructor
NegationFSM - Class in org.apache.ctakes.smokingstatus.machine: Uses one or more finite state machines to detect dates in the given input of tokens.
NegationFSM() - Constructor for class org.apache.ctakes.smokingstatus.machine.NegationFSM: Constructor
NegationIndicator - Class in org.apache.ctakes.core.fsm.output
NegationIndicator(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.NegationIndicator
NegationManualDepContextAnalyzer - Class in org.apache.ctakes.assertion.util: Uses one or more finite state machines to detect dates in the given input of tokens.
NegationManualDepContextAnalyzer() - Constructor for class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
negationStatus - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
negativeSign - Static variable in class org.apache.ctakes.core.fsm.adapters.IntegerTokenAdapter
negativeSign - Static variable in class org.apache.ctakes.core.fsm.token.adapter.IntegerTokenAdapter
NegContextInitializerImpl - Class in org.apache.ctakes.drugner.ae.impl
NegContextInitializerImpl() - Constructor for class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
negDemInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
NEGEX_CORPUS - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
NEGEX_CORPUS_PREPROCESSED - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
NEGEX_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
NEGEX_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
NEGEX_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
NEGEX_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
NEGEX_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
NEGEX_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
NegExAnnotation - Class in org.apache.ctakes.assertion.cr: parses a line of data from the negex gold standard For the few instances where there is somethign wrong with the gold standard, corrects/rejects some mistakes in gold standard (e.g.
NegExAnnotation(String) - Constructor for class org.apache.ctakes.assertion.cr.NegExAnnotation
NegexAnnotator - Class in org.apache.ctakes.ytex.uima.annotators: Negex adapted to cTAKES.
NegexAnnotator() - Constructor for class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
NegexAnnotator.NamedEntityTargetAnnoFilter - Class in org.apache.ctakes.ytex.uima.annotators: only bother with IdentifiedAnnotations that have concepts
NegexAnnotator.NamedEntityTargetAnnoFilter() - Constructor for class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NamedEntityTargetAnnoFilter
NegexAnnotator.NegexRule - Class in org.apache.ctakes.ytex.uima.annotators
NegexAnnotator.NegexRule() - Constructor for class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
NegexAnnotator.NegexRule(Pattern, String, String) - Constructor for class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
NegexAnnotator.NegexToken - Class in org.apache.ctakes.ytex.uima.annotators
NegexAnnotator.NegexToken(int, int, NegexAnnotator.NegexRule) - Constructor for class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
NegexAnnotator.TargetAnnoFilter - Interface in org.apache.ctakes.ytex.uima.annotators
NegExCorpusReader - Class in org.apache.ctakes.assertion.cr: Reads lines from file named by AssertionConst.NEGEX_CORPUS If use the main() method, uses this collection reader to read the corpus and then uses the XMI writer to write the XMI to directory given by AssertionConst.NEGEX_CORPUS_PREPROCESSED
NegExCorpusReader() - Constructor for class org.apache.ctakes.assertion.cr.NegExCorpusReader
NegExCorpusReader(boolean) - Constructor for class org.apache.ctakes.assertion.cr.NegExCorpusReader
NegIndicatorFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect dates in the given input of tokens.
NegIndicatorFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.NegIndicatorFSM: Constructor
negNeInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
negPronInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
NEMarkable - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
NEMarkable() - Constructor for class org.apache.ctakes.coreference.type.NEMarkable: Never called.
NEMarkable(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.NEMarkable: Internal - constructor used by generator
NEMarkable(JCas) - Constructor for class org.apache.ctakes.coreference.type.NEMarkable
NEMarkable(JCas, int, int) - Constructor for class org.apache.ctakes.coreference.type.NEMarkable
NEMarkable_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
NEMarkable_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.NEMarkable_Type: initialize variables to correspond with Cas Type and Features
nEntityMentionsBetween - Variable in class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor: Number of named entities between the two mentions
neOut - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
NEPredicateEventAnnotator - Class in org.apache.ctakes.temporal.ae
NEPredicateEventAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.NEPredicateEventAnnotator
neRegexDao - Variable in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
NERTypeIdentifier - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
neTreeOut - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
NEW_LINE - Static variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: System new line character
NEWLINE - Variable in class org.apache.ctakes.core.ae.SentenceDetector
NEWLINE - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
NEWLINE - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
NewlineToken - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a newline rather than a punctuation, symbol, contraction, word, or number.
NewlineToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.NewlineToken: Never called.
NewlineToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NewlineToken: Internal - constructor used by generator
NewlineToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NewlineToken
NewlineToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NewlineToken
NewlineToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a newline rather than a punctuation, symbol, contraction, word, or number.
NewlineToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NewlineToken_Type: initialize variables to correspond with Cas Type and Features
NewlineTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
NewlineTokenAdapter(NewlineToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.NewlineTokenAdapter
newTextNode() - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor: Called when a fully contiguous text node has been found.
next() - Method in class org.apache.ctakes.core.util.FSListIterator
nextID - Static variable in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
nextX(TreebankNode) - Static method in class org.apache.ctakes.coreference.util.HobbsTreeNavigator
nFolds - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
ngrams - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
nMod - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.SliceEvaluator
NO - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
NO - Static variable in interface org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser
NO_ANNOTATION_TYPE_SPECIFIED - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
NO_ENTITY_ID - Static variable in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
NO_RELATION_CATEGORY - Static variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
NO_RELATION_CATEGORY - Static variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
NO_SPLIT - Static variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Constant indicates no sentence split.
NO_WINDOW_SIZE_SPECIFIED - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
noAdditionalEventsInBetween(JCas, EventMention, EventMention) - Static method in class org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
NOCHANGE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
NOCHANGE_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
noCleartk - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
Node - Class in org.apache.ctakes.ytex.kernel.tree
Node() - Constructor for class org.apache.ctakes.ytex.kernel.tree.Node
NodeAttributeKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: Extract a node attribute and run the delegate kernel on the attribute.
NodeAttributeKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
nodeCUI - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel: id of this concept
nodeFromRow(NodeMappingInfo, Map<String, Object>) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
nodeIndex - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel
NodeKey - Class in org.apache.ctakes.ytex.kernel.tree
NodeKey(Node) - Constructor for class org.apache.ctakes.ytex.kernel.tree.NodeKey
NodeMappingInfo - Class in org.apache.ctakes.ytex.kernel.tree
NodeMappingInfo() - Constructor for class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
NodeMappingInfo(String, Set<String>) - Constructor for class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
nodeMarkable(JCas, int, int) - Static method in class org.apache.ctakes.coreference.util.MarkableTreeUtils
nodeQueryMappingInfos - Variable in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
nodeToDocument(Node) - Static method in class org.apache.ctakes.jdl.data.xml.DomUtil
nodeToStr(Node) - Static method in class org.apache.ctakes.jdl.data.xml.DomUtil
nodeType - Variable in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
nodeType - Variable in class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
nodeTypes - Variable in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
nominalAttributeMap - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: map of nominal attribute - [nominal attribute value - attribute index].
NominalAttributeValue - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
NominalAttributeValue() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue: Never called.
NominalAttributeValue(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue: Internal - constructor used by generator
NominalAttributeValue(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue
NominalAttributeValue(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue
NominalAttributeValue_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
NominalAttributeValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type: initialize variables to correspond with Cas Type and Features
nominalWordValueMap - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: nominal attribute names and values
nominalWordValueMap - Variable in class org.apache.ctakes.ytex.kernel.SparseData: nominal attribute names and values
NON_MENTION - Static variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
nonDetSubstr(String) - Static method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
NonIndicator - Class in org.apache.ctakes.drugner.fsm.output.util
NonIndicator(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.NonIndicator
NonIndicatorFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect dates in the given input of tokens.
NonIndicatorFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.NonIndicatorFSM: Constructor
NonSmokerNamedEntityAnnotation - Class in org.apache.ctakes.smokingstatus.type: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
NonSmokerNamedEntityAnnotation() - Constructor for class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation: Never called.
NonSmokerNamedEntityAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation: Internal - constructor used by generator
NonSmokerNamedEntityAnnotation(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation
NonSmokerNamedEntityAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation
NonSmokerNamedEntityAnnotation_Type - Class in org.apache.ctakes.smokingstatus.type: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
NonSmokerNamedEntityAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation_Type: initialize variables to correspond with Cas Type and Features
NonSmokerNamedEntityLookupConsumerImpl - Class in org.apache.ctakes.smokingstatus.lookup.ae: copied from edu.may.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl in the "Dictionary Lookup" project to use "NonSmokerNamedEntityAnnotation" instead of NamedEntityAnnotation
NonSmokerNamedEntityLookupConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.smokingstatus.lookup.ae.NonSmokerNamedEntityLookupConsumerImpl
NonTerminalConsumer - Interface in org.apache.ctakes.core.cc: Extends the CasConsumer interface to provide a method for getting output in XML form.
NonTerminalEndState - Class in org.apache.ctakes.core.fsm.state
NonTerminalEndState(String) - Constructor for class org.apache.ctakes.core.fsm.state.NonTerminalEndState
nonWhiteSpacePattern - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
norm - Variable in class org.apache.ctakes.utils.kernel.PolyKernel
norm - Variable in class org.apache.ctakes.ytex.kernel.tree.Node: Caching the norm externally, e.g.
normalHits - Variable in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
normalize - Variable in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
normalizedDistance(String, String) - Static method in class org.apache.ctakes.coreference.util.EditDistance
NormalizedFilesInDirectoryCasConsumer - Class in org.apache.ctakes.core.cc: For each CAS a local file with the document text is written to a directory specifed by a parameter.
NormalizedFilesInDirectoryCasConsumer() - Constructor for class org.apache.ctakes.core.cc.NormalizedFilesInDirectoryCasConsumer
normalizedLaplacian - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
normalizeEventText(JCas, Annotation) - Static method in class org.apache.ctakes.temporal.duration.Utils: Keep UMLS concepts and non-verbs intact.
normalizeName(String) - Static method in class org.apache.ctakes.assertion.cr.XMLReader: Convert Argument_CU and Related_to_CU to Argument and Related_to.
normalizeRoleName(String) - Static method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader: Convert Argument_CU and Related_to_CU to Argument and Related_to.
normalizeRoleName(String) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader: Convert Argument_CU and Related_to_CU to Argument and Related_to.
normalizers - Variable in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
normalizers - Variable in class org.apache.ctakes.utils.kernel.PolyKernel
normalizeToDomain(String) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine: Looks in the domain string (path) for meaningful corpus names
normCache - Variable in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
normCacheMap - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
normCacheMap - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
NormKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: Return norm of delegate kernel: k(x,y)/sqrt(k(x,x)*k(y,y).
NormKernel(Kernel) - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
NormKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
NOT_NEGATED - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
NOT_PRESENT - Static variable in class org.apache.ctakes.utils.env.EnvironmentVariable
noteVerb - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
NP - Class in org.apache.ctakes.typesystem.type.syntax: A noun phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.NP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
NP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.NP: Never called.
NP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NP: Internal - constructor used by generator
NP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NP
NP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NP
NP_Type - Class in org.apache.ctakes.typesystem.type.syntax: A noun phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.NP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
NP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NP_Type: initialize variables to correspond with Cas Type and Features
nPreviousClassifications - Variable in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
npv - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
nSlice - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl.SliceEvaluator
nTokensBetween - Variable in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor: Number of words between the mentions
nTokensBetween - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor: Number of words between the mentions
nTokensBetween - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor: Number of words between the mentions
nTokensBetween - Variable in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor: Number of words between the mentions
NULL_TREE - Static variable in class org.apache.ctakes.assertion.util.AssertionTreeUtils
NullAnnotator - Class in org.apache.ctakes.core.ae: This annotator does nothing.
NullAnnotator() - Constructor for class org.apache.ctakes.core.ae.NullAnnotator
nullSafeGet(ResultSet, String[], Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
nullSafeGet(ResultSet, String[], SessionImplementor, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
nullSafeSet(PreparedStatement, Object, int) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
nullSafeSet(PreparedStatement, Object, int, SessionImplementor) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
nullToEmptyString(String) - Static method in class org.apache.ctakes.ytex.dao.DBUtil
nullToEmptyString(String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl: todo for oracle need to handle empty strings differently
NUM_FIRST - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
NUM_FIRST - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
NUM_LAST - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
NUM_LAST - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
NUM_MIDDLE - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
NUM_MIDDLE - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
NUM_NONE - Static variable in interface org.apache.ctakes.core.fsm.token.WordToken
NUM_NONE - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token
NUM_OVERLAP_BITS - Variable in class org.apache.ctakes.core.ae.OverlapAnnotator
NUM_WIKI_HITS - Static variable in class org.apache.ctakes.coreference.util.SvmVectorCreator
number(Markable) - Method in class org.apache.ctakes.coreference.util.AttributeCalculator
NumberCondition - Class in org.apache.ctakes.core.fsm.condition
NumberCondition() - Constructor for class org.apache.ctakes.core.fsm.condition.NumberCondition
NumberOfEventsInTheSameSentenceExtractor - Class in org.apache.ctakes.temporal.ae.feature: Count the number of EventMentions in the same sentence as the two arguments, used for features for within sentence event-event relation discovery
NumberOfEventsInTheSameSentenceExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.NumberOfEventsInTheSameSentenceExtractor
NumberOfEventTimeBetweenCandidatesExtractor - Class in org.apache.ctakes.temporal.ae.feature: Count the number of EventMention and TimeMention in between two arguments as features
NumberOfEventTimeBetweenCandidatesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.NumberOfEventTimeBetweenCandidatesExtractor
NumberToken - Interface in org.apache.ctakes.core.fsm.token
NumberTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
NumberTokenAdapter(NumToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.NumberTokenAdapter
NumberTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter
NumberTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.NumberTokenAdapter
numCommonSubtrees(Parse, Parse) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
numDemFeats - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
numDocs - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
numericAttributeMap - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: map of numeric attribute - attribute index.
NumericAttributeValue - Class in org.apache.ctakes.smokingstatus.type.libsvm: Corresponds to the ARFF numeric attributes.
NumericAttributeValue() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue: Never called.
NumericAttributeValue(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue: Internal - constructor used by generator
NumericAttributeValue(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue
NumericAttributeValue(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue
NumericAttributeValue_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm: Corresponds to the ARFF numeric attributes.
NumericAttributeValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type: initialize variables to correspond with Cas Type and Features
numericTypes - Static variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
numericWords - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: numeric attribute labels
numericWords - Variable in class org.apache.ctakes.ytex.kernel.SparseData: numeric attribute labels
numFeatures - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
numFeatures - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
numFeatures - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
numFeatures - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
numFeatures - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
numLogs - Static variable in class org.apache.ctakes.utils.wiki.ApproximateMath
numNEFeats - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
numNgrams(Markable) - Method in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
numOfNearestNeighbors - Variable in class org.apache.ctakes.temporal.utils.SMOTEplus
numPronFeats - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
numRoots - Static variable in class org.apache.ctakes.utils.wiki.ApproximateMath
NUMTHREADS - Static variable in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
NUMTHREADS - Static variable in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
NumToken - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a number rather than a punctuation, symbol, newline, word, or contraction.
NumToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.NumToken: Never called.
NumToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NumToken: Internal - constructor used by generator
NumToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NumToken
NumToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NumToken
NumToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a number rather than a punctuation, symbol, newline, word, or contraction.
NumToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.NumToken_Type: initialize variables to correspond with Cas Type and Features
numVecs - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
numWords - Variable in class org.apache.ctakes.utils.distsem.WordVectorReader

O

O - Class in org.apache.ctakes.typesystem.type.syntax: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
O() - Constructor for class org.apache.ctakes.typesystem.type.syntax.O: Never called.
O(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.O: Internal - constructor used by generator
O(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.O
O(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.O
o1 - Variable in class org.apache.ctakes.ytex.kernel.OrderedPair
o1 - Variable in class org.apache.ctakes.ytex.kernel.Pair
o2 - Variable in class org.apache.ctakes.ytex.kernel.OrderedPair
o2 - Variable in class org.apache.ctakes.ytex.kernel.Pair
O_Type - Class in org.apache.ctakes.typesystem.type.syntax: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
O_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.O_Type: initialize variables to correspond with Cas Type and Features
ObjectFactoryBind - Class in org.apache.ctakes.jdl.data.xml.jaxb: Bind JAXB factory.
ObjectFactoryBind() - Constructor for class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind
objectFactoryMapping - Static variable in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
ObjectFactoryUtil - Class in org.apache.ctakes.jdl.data.xml.jaxb: Utility to mange JAXB factory.
ObjectFactoryUtil() - Constructor for class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil
objects - Static variable in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
ObjPair<T1,T2> - Class in org.apache.ctakes.ytex.kernel.model
ObjPair(T1, T2) - Constructor for class org.apache.ctakes.ytex.kernel.model.ObjPair
obtainCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: obtains a collection mapped with key.
obtainCollection(K) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: obtains a collection mapped with key.
obtainCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: obtains a collection mapped with key.
obtainCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: obtains a collection mapped with key.
obtainCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: obtains a collection mapped with key.
obtainCollection(K) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: obtains a collection mapped with key.
OddsRatioFeatureSelection<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Selects features via Odds Ratio statistics between the features extracted from its sub-extractor and the outcome values they are paired with in classification instances.
OddsRatioFeatureSelection(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
OddsRatioFeatureSelection(String, double) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
OddsRatioFeatureSelection(String, double, String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
OddsRatioFeatureSelection.OddsRatioScorer<OUTCOME_T> - Class in org.apache.ctakes.temporal.ae.feature.selection: Helper class for aggregating and computing mutual Odds Ratio statistics
OddsRatioFeatureSelection.OddsRatioScorer(String) - Constructor for class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
oddsRatioFunction - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
oddsRatioThreshold - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
ODIEVectorFileWriter - Class in org.apache.ctakes.coreference.cc
ODIEVectorFileWriter() - Constructor for class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
OffsetComparator - Class in org.apache.ctakes.core.nlp.tokenizer: Sorts Token objects by their offset.
OffsetComparator() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.OffsetComparator
oid - Variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
OINTMENT - Static variable in class org.apache.ctakes.drugner.elements.FormElement
ONE - Static variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
OntologyConcept - Class in org.apache.ctakes.typesystem.type.refsem: Ontologies (e.g., SNOMED-CT) provide an expert semantic representation for concepts.
OntologyConcept() - Constructor for class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: Never called.
OntologyConcept(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: Internal - constructor used by generator
OntologyConcept(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.OntologyConcept
OntologyConcept_Type - Class in org.apache.ctakes.typesystem.type.refsem: Ontologies (e.g., SNOMED-CT) provide an expert semantic representation for concepts.
OntologyConcept_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type: initialize variables to correspond with Cas Type and Features
openConnection() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection: Attempts to establish a connection.
OpenNLPPOSCollectionReader - Class in org.apache.ctakes.postagger: This collection reader reads in part-of-speech training/test data in the OpenNLP format.
OpenNLPPOSCollectionReader() - Constructor for class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader
OPT_XDL_CONN - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_CONN_DESCR - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_CONN_LONG - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_DATA - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_DATA_DESCR - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_DATA_LONG - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_LOAD - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_LOAD_DESCR - Static variable in class org.apache.ctakes.jdl.AppMain
OPT_XDL_LOAD_LONG - Static variable in class org.apache.ctakes.jdl.AppMain
optionKey - Variable in enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption
options - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
options - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
options - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
options - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
options - Static variable in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances
options - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
OR_RELATION - Static variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl
oracle - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
ORAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
ORAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
OrangeBookFilterConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: Implementation that takes Rxnorm dictionary lookup hits and stores only the ones that are also present in the Orange Book.
OrangeBookFilterConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
OrangeBookFilterConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
OrderedPair<T extends java.lang.Comparable<T>> - Class in org.apache.ctakes.ytex.kernel: simple pair class used for cache keys where the result is symmetric, e.g.
OrderedPair(T, T) - Constructor for class org.apache.ctakes.ytex.kernel.OrderedPair
org.apache.ctakes.assertion.attributes - package org.apache.ctakes.assertion.attributes
org.apache.ctakes.assertion.attributes.features - package org.apache.ctakes.assertion.attributes.features
org.apache.ctakes.assertion.attributes.features.selection - package org.apache.ctakes.assertion.attributes.features.selection
org.apache.ctakes.assertion.attributes.generic - package org.apache.ctakes.assertion.attributes.generic
org.apache.ctakes.assertion.attributes.history - package org.apache.ctakes.assertion.attributes.history
org.apache.ctakes.assertion.attributes.subject - package org.apache.ctakes.assertion.attributes.subject
org.apache.ctakes.assertion.cc - package org.apache.ctakes.assertion.cc
org.apache.ctakes.assertion.cr - package org.apache.ctakes.assertion.cr
org.apache.ctakes.assertion.eval - package org.apache.ctakes.assertion.eval
org.apache.ctakes.assertion.medfacts - package org.apache.ctakes.assertion.medfacts
org.apache.ctakes.assertion.medfacts.cleartk - package org.apache.ctakes.assertion.medfacts.cleartk
org.apache.ctakes.assertion.medfacts.cleartk.extractors - package org.apache.ctakes.assertion.medfacts.cleartk.extractors
org.apache.ctakes.assertion.medfacts.i2b2.api - package org.apache.ctakes.assertion.medfacts.i2b2.api
org.apache.ctakes.assertion.medfacts.types - package org.apache.ctakes.assertion.medfacts.types
org.apache.ctakes.assertion.pipelines - package org.apache.ctakes.assertion.pipelines
org.apache.ctakes.assertion.train - package org.apache.ctakes.assertion.train
org.apache.ctakes.assertion.util - package org.apache.ctakes.assertion.util
org.apache.ctakes.assertion.zoner.types - package org.apache.ctakes.assertion.zoner.types
org.apache.ctakes.chunker.ae - package org.apache.ctakes.chunker.ae
org.apache.ctakes.chunker.ae.adjuster - package org.apache.ctakes.chunker.ae.adjuster
org.apache.ctakes.clinicalpipeline - package org.apache.ctakes.clinicalpipeline
org.apache.ctakes.clinicalpipeline.ae - package org.apache.ctakes.clinicalpipeline.ae
org.apache.ctakes.clinicalpipeline.runtime - package org.apache.ctakes.clinicalpipeline.runtime
org.apache.ctakes.constituency.parser - package org.apache.ctakes.constituency.parser
org.apache.ctakes.constituency.parser.ae - package org.apache.ctakes.constituency.parser.ae
org.apache.ctakes.constituency.parser.treekernel - package org.apache.ctakes.constituency.parser.treekernel
org.apache.ctakes.constituency.parser.uima.co - package org.apache.ctakes.constituency.parser.uima.co
org.apache.ctakes.constituency.parser.uima.type - package org.apache.ctakes.constituency.parser.uima.type
org.apache.ctakes.constituency.parser.util - package org.apache.ctakes.constituency.parser.util
org.apache.ctakes.contexttokenizer.ae - package org.apache.ctakes.contexttokenizer.ae
org.apache.ctakes.core.ae - package org.apache.ctakes.core.ae
org.apache.ctakes.core.cc - package org.apache.ctakes.core.cc
org.apache.ctakes.core.ci - package org.apache.ctakes.core.ci
org.apache.ctakes.core.cpe - package org.apache.ctakes.core.cpe
org.apache.ctakes.core.cr - package org.apache.ctakes.core.cr
org.apache.ctakes.core.fsm.adapters - package org.apache.ctakes.core.fsm.adapters: This package contains adapters for JCas token objects comforming to the input interfaces used by the FSM project.
org.apache.ctakes.core.fsm.condition - package org.apache.ctakes.core.fsm.condition
org.apache.ctakes.core.fsm.machine - package org.apache.ctakes.core.fsm.machine
org.apache.ctakes.core.fsm.output - package org.apache.ctakes.core.fsm.output
org.apache.ctakes.core.fsm.state - package org.apache.ctakes.core.fsm.state
org.apache.ctakes.core.fsm.token - package org.apache.ctakes.core.fsm.token
org.apache.ctakes.core.fsm.token.adapter - package org.apache.ctakes.core.fsm.token.adapter
org.apache.ctakes.core.knowtator - package org.apache.ctakes.core.knowtator
org.apache.ctakes.core.nlp.tokenizer - package org.apache.ctakes.core.nlp.tokenizer
org.apache.ctakes.core.resource - package org.apache.ctakes.core.resource
org.apache.ctakes.core.sentence - package org.apache.ctakes.core.sentence
org.apache.ctakes.core.util - package org.apache.ctakes.core.util
org.apache.ctakes.coreference.ae - package org.apache.ctakes.coreference.ae
org.apache.ctakes.coreference.cc - package org.apache.ctakes.coreference.cc
org.apache.ctakes.coreference.eval.helpers - package org.apache.ctakes.coreference.eval.helpers
org.apache.ctakes.coreference.treekernel.training - package org.apache.ctakes.coreference.treekernel.training
org.apache.ctakes.coreference.type - package org.apache.ctakes.coreference.type
org.apache.ctakes.coreference.util - package org.apache.ctakes.coreference.util
org.apache.ctakes.dependency.parser - package org.apache.ctakes.dependency.parser
org.apache.ctakes.dependency.parser.ae - package org.apache.ctakes.dependency.parser.ae
org.apache.ctakes.dependency.parser.ae.util - package org.apache.ctakes.dependency.parser.ae.util
org.apache.ctakes.dependency.parser.cr - package org.apache.ctakes.dependency.parser.cr
org.apache.ctakes.dependency.parser.util - package org.apache.ctakes.dependency.parser.util
org.apache.ctakes.dictionary.assertion - package org.apache.ctakes.dictionary.assertion
org.apache.ctakes.dictionary.lookup - package org.apache.ctakes.dictionary.lookup
org.apache.ctakes.dictionary.lookup.ae - package org.apache.ctakes.dictionary.lookup.ae
org.apache.ctakes.dictionary.lookup.algorithms - package org.apache.ctakes.dictionary.lookup.algorithms
org.apache.ctakes.dictionary.lookup.filter - package org.apache.ctakes.dictionary.lookup.filter
org.apache.ctakes.dictionary.lookup.jdbc - package org.apache.ctakes.dictionary.lookup.jdbc
org.apache.ctakes.dictionary.lookup.lucene - package org.apache.ctakes.dictionary.lookup.lucene
org.apache.ctakes.dictionary.lookup.phrasebuilder - package org.apache.ctakes.dictionary.lookup.phrasebuilder
org.apache.ctakes.dictionary.lookup.strtable - package org.apache.ctakes.dictionary.lookup.strtable
org.apache.ctakes.dictionary.lookup.vo - package org.apache.ctakes.dictionary.lookup.vo
org.apache.ctakes.dictionary.lookup2.ae - package org.apache.ctakes.dictionary.lookup2.ae
org.apache.ctakes.dictionary.lookup2.concept - package org.apache.ctakes.dictionary.lookup2.concept
org.apache.ctakes.dictionary.lookup2.consumer - package org.apache.ctakes.dictionary.lookup2.consumer
org.apache.ctakes.dictionary.lookup2.dictionary - package org.apache.ctakes.dictionary.lookup2.dictionary
org.apache.ctakes.dictionary.lookup2.term - package org.apache.ctakes.dictionary.lookup2.term
org.apache.ctakes.dictionary.lookup2.textspan - package org.apache.ctakes.dictionary.lookup2.textspan
org.apache.ctakes.dictionary.lookup2.util - package org.apache.ctakes.dictionary.lookup2.util
org.apache.ctakes.dictionary.lookup2.util.collection - package org.apache.ctakes.dictionary.lookup2.util.collection
org.apache.ctakes.drugner - package org.apache.ctakes.drugner
org.apache.ctakes.drugner.ae - package org.apache.ctakes.drugner.ae
org.apache.ctakes.drugner.ae.impl - package org.apache.ctakes.drugner.ae.impl
org.apache.ctakes.drugner.cc - package org.apache.ctakes.drugner.cc
org.apache.ctakes.drugner.elements - package org.apache.ctakes.drugner.elements
org.apache.ctakes.drugner.fsm.elements.conditions - package org.apache.ctakes.drugner.fsm.elements.conditions
org.apache.ctakes.drugner.fsm.machines.elements - package org.apache.ctakes.drugner.fsm.machines.elements
org.apache.ctakes.drugner.fsm.machines.util - package org.apache.ctakes.drugner.fsm.machines.util
org.apache.ctakes.drugner.fsm.output.elements - package org.apache.ctakes.drugner.fsm.output.elements
org.apache.ctakes.drugner.fsm.output.util - package org.apache.ctakes.drugner.fsm.output.util
org.apache.ctakes.drugner.fsm.states.util - package org.apache.ctakes.drugner.fsm.states.util
org.apache.ctakes.drugner.type - package org.apache.ctakes.drugner.type
org.apache.ctakes.examples.ae - package org.apache.ctakes.examples.ae
org.apache.ctakes.examples.pipelines - package org.apache.ctakes.examples.pipelines
org.apache.ctakes.jdl - package org.apache.ctakes.jdl: Copied from https://code.google.com/p/jdl-prj/ Following modifications: fixed batch insert support specification of tab as delimiter disable text encapsulators by defalt in CsvLoader change package names
org.apache.ctakes.jdl.common - package org.apache.ctakes.jdl.common: Common utility.
org.apache.ctakes.jdl.data.base - package org.apache.ctakes.jdl.data.base: Database.
org.apache.ctakes.jdl.data.loader - package org.apache.ctakes.jdl.data.loader: Loader of data.
org.apache.ctakes.jdl.data.xml - package org.apache.ctakes.jdl.data.xml: XML data.
org.apache.ctakes.jdl.data.xml.jaxb - package org.apache.ctakes.jdl.data.xml.jaxb: JAXB utility.
org.apache.ctakes.lvg.ae - package org.apache.ctakes.lvg.ae
org.apache.ctakes.lvg.resource - package org.apache.ctakes.lvg.resource
org.apache.ctakes.necontexts - package org.apache.ctakes.necontexts
org.apache.ctakes.necontexts.negation - package org.apache.ctakes.necontexts.negation
org.apache.ctakes.necontexts.status - package org.apache.ctakes.necontexts.status
org.apache.ctakes.postagger - package org.apache.ctakes.postagger
org.apache.ctakes.preprocessor - package org.apache.ctakes.preprocessor
org.apache.ctakes.preprocessor.ae - package org.apache.ctakes.preprocessor.ae
org.apache.ctakes.preprocessor.test - package org.apache.ctakes.preprocessor.test
org.apache.ctakes.relationextractor.ae - package org.apache.ctakes.relationextractor.ae
org.apache.ctakes.relationextractor.ae.baselines - package org.apache.ctakes.relationextractor.ae.baselines
org.apache.ctakes.relationextractor.ae.features - package org.apache.ctakes.relationextractor.ae.features
org.apache.ctakes.relationextractor.data - package org.apache.ctakes.relationextractor.data
org.apache.ctakes.relationextractor.data.analysis - package org.apache.ctakes.relationextractor.data.analysis
org.apache.ctakes.relationextractor.eval - package org.apache.ctakes.relationextractor.eval
org.apache.ctakes.relationextractor.knowtator - package org.apache.ctakes.relationextractor.knowtator
org.apache.ctakes.relationextractor.pipelines - package org.apache.ctakes.relationextractor.pipelines
org.apache.ctakes.sideeffect.ae - package org.apache.ctakes.sideeffect.ae
org.apache.ctakes.sideeffect.cc - package org.apache.ctakes.sideeffect.cc
org.apache.ctakes.sideeffect.type - package org.apache.ctakes.sideeffect.type
org.apache.ctakes.sideeffect.util - package org.apache.ctakes.sideeffect.util
org.apache.ctakes.smokingstatus - package org.apache.ctakes.smokingstatus
org.apache.ctakes.smokingstatus.ae - package org.apache.ctakes.smokingstatus.ae
org.apache.ctakes.smokingstatus.cc - package org.apache.ctakes.smokingstatus.cc
org.apache.ctakes.smokingstatus.context - package org.apache.ctakes.smokingstatus.context
org.apache.ctakes.smokingstatus.context.negation - package org.apache.ctakes.smokingstatus.context.negation
org.apache.ctakes.smokingstatus.i2b2.type - package org.apache.ctakes.smokingstatus.i2b2.type
org.apache.ctakes.smokingstatus.lookup.ae - package org.apache.ctakes.smokingstatus.lookup.ae
org.apache.ctakes.smokingstatus.machine - package org.apache.ctakes.smokingstatus.machine
org.apache.ctakes.smokingstatus.MLutil - package org.apache.ctakes.smokingstatus.MLutil
org.apache.ctakes.smokingstatus.patientLevel - package org.apache.ctakes.smokingstatus.patientLevel
org.apache.ctakes.smokingstatus.type - package org.apache.ctakes.smokingstatus.type
org.apache.ctakes.smokingstatus.type.libsvm - package org.apache.ctakes.smokingstatus.type.libsvm
org.apache.ctakes.smokingstatus.util - package org.apache.ctakes.smokingstatus.util
org.apache.ctakes.template.filler.ae - package org.apache.ctakes.template.filler.ae
org.apache.ctakes.temporal.ae - package org.apache.ctakes.temporal.ae
org.apache.ctakes.temporal.ae.baselines - package org.apache.ctakes.temporal.ae.baselines
org.apache.ctakes.temporal.ae.feature - package org.apache.ctakes.temporal.ae.feature
org.apache.ctakes.temporal.ae.feature.duration - package org.apache.ctakes.temporal.ae.feature.duration
org.apache.ctakes.temporal.ae.feature.selection - package org.apache.ctakes.temporal.ae.feature.selection
org.apache.ctakes.temporal.ae.feature.treekernel - package org.apache.ctakes.temporal.ae.feature.treekernel
org.apache.ctakes.temporal.data.analysis - package org.apache.ctakes.temporal.data.analysis
org.apache.ctakes.temporal.duration - package org.apache.ctakes.temporal.duration
org.apache.ctakes.temporal.eval - package org.apache.ctakes.temporal.eval
org.apache.ctakes.temporal.pipelines - package org.apache.ctakes.temporal.pipelines
org.apache.ctakes.temporal.utils - package org.apache.ctakes.temporal.utils
org.apache.ctakes.typesystem.type.constants - package org.apache.ctakes.typesystem.type.constants
org.apache.ctakes.typesystem.type.refsem - package org.apache.ctakes.typesystem.type.refsem
org.apache.ctakes.typesystem.type.relation - package org.apache.ctakes.typesystem.type.relation
org.apache.ctakes.typesystem.type.structured - package org.apache.ctakes.typesystem.type.structured
org.apache.ctakes.typesystem.type.syntax - package org.apache.ctakes.typesystem.type.syntax
org.apache.ctakes.typesystem.type.temporary.assertion - package org.apache.ctakes.typesystem.type.temporary.assertion
org.apache.ctakes.typesystem.type.textsem - package org.apache.ctakes.typesystem.type.textsem
org.apache.ctakes.typesystem.type.textspan - package org.apache.ctakes.typesystem.type.textspan
org.apache.ctakes.typesystem.type.util - package org.apache.ctakes.typesystem.type.util
org.apache.ctakes.utils.build - package org.apache.ctakes.utils.build
org.apache.ctakes.utils.distsem - package org.apache.ctakes.utils.distsem
org.apache.ctakes.utils.env - package org.apache.ctakes.utils.env
org.apache.ctakes.utils.kernel - package org.apache.ctakes.utils.kernel
org.apache.ctakes.utils.struct - package org.apache.ctakes.utils.struct
org.apache.ctakes.utils.test - package org.apache.ctakes.utils.test
org.apache.ctakes.utils.tree - package org.apache.ctakes.utils.tree
org.apache.ctakes.utils.wiki - package org.apache.ctakes.utils.wiki
org.apache.ctakes.utils.xcas_comparison - package org.apache.ctakes.utils.xcas_comparison
org.apache.ctakes.ytex - package org.apache.ctakes.ytex
org.apache.ctakes.ytex.dao - package org.apache.ctakes.ytex.dao
org.apache.ctakes.ytex.kernel - package org.apache.ctakes.ytex.kernel
org.apache.ctakes.ytex.kernel.dao - package org.apache.ctakes.ytex.kernel.dao
org.apache.ctakes.ytex.kernel.evaluator - package org.apache.ctakes.ytex.kernel.evaluator
org.apache.ctakes.ytex.kernel.metric - package org.apache.ctakes.ytex.kernel.metric
org.apache.ctakes.ytex.kernel.model - package org.apache.ctakes.ytex.kernel.model
org.apache.ctakes.ytex.kernel.pagerank - package org.apache.ctakes.ytex.kernel.pagerank
org.apache.ctakes.ytex.kernel.tree - package org.apache.ctakes.ytex.kernel.tree
org.apache.ctakes.ytex.kernel.wsd - package org.apache.ctakes.ytex.kernel.wsd
org.apache.ctakes.ytex.libsvm - package org.apache.ctakes.ytex.libsvm
org.apache.ctakes.ytex.R - package org.apache.ctakes.ytex.R
org.apache.ctakes.ytex.semil - package org.apache.ctakes.ytex.semil
org.apache.ctakes.ytex.sparsematrix - package org.apache.ctakes.ytex.sparsematrix
org.apache.ctakes.ytex.svmlight - package org.apache.ctakes.ytex.svmlight
org.apache.ctakes.ytex.tools - package org.apache.ctakes.ytex.tools
org.apache.ctakes.ytex.tools.docanalyzer - package org.apache.ctakes.ytex.tools.docanalyzer
org.apache.ctakes.ytex.uima - package org.apache.ctakes.ytex.uima
org.apache.ctakes.ytex.uima.annotators - package org.apache.ctakes.ytex.uima.annotators
org.apache.ctakes.ytex.uima.dao - package org.apache.ctakes.ytex.uima.dao
org.apache.ctakes.ytex.uima.lookup.ae - package org.apache.ctakes.ytex.uima.lookup.ae
org.apache.ctakes.ytex.uima.mapper - package org.apache.ctakes.ytex.uima.mapper
org.apache.ctakes.ytex.uima.model - package org.apache.ctakes.ytex.uima.model
org.apache.ctakes.ytex.uima.resource - package org.apache.ctakes.ytex.uima.resource
org.apache.ctakes.ytex.uima.types - package org.apache.ctakes.ytex.uima.types
org.apache.ctakes.ytex.umls.dao - package org.apache.ctakes.ytex.umls.dao
org.apache.ctakes.ytex.umls.model - package org.apache.ctakes.ytex.umls.model
org.apache.ctakes.ytex.web.search - package org.apache.ctakes.ytex.web.search
org.apache.ctakes.ytex.weka - package org.apache.ctakes.ytex.weka
org.apache.ctakes.ytex.ws - package org.apache.ctakes.ytex.ws
organizeByOffset(Iterator<LookupHit>) - Static method in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl: Organizes the LookupHit objects by begin and end offsets.
OTHER - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
OTHER - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
OTHER_DEPPATH - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
OTHER_DEPTOK - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
OTHER_OR - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
OTHER_SRLARG - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
OTHER_TOKEN - Static variable in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
OtherDesig - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
otherVerb - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
out - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
out - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
out - Variable in class org.apache.ctakes.constituency.parser.uima.co.ParserTreeWriterConsumer
out - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
OUTCOME1 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
OUTCOME2 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
OUTCOME3 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
outdir - Variable in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: directory to export files to, with trailing separator added on if necessary
outFile - Variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation.Options
outFile - Variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
outFile - Variable in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
outputDir - Variable in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances.Options
outputDir - Variable in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
outputDir - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
outputDir - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML
outputDir - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML
outputDirectory - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
outputDirectory - Variable in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.SerializeDocumentToXMI
outputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline.Options
outputDirectoryName - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
outputFile - Variable in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
outputFile - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
outputFile - Static variable in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
outputFile - Variable in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.RelationContextPrinter
outputFile - Variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.Options
outputFile - Variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
outputFile - Variable in class org.apache.ctakes.temporal.duration.EventEventDurationStatistics.AnalyseRelationArgumentDuration
outputFile - Variable in class org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.AnalyseRelationArgumentDuration
outputFile - Variable in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
outputFilePath - Variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
outputGramMatrix(double[][], SortedSet<Long>, String) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
outputInstanceData(InstanceData, String) - Method in interface org.apache.ctakes.ytex.sparsematrix.InstanceDataExporter
outputInstanceData(InstanceData, String, String, String, String, boolean) - Method in interface org.apache.ctakes.ytex.sparsematrix.InstanceDataExporter
outputInstanceData(InstanceData, String) - Method in class org.apache.ctakes.ytex.sparsematrix.InstanceDataExporterImpl
outputInstanceData(InstanceData, String, String, String, String, boolean) - Method in class org.apache.ctakes.ytex.sparsematrix.InstanceDataExporterImpl
outputInstanceIds(String, SortedMap<Integer, Map<String, Integer>>, String) - Method in interface org.apache.ctakes.ytex.libsvm.LibSVMUtil
outputInstanceIds(String, SortedMap<Integer, Map<String, Integer>>, String) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl
outputRoot - Variable in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.Options
outputRoot - Variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors.Options
outputSentenceTokens(String, Iterable<String>) - Method in class org.apache.ctakes.core.cc.SentenceTokensPrinter
OV - Static variable in interface org.apache.ctakes.temporal.utils.TimeRelationConstants
overlap(int[], int[]) - Static method in class org.apache.ctakes.coreference.eval.helpers.Span
OVERLAP_A_ENV_B - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator: A completely envelopes B
OVERLAP_B_ENV_A - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator: B completely envelopes A
OVERLAP_EXACT - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator: A and B have identical offsets
OVERLAP_NONE - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator: No overlap at all between A and B
OVERLAP_PARTIAL - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator: A and B only partially overlap
OverlapAnnotator - Class in org.apache.ctakes.core.ae
OverlapAnnotator() - Constructor for class org.apache.ctakes.core.ae.OverlapAnnotator
OverlapAnnotator.Action - Interface in org.apache.ctakes.core.ae: Generic interface for performing an action if the overlap constraint is met between annotations A and B.
OverlapAnnotator.DeleteActionImpl - Class in org.apache.ctakes.core.ae: Implementation that deletes either the A, B, or both.
OverlapAnnotator.DeleteActionImpl(byte) - Constructor for class org.apache.ctakes.core.ae.OverlapAnnotator.DeleteActionImpl
OverlapAnnotator.ModifyActionImpl - Class in org.apache.ctakes.core.ae: Implementation that modifies feature values of either annotation A or B.
OverlapAnnotator.ModifyActionImpl(byte, byte, byte) - Constructor for class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
OverlapJCasTermAnnotator - Class in org.apache.ctakes.dictionary.lookup2.ae: Checks for terms that overlap a window.
OverlapJCasTermAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
OverlappedHeadFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature: Extract the overlapping head words of two arguments.
OverlappedHeadFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.OverlappedHeadFeaturesExtractor

P

p1 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
p2 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
p3 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
pagerankIter(double[], Map<Integer, Double>, ConceptGraph, double, double, Set<Integer>) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
pagerankIter(double[], Map<Integer, Double>, ConceptGraph, double, double) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
pagerankIter(Map<Integer, Double>, Map<Integer, Double>, ConceptGraph, double, double) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl: perform one iteration of pagerank
PageRankMetric - Class in org.apache.ctakes.ytex.kernel.metric
PageRankMetric(ConceptSimilarityService, PageRankService) - Constructor for class org.apache.ctakes.ytex.kernel.metric.PageRankMetric
pageRankService - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
pageRankService - Variable in class org.apache.ctakes.ytex.kernel.metric.PageRankMetric
PageRankService - Interface in org.apache.ctakes.ytex.kernel.pagerank
PageRankServiceImpl - Class in org.apache.ctakes.ytex.kernel.pagerank
PageRankServiceImpl() - Constructor for class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
Pair - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
Pair() - Constructor for class org.apache.ctakes.coreference.type.Pair: Never called.
Pair(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.Pair: Internal - constructor used by generator
Pair(JCas) - Constructor for class org.apache.ctakes.coreference.type.Pair
Pair - Class in org.apache.ctakes.typesystem.type.util: An Attribute-Value tuple.
Pair() - Constructor for class org.apache.ctakes.typesystem.type.util.Pair: Never called.
Pair(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.util.Pair: Internal - constructor used by generator
Pair(JCas) - Constructor for class org.apache.ctakes.typesystem.type.util.Pair
Pair<T> - Class in org.apache.ctakes.ytex.kernel: simple object pair implementation
Pair(T, T) - Constructor for class org.apache.ctakes.ytex.kernel.Pair
PAIR_CONCEPT_FACTORY_NAME - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
PAIR_DICTIONARY_NAME - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: pairings must have specified dictionaries and concept factories
Pair_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
Pair_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.Pair_Type: initialize variables to correspond with Cas Type and Features
Pair_Type - Class in org.apache.ctakes.typesystem.type.util: An Attribute-Value tuple.
Pair_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.util.Pair_Type: initialize variables to correspond with Cas Type and Features
PairAttributeCalculator - Class in org.apache.ctakes.coreference.util
PairAttributeCalculator(JCas, Markable, Markable) - Constructor for class org.apache.ctakes.coreference.util.PairAttributeCalculator
Pairs - Class in org.apache.ctakes.typesystem.type.util: A brute force "hash" that stores multiple Pairs in a list.
Pairs() - Constructor for class org.apache.ctakes.typesystem.type.util.Pairs: Never called.
Pairs(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.util.Pairs: Internal - constructor used by generator
Pairs(JCas) - Constructor for class org.apache.ctakes.typesystem.type.util.Pairs
PAIRS_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
Pairs_Type - Class in org.apache.ctakes.typesystem.type.util: A brute force "hash" that stores multiple Pairs in a list.
Pairs_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.util.Pairs_Type: initialize variables to correspond with Cas Type and Features
PairType - Enum in org.apache.ctakes.coreference.eval.helpers
PairType() - Constructor for enum org.apache.ctakes.coreference.eval.helpers.PairType
pAlgo - Static variable in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser
Paragraph - Class in org.apache.ctakes.typesystem.type.textspan: A text span corresponding to a paragraph, typically containing multiple sentences.
Paragraph() - Constructor for class org.apache.ctakes.typesystem.type.textspan.Paragraph: Never called.
Paragraph(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Paragraph: Internal - constructor used by generator
Paragraph(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Paragraph
Paragraph(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Paragraph
PARAGRAPH_PATTERN - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change split paragraphs on this pattern
Paragraph_Type - Class in org.apache.ctakes.typesystem.type.textspan: A text span corresponding to a paragraph, typically containing multiple sentences.
Paragraph_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Paragraph_Type: initialize variables to correspond with Cas Type and Features
paragraphPattern - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change
param1 - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
param1 - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
param1 - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
param1 - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
param2 - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
param2 - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
param2 - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
param2 - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
PARAM_ALLOWED_CLASSES - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Name of configuration parameter that determines the allowed Classification values.
PARAM_ANAFORA_DIRECTORY - Static variable in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
PARAM_ANAFORA_XML_SUFFIXES - Static variable in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
PARAM_ANNOTATION_CLASSES - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyFromGold
PARAM_ANNOTATION_TYPE - Static variable in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl: Specifies the parameter AnnotationType to iterate on, specified in the descriptor file.
PARAM_CHUNK_PATTERN - Static variable in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: The pattern of chunks that trigger an adjustment.
PARAM_CHUNKER_CREATOR_CLASS - Static variable in class org.apache.ctakes.chunker.ae.Chunker
PARAM_CHUNKER_MODEL_FILE - Static variable in class org.apache.ctakes.chunker.ae.Chunker
PARAM_CLASSIFY_BOTH_DIRECTIONS - Static variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
PARAM_CMD_CACHE_FILE - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_COMMENT - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
PARAM_COMMENT_STRING - Static variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader: Optional parameter specifies a comment string.
PARAM_DB_CONN_RESRC - Static variable in class org.apache.ctakes.core.cc.AbstractJdbcWriter
PARAM_DB_CONN_RESRC - Static variable in class org.apache.ctakes.core.cr.JdbcCollectionReader: Name of external resource for database connection.
PARAM_DELIMITER - Static variable in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
PARAM_DELIMITER - Static variable in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
PARAM_DELIMITER - Static variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: The name of the parameter that is specifies the delimiter for the output file.
PARAM_DEST_CLASS - Static variable in class org.apache.ctakes.core.ae.CopyAnnotator
PARAM_DOCID_COLS - Static variable in class org.apache.ctakes.core.cr.JdbcCollectionReader: Optional parameter.
PARAM_DOCID_DELIMITER - Static variable in class org.apache.ctakes.core.cr.JdbcCollectionReader: Optional parameter.
PARAM_DOCTEXT_COL - Static variable in class org.apache.ctakes.core.cr.JdbcCollectionReader: Name of column from resultset that contains the document text.
PARAM_DRIVER_CLASS - Static variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl: JDBC driver ClassName.
PARAM_DRIVER_CLASS - Static variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl: JDBC driver ClassName.
PARAM_DTD_FILE - Static variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
PARAM_ENCODING - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Name of configuration parameter that contains the character encoding used by the input files.
PARAM_ENCODING - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader: Name of configuration parameter that contains the character encoding used by the input files.
PARAM_EXC_TAGS_PRP - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: optional part of speech tags for tokens that should not be used for lookup
PARAM_EXCLUSION_WORDS - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_EXTEND_TO_INCLUDE_TOKEN - Static variable in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: The index of the token (within the pattern) to extend the end offset to include.
PARAM_EXTENSIONS - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Name of optional configuration parameter that specifies the extensions of the files that the collection reader will read.
PARAM_EXTENSIONS - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader: Name of optional configuration parameter that specifies the extensions of the files that the collection reader will read.
PARAM_FAILUNKNOWN - Static variable in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes: Name of the configuration parameter that must be set to indicate if the execution fails if an encountered type is unknown
PARAM_FAILUNKNOWN - Static variable in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes: Name of the configuration parameter that must be set to indicate if the execution fails if an encountered type is unknown
PARAM_FEATURE_CONFIG - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_FEATURE_SELECTION_THRESHOLD - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_FEATURE_SELECTION_THRESHOLD - Static variable in class org.apache.ctakes.temporal.ae.EventAnnotator
PARAM_FEATURE_SELECTION_THRESHOLD - Static variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
PARAM_FEATURE_SELECTION_URI - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_FEATURE_SELECTION_URI - Static variable in class org.apache.ctakes.temporal.ae.EventAnnotator
PARAM_FEATURE_SELECTION_URI - Static variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
PARAM_FIELD_SEPERATOR - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
PARAM_FILES - Static variable in class org.apache.ctakes.assertion.eval.XMIReader
PARAM_FILES - Static variable in class org.apache.ctakes.core.cr.TextReader
PARAM_FILES - Static variable in class org.apache.ctakes.core.cr.XMIReader
PARAM_FILES - Static variable in class org.apache.ctakes.dependency.parser.ae.util.XMIReader
PARAM_FILES - Static variable in class org.apache.ctakes.relationextractor.eval.XMIReader
PARAM_FNMATCH - Static variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
PARAM_FRAGS - Static variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
PARAM_GOLD_DIR - Static variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
PARAM_GOLD_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveNonUMLSEvents
PARAM_GOLD_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveNonUMLSEvents
PARAM_GOLD_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveNonUMLSEtEvents
PARAM_GOLD_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations
PARAM_GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_GOLDVIEW_NAME - Static variable in class org.apache.ctakes.temporal.eval.RemoveTreeAlignedMentions
PARAM_HYPHEN_FILE - Static variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
PARAM_ID_DELIMETER - Static variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader: Name of optional configuration parameter that specifies a character (or string) that delimits the id of the document from the text of the document.
PARAM_IGNORE_BLANK_LINES - Static variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader: Optional parameter determines whether a blank line will be processed as a document or will be ignored.
PARAM_IGNORE_SECTIONS - Static variable in class org.apache.ctakes.sideeffect.ae.PSESentenceAnnotator
PARAM_IGNORE_SECTIONS - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Sections NOT to be entered in ClassifiableEntries
PARAM_IGNORE_WORDS - Static variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster: The list of words ("and" "&") to ignore in pattern matching.
PARAM_INPUT_DIR - Static variable in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
PARAM_INPUT_FILE - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
PARAM_INPUT_FILE_NAME - Static variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader: This parameter will be used the descriptor file to specify the location of the file that will be run through this collection reader.
PARAM_INPUTDIR - Static variable in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
PARAM_INPUTDIR - Static variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
PARAM_INPUTDIR - Static variable in class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes: Name of configuration parameter that must be set to the path of a directory containing the XMI files.
PARAM_INPUTDIR - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Name of configuration parameter that must be set to the path of a directory containing input files.
PARAM_INPUTDIR - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader: Name of configuration parameter that must be set to the path of a directory containing input files.
PARAM_INPUTDIR - Static variable in class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes: Name of configuration parameter that must be set to the path of a directory containing the XMI files.
PARAM_ISOLATION - Static variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl: Transaction isolation level.
PARAM_ISOLATION - Static variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl: Transaction isolation level.
PARAM_KEEP_ALIVE - Static variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl: Flag that determines whether to keep JDBC connection open no matter what.
PARAM_KEEP_ALIVE - Static variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl: Flag that determines whether to keep JDBC connection open no matter what.
PARAM_KNOWTATOR_XML_DIRECTORY - Static variable in class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
PARAM_LANGUAGE - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Name of optional configuration parameter that contains the language of the documents in the input directory.
PARAM_LANGUAGE - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader: Name of optional configuration parameter that contains the language of the documents in the input directory.
PARAM_LANGUAGE - Static variable in class org.apache.ctakes.core.cr.LinesFromFileCollectionReader: Name of optional configuration parameter that contains the language of the documents in the input directory.
PARAM_LEMMA_CACHE_FILE_LOCATION - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator: Value is "LemmaCacheFileLocation".
PARAM_LEMMA_CACHE_FILE_LOCATION - Static variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Value is "LemmaCacheFileLocation".
PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator: Value is "LemmaCacheFrequencyCutoff".
PARAM_LEMMA_CACHE_FREQUENCY_CUTOFF - Static variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Value is "LemmaCacheFrequencyCutoff".
PARAM_LEMMA_FREQ_CUTOFF - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_LEMMATIZER_DATA_FILE - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
PARAM_LEMMATIZER_DATA_FILE - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
PARAM_LVGCMDAPI_RESRC_KEY - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_MAP_THYME - Static variable in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
PARAM_METHOD_MAP - Static variable in class org.apache.ctakes.core.ae.CopyAnnotator
PARAM_MIN_SPAN_PRP - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: optional minimum span for tokens that should not be used for lookup
PARAM_MODEL_FILENAME - Static variable in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
PARAM_NAME_DECODING_INPUT_DIRECTORY - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
PARAM_NAME_DECODING_OUTPUT_DIRECTORY - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
PARAM_NAME_MODEL_DIRECTORY - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
PARAM_NAME_TRAINING_INPUT_DIRECTORY - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
PARAM_NUMREADS - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads: Arguement to equate to # of times it should read the files.
PARAM_OUTFILE - Static variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
PARAM_OUTPUT_DIR - Static variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
PARAM_OUTPUT_DIR - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML
PARAM_OUTPUT_DIR - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML
PARAM_OUTPUT_DIRECTORY - Static variable in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.SerializeDocumentToXMI
PARAM_OUTPUT_DIRECTORY_NAME - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances: The parameter name for the configuration parameter that specifies the output directory
PARAM_OUTPUT_FILE - Static variable in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
PARAM_OUTPUT_FILE - Static variable in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
PARAM_OUTPUT_FILE - Static variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: The name of the parameter that is specifies the path of the output file.
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.core.cc.FilesInDirectoryCasConsumer
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.core.cc.NormalizedFilesInDirectoryCasConsumer
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.core.cc.SentenceTokensPrinter
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.core.cc.TokenOffsetsCasConsumer
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes: Name of configuration parameter that must be set to the path of a directory into which the output files will be written.
PARAM_OUTPUTDIR - Static variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
PARAM_PARSE_SECTIONS - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Name of configuration parameter that determines whether section headers will be parsed out and Segments made to cover the section text.
PARAM_PARSER_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
PARAM_PARSER_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
PARAM_PARSERMODEL - Static variable in class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
PARAM_PASSWORD - Static variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl: Password for db authentication.
PARAM_PASSWORD - Static variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl: Password for db authentication.
PARAM_PORTION_OF_DATA_TO_USE - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_POS_MODEL_FILE - Static variable in class org.apache.ctakes.postagger.POSTagger
PARAM_POS_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
PARAM_POST_LEMMAS - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator: Value is "PostLemmas".
PARAM_POST_LEMMAS - Static variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Value is "PostLemmas".
PARAM_PRED_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
PARAM_PREFIX - Static variable in class org.apache.ctakes.core.util.CtakesFileNamer: The parameter name for the configuration parameter that specifies a fixed prefix for all returned file names.
PARAM_PRINT_ANN - Static variable in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
PARAM_PRINT_ERRORS - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE - Static variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE - Static variable in class org.apache.ctakes.temporal.ae.EventAnnotator
PARAM_PROBABILITY_OF_KEEPING_DEFAULT_EXAMPLE - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
PARAM_RECURSE - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
PARAM_RECURSE - Static variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.Overlap2Contains
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveEventEventRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveEventEventRelations
PARAM_RELATION_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations
PARAM_ROLE_MODEL_FILE_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
PARAM_SAVE_ANN - Static variable in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
PARAM_SD_MODEL_FILE - Static variable in class org.apache.ctakes.core.ae.SentenceDetector
PARAM_SECTIONS_FILE - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
PARAM_SEGMENT_ID - Static variable in class org.apache.ctakes.core.ae.SimpleSegmentAnnotator
PARAM_SEGMENTS_MEDICATION_RELATED - Static variable in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: This identifies the section ids that will be considered in generating DrugMentionAnnotaitons
PARAM_SEGMENTS_TO_SKIP - Static variable in class org.apache.ctakes.core.ae.SentenceDetector: Value is "SegmentsToSkip".
PARAM_SEGMENTS_TO_SKIP - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator: Value is "SegmentsToSkip".
PARAM_SEGMENTS_TO_SKIP - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB: Value is "SegmentsToSkip".
PARAM_SEGMENTS_TO_SKIP - Static variable in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator: Value is "sectionOverrideSet".
PARAM_SEGMENTS_TO_SKIP - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: Value is "SegmentsToSkip".
PARAM_SEMDIR - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
PARAM_SENTENCE_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations
PARAM_SENTENCE_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations
PARAM_SENTENCE_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations
PARAM_SENTENCE_VIEW - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations
PARAM_SET_DEFAULTS - Static variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
PARAM_SET_DEFAULTS - Static variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
PARAM_SKIP_SEGMENTS - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_SMOKING_STATUS_DESC_STEP1KEY - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Name of configuration parameter that must be set to the filepath of the UIMA descriptor ProductionPostSentenceAggregate.xml
PARAM_SMOKING_STATUS_DESC_STEP2KEY - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
PARAM_SMOTE_NUM_NEIGHBORS - Static variable in class org.apache.ctakes.temporal.ae.EventAnnotator
PARAM_SMOTE_NUM_NEIGHBORS - Static variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
PARAM_SOURCE_CLASS - Static variable in class org.apache.ctakes.core.ae.CopyAnnotator
PARAM_SQL - Static variable in class org.apache.ctakes.core.cr.JdbcCollectionReader: SQL statement to retrieve the document.
PARAM_STOPS - Static variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
PARAM_SUFFIX - Static variable in class org.apache.ctakes.core.util.CtakesFileNamer: The parameter name for the configuration parameter that specifies a fixed suffix for all returned file names.
PARAM_TEXT_DIRECTORY - Static variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
PARAM_TEXT_DIRECTORY - Static variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
PARAM_TIMEX_VIEW - Static variable in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
PARAM_TIMEX_VIEW - Static variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
PARAM_TIMEX_VIEW - Static variable in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
PARAM_TIMEX_VIEW - Static variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
PARAM_TREES - Static variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
PARAM_TRUTH_FILE - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Name of configuration parameter that must be set to the filepath of the delimited truth file.
PARAM_TRUTH_FILE_DELIMITER - Static variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Name of configuration parameter that describes the character delimiter used in the delimited truth file.
PARAM_URL - Static variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl: JDBC URL that specifies db network location and db name.
PARAM_URL - Static variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl: JDBC URL that specifies db network location and db name.
PARAM_USE_CMD_CACHE - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_USE_LEMMA_CACHE - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator: Value is "UseLemmaCache".
PARAM_USE_LEMMA_CACHE - Static variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Value is "UseLemmaCache".
PARAM_USE_LEMMATIZER - Static variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
PARAM_USE_SEGMENTS - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
PARAM_USERNAME - Static variable in class org.apache.ctakes.core.resource.JdbcConnectionResourceImpl: Username for db authentication.
PARAM_USERNAME - Static variable in class org.apache.ctakes.ytex.uima.resource.InitableJdbcConnectionResourceImpl: Username for db authentication.
PARAM_VALUE_FILE_RESRC - Static variable in class org.apache.ctakes.core.cr.JdbcCollectionReader: Optional parameter.
PARAM_VECTOR_TABLE - Static variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate
PARAM_VECTORS - Static variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
PARAM_WINDOW_ANNOT_PRP - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: specifies the type of window to use for lookup
PARAM_WORD_FREQ_FILE - Static variable in class org.apache.ctakes.core.cc.TokenFreqCasConsumer: The name of the parameter that is specifies the path of the output file in the descriptor file.
PARAM_WORDS_IN_PATTERN - Static variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster: The list of words ("none", "no", etc) used in the pattern
PARAM_XMI_DIRECTORY - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader
PARAM_XMI_DIRECTORY - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIWriter
PARAM_XML_SCHEME_NAME - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances: The parameter name for the configuration parameter that provides the name of the XML scheme to use.
PARAM_XT_MAP - Static variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
parameterGrid(List<String>, Object...) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil: recursively generate parameter grid
parameterSettings - Variable in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
ParameterSettings - Class in org.apache.ctakes.relationextractor.eval: Holds a set of parameters for a relation extraction model
ParameterSettings(Class<? extends <any>>, Object[], String[]) - Constructor for class org.apache.ctakes.relationextractor.eval.ParameterSettings
ParameterSettings(Class<? extends <any>>, String[]) - Constructor for class org.apache.ctakes.relationextractor.eval.ParameterSettings
parameterSettings - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
params - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
ParamUtil - Class in org.apache.ctakes.core.util
ParamUtil() - Constructor for class org.apache.ctakes.core.util.ParamUtil
parent - Variable in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
parent - Variable in class org.apache.ctakes.utils.tree.SimpleTree
parentAnnoBaseId - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
parentAnnotationId - Variable in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
parentConceptEvalThreshold - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
parentConceptTopThreshold - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
ParentPtrTree - Class in org.apache.ctakes.coreference.util
ParentPtrTree(int) - Constructor for class org.apache.ctakes.coreference.util.ParentPtrTree
ParentPtrTree(int[][]) - Constructor for class org.apache.ctakes.coreference.util.ParentPtrTree
parents - Variable in class org.apache.ctakes.coreference.util.ParentPtrTree
parents - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel: parents of this concept
parentsArray - Variable in class org.apache.ctakes.ytex.kernel.model.ConcRel: for java object serialization, need to avoid default serializer behavior of writing out entire object graph.
parentTag - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
parentUimaTypeId - Variable in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
parse(URI) - Method in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
parse(JCas, String) - Static method in class org.apache.ctakes.core.util.DateParser: First try parsing full date (month, day and year) using java.util.Date If that fails, try extracting at least part of the date
parse() - Method in class org.apache.ctakes.jdl.data.xml.DomParser: DOM parser.
parse() - Method in class org.apache.ctakes.jdl.data.xml.SaxParser: SAX Parser.
parse(String) - Method in class org.apache.ctakes.jdl.data.xml.SaxParser
parseBsvFile(File) - Static method in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory: Create a collection of RareWordTermMapCreator.CuiTerm Objects by parsing a bsv file.
parseBsvFile(File) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary: Create a collection of RareWordTermMapCreator.CuiTerm Objects by parsing a bsv file.
parseClassIds(BufferedReader) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: parse class ids from first line in prediction file.
parseConceptFactories(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Creates concept factories by parsing the section defined by {@link this.CONCEPT_FACTORY_KEY
parseConceptFactory(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Creates a dictionary by parsing each child element of this.DICTIONARIES_KEY
parseConcepts(String) - Static method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
parseConsumerXml(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Creates a term consumer by parsing section defined by this.CONSUMER_KEY
parseDescriptor(File, UimaContext, int) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
parseDescriptor(File, UimaContext) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
parseDescriptor(File, UimaContext, int) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
parseDescriptor(File, UimaContext) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
parseDescriptor(File, UimaContext) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Initiates the parsing of the XML descriptor file containing definition of dictionaries and a consumer for the Rare Word Term dictionary paradigm
parseDictionaries(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
parseDictionaries(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
parseDictionaries(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Creates dictionary engines by parsing the section defined by this.DICTIONARIES_KEY
parseDictionary(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Creates a dictionary by parsing each child element of this.DICTIONARIES_KEY
parseDictionaryXml(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
parseDictionaryXml(UimaContext, Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
parseDirectory(File, File) - Method in interface org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser
parseDirectory(File, File) - Method in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser: parse directory.
parseDirectory(File, File) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: parse directory.
parseDirectory(File, File) - Method in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
parseDoubleOption(Pattern, String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser: parse a number out of the libsvm command line that matches the specified pattern.
parseDoubleValue(Object) - Method in class org.apache.ctakes.drugner.DrugMention
parseExtractor - Variable in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
parseExtractor - Variable in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
parseExtractor - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
ParseFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
ParseFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.ParseFeatureExtractor
parseFoldFromFileName(String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil: extract fold from file name produced by file util
parseInstanceIds(String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
parseInt(String, Logger) - Static method in class org.apache.ctakes.core.ae.SentenceDetector
parseInt(Object, String, int) - Static method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
parseInt(String, Logger) - Static method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
parseIntOption(Pattern, String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser: parse a number out of the libsvm command line that matches the specified pattern.
parseIntValue(Object) - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
parseIntValue(Object) - Method in class org.apache.ctakes.drugner.DrugMention
parseLabelFromFileName(String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil: extract label from file name produced by file util
parseLookupBindingXml(UimaContext, Map<String, DictionaryEngine>, Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
parseLookupBindingXml(UimaContext, Map<String, DictionaryEngine>, Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
parseMetrics(String) - Static method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
parseModel(String) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: parse svm-train model file to get the number of support vectors.
parseOptions(SVMClassifierEvaluation, String) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser
parseOptions(SemiLClassifierEvaluation, String, Properties, String) - Method in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser: parse options out of file, into object.
parseOverlapTypeString(String) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator: Parses the overlap type string and populates the user bitset.
parsePairingNames(Element, String) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser
parsePredictedClasses(ClassifierEvaluation, String, List<BaseClassifierEvaluationParser.InstanceClassInfo>, boolean, <any>) - Method in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser: parse class predictions for test instances out of semil output.
parsePredictions(String, String, Properties, String, SVMClassifierEvaluation) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: parse predicted class ids, probabilities; correlate to target class ids and instance ids.
parsePredictions(String, String, Properties, String, SVMClassifierEvaluation) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightParser: Parse svm-classify input (instance file) and predictions (prediction file).
parsePropertiesXml(Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities
parsePropertiesXml(Element) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilitiesRefactor
parsePropertiesXml(Element) - Static method in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: Builds a collection of key, value properties
parser - Variable in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
parser - Variable in class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
parser - Variable in class org.apache.ctakes.constituency.parser.MaxentParserWrapper
parser - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
parser - Variable in class org.apache.ctakes.jdl.data.loader.CsvLoader
parseRegex(String) - Method in class org.apache.ctakes.drugner.DrugMention
parseResults(File, File, SVMClassifierEvaluation, Properties) - Method in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser
parseResults(File, File, String, String, SVMClassifierEvaluation, Properties) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: parse the results in the specified output dir.
parseResults(File, File, String, String, SVMClassifierEvaluation, Properties) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightParser: parse output.txt - contains vcdim and number support vectors
ParserEvaluationAnnotator - Class in org.apache.ctakes.constituency.parser.ae
ParserEvaluationAnnotator() - Constructor for class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
parserModel - Variable in class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
parserModelFileName - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
parserModelUri - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
parserPredFileName - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
parserRoleFileName - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
ParserTreeWriterConsumer - Class in org.apache.ctakes.constituency.parser.uima.co
ParserTreeWriterConsumer() - Constructor for class org.apache.ctakes.constituency.parser.uima.co.ParserTreeWriterConsumer
parseRunFromFileName(String) - Static method in class org.apache.ctakes.ytex.kernel.FileUtil: extract run from file name produced by file util
ParserWrapper - Interface in org.apache.ctakes.constituency.parser
parseScopeOrder(String[]) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
parseSemiLOutput(File, String, Properties, File, List<BaseClassifierEvaluationParser.InstanceClassInfo>) - Method in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser: parse semil output file
parseSlotMention(Element, String) - Method in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
ParseSpanFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
ParseSpanFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.ParseSpanFeatureExtractor
parseStengthValue(Object) - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
parseStr - Variable in class org.apache.ctakes.constituency.parser.MaxentParserWrapper
parseSvmlinOutput(File, File, SVMClassifierEvaluation, String, Properties, List<BaseClassifierEvaluationParser.InstanceClassInfo>, <any>) - Method in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser: support multi-class classification
parseTextDoublesMap(File, Charset) - Static method in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor
parseTextDoublesMap(File, Charset) - Static method in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor
parseTrainOutput(SVMClassifierEvaluation, String) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightParser: Number of SV: 133 (including 0 at upper bound) L1 loss: loss=0.00000 Norm of weight vector: |w|=2.09380 Norm of longest example vector: |x|=16.91153 Estimated VCdim of classifier: VCdim<=684.90185
parseWeight(String) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: parse the weight options out of the libsvm command line.
parseYN(String) - Static method in class org.apache.ctakes.ytex.uima.model.BooleanUtil
parsingCLI(String[]) - Static method in class org.apache.ctakes.jdl.AppMain
PartOfSpeechFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
PartOfSpeechFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor
PASS_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
password - Variable in class org.apache.ctakes.jdl.data.base.JdlConnection
pat - Variable in class org.apache.ctakes.sideeffect.util.PatternMatch
PATCH - Static variable in class org.apache.ctakes.drugner.elements.FormElement
path - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
patHeader - Static variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
PathMetric - Class in org.apache.ctakes.ytex.kernel.metric
PathMetric(ConceptSimilarityService) - Constructor for class org.apache.ctakes.ytex.kernel.metric.PathMetric
pathToDrugInclusions - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
pathToString(LinkedList<ConllDependencyNode>) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: This will convert a path into a string lexicalized at the end points with arc labels and POS tags in between
pathToString(LinkedList<ConllDependencyNode>) - Static method in class org.apache.ctakes.temporal.ae.feature.DependencyParseUtils: This will convert a path into a string lexicalized at the end points with arc labels and POS tags in between
PATIENT_LEVEL_PROCESSING - Static variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer: Specifies whether post process should be run which provides the patient level classification
patientId - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
PatientLevelSmokingStatus - Class in org.apache.ctakes.smokingstatus.patientLevel: Patient-level smoking status classification used for the AMIA 2009 paper From PatientLevelSmokingStatus_Jan09.java revised frequency based except for assigning past smoker if exists only past and non-smoker
PatientLevelSmokingStatus() - Constructor for class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
patientSmokingStatus - Variable in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
patientsStatuses - Static variable in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
patResult - Static variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
pattern - Variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
pattern - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
PatternMatch - Class in org.apache.ctakes.sideeffect.util: Regular expression pattern match class used in SideEffectAnnotaor: Constructor: PatternMatch(String expr, String in, List kw): "expr" is an regular expression.
PatternMatch(String, String, List<String>) - Constructor for class org.apache.ctakes.sideeffect.util.PatternMatch
PatternMatch(String, String) - Constructor for class org.apache.ctakes.sideeffect.util.PatternMatch
patterns - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
patts - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.DependencyPathRegexpFeatureExtractor
paused() - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
paused() - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the CPM is paused.
pCost - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser
PcsClassifierAnnotator_libsvm - Class in org.apache.ctakes.smokingstatus.ae
PcsClassifierAnnotator_libsvm() - Constructor for class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
pDegree - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser
pearFile - Variable in class org.apache.ctakes.utils.build.InstallPearSilently.RunInstallation
pendingArr - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
pendingIntArr - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
pendingList - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
pendingRef - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
percentLabeled - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
performAction(Annotation, Annotation) - Method in interface org.apache.ctakes.core.ae.OverlapAnnotator.Action
performAction(Annotation, Annotation) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator.DeleteActionImpl
performAction(Annotation, Annotation) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
performLookup(JCas, LookupSpec, List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator: Executes the lookup algorithm on the lookup tokens.
performLookup(LookupAlgorithm, List<LookupToken>, Map<String, List<LookupAnnotation>>) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator: Executes the lookup algorithm on the lookup tokens.
performRecordResolution(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
PERIOD - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
PERIOD_PATTERN - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change split sentences periods after which this pattern is seen
periodPattern - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change
PermutationUtil - Class in org.apache.ctakes.dictionary.lookup.algorithms
PermutationUtil() - Constructor for class org.apache.ctakes.dictionary.lookup.algorithms.PermutationUtil
PersonTitleAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
PersonTitleAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation: Never called.
PersonTitleAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation: Internal - constructor used by generator
PersonTitleAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
PersonTitleAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
PersonTitleAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
PersonTitleAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type: initialize variables to correspond with Cas Type and Features
PersonTitleFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect measurements in the given input of tokens.
PersonTitleFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.PersonTitleFSM: Constructor
PersonTitleToken - Class in org.apache.ctakes.core.fsm.output
PersonTitleToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.PersonTitleToken
PETFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
PETFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PETFeatureExtractor
pFold - Static variable in class org.apache.ctakes.ytex.kernel.FileUtil
pGamma - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser
pGamma - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser: parse options
phrase - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.CuePhrase
PhraseBuilder - Interface in org.apache.ctakes.dictionary.lookup.phrasebuilder: Interface for building phrases from LookupToken objects.
phraseChunking - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
PhraseChunkingExtractor - Class in org.apache.ctakes.relationextractor.ae.features
PhraseChunkingExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor
PhraseTypeChunkCreator - Class in org.apache.ctakes.chunker.ae: This chunker creator creates annotations of type org.apache.ctakes.typesystem.type.* and sets the chunkType feature of the annotation to the passed in parameter chunkType.
PhraseTypeChunkCreator() - Constructor for class org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator
PILL - Static variable in class org.apache.ctakes.drugner.elements.FormElement
ping(Properties) - Static method in class org.apache.ctakes.ytex.tools.DBPing
pKernel - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser
pLabel - Static variable in class org.apache.ctakes.ytex.kernel.FileUtil
pLabel - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
placeMap(Map<K, V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: places each value of a map into a collection mapped with the appropriate key
placeMap(Map<K, V>) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: places each value of a map into a collection mapped with the appropriate key
placeMap(Map<K, V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: places each value of a map into a collection mapped with the appropriate key
placeMap(Map<K, V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: places each value of a map into a collection mapped with the appropriate key
placeMap(Map<K, V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: places each value of a map into a collection mapped with the appropriate key
placeMap(Map<K, V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: places each value of a map into a collection mapped with the appropriate key
placeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: places value into a collection mapped with key
placeValue(K, V) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: places value into a collection mapped with key
placeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: places value into a collection mapped with key
placeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: places value into a collection mapped with key
placeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: places value into a collection mapped with key
placeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: places value into a collection mapped with key
pLambaU - Static variable in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser
pLambda - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
pLambdaW - Static variable in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser
pLaplacian - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
pMu - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
polarity - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
PolarityCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
PolarityCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
PolarityCotrainingTests - Class in org.apache.ctakes.assertion.train: For each assertion attribute (polarity, conditional, etc), run against the test directories for that attribute, using models that are under the models-dir.
PolarityCotrainingTests() - Constructor for class org.apache.ctakes.assertion.train.PolarityCotrainingTests
PolarityCotrainingTests.TestPair - Class in org.apache.ctakes.assertion.train
PolarityCotrainingTests.TestPair(String, String) - Constructor for class org.apache.ctakes.assertion.train.PolarityCotrainingTests.TestPair
PolarityCotrainingTrain - Class in org.apache.ctakes.assertion.train: For each assertion attribute (polarity, conditional, etc), train a model using the data in the training directories for that attribute, and store the model under the models-dir Note that this uses constants within AssertionConst for the directory names.
PolarityCotrainingTrain() - Constructor for class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
PolarityDomainAdaptationTests - Class in org.apache.ctakes.assertion.train: For each assertion attribute (polarity, conditional, etc), run against the test directories for that attribute, using models that are under the models-dir.
PolarityDomainAdaptationTests() - Constructor for class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
PolarityDomainAdaptationTests.TestPair - Class in org.apache.ctakes.assertion.train
PolarityDomainAdaptationTests.TestPair(String, String) - Constructor for class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests.TestPair
PolarityDomainAdaptationTrain - Class in org.apache.ctakes.assertion.train: For each assertion attribute (polarity, conditional, etc), train a model using the data in the training directories for that attribute, and store the model under the models-dir Note that this uses constants within AssertionConst for the directory names.
PolarityDomainAdaptationTrain() - Constructor for class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
PolarityFedaCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
PolarityFedaCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
PolarityModifier - Class in org.apache.ctakes.typesystem.type.textsem: Used to indicate that a procedure or assertion did not occur or does not exist.
PolarityModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.PolarityModifier: Never called.
PolarityModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PolarityModifier: Internal - constructor used by generator
PolarityModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PolarityModifier
PolarityModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PolarityModifier
PolarityModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Used to indicate that a procedure or assertion did not occur or does not exist.
PolarityModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type: initialize variables to correspond with Cas Type and Features
PolyKernel - Class in org.apache.ctakes.utils.kernel
PolyKernel(int, double, boolean) - Constructor for class org.apache.ctakes.utils.kernel.PolyKernel
PolyKernel() - Constructor for class org.apache.ctakes.utils.kernel.PolyKernel
populateMinorityClass() - Method in class org.apache.ctakes.temporal.utils.SMOTEplus
populateSvmlinParameters(File, File, Properties, Properties) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil: set following properties in props [codeFile basename].dataFile [codeFile basename].kernel.evalLines [labelFile basename].param.R
populateTlinkTypesArray(List<BinaryTextRelation>) - Method in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
portionOfDataToUse - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
portionOfDataToUse - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
pos - Variable in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
pos - Variable in class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor
POS_DATA_FILE_PARAM - Static variable in class org.apache.ctakes.postagger.OpenNLPPOSCollectionReader: "PosDataFile" is a required, single, string parameter that specifies the location of a data file that contains part-of-speech data in it.
POS_MODEL_FILE_PARAM - Static variable in class org.apache.ctakes.postagger.POSTagger: "PosModelFile" is a required, single, string parameter that contains the file name of the part of speech tagger model.
POS_TAGGER_PATH - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
posAnaphInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
posDemInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
positions - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile
positiveClass - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
positiveClass - Variable in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
positiveClass - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
positiveClass - Variable in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
posModelPath - Variable in class org.apache.ctakes.postagger.POSTagger
posModelUri - Variable in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
posNeInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
posPronInst - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
posSet - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator.LemmaLocalClass
posSet - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator.LemmaLocalClass
possible - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
possibleContractionEndings - Static variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
possibleContractionEndings - Static variable in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB
possibleFinalPunctuation - Variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
postagger - Variable in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
POSTagger - Class in org.apache.ctakes.postagger
POSTagger() - Constructor for class org.apache.ctakes.postagger.POSTagger
POSTCOORD_NMOD - Static variable in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
POSTCOORD_NMOD - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
postLemmas - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
postLemmas - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
PostLookupFilter - Interface in org.apache.ctakes.dictionary.lookup.filter
PostLookupFilterGroupImpl - Class in org.apache.ctakes.dictionary.lookup.filter: Groups multiple PostLookupFilter objects together and applies boolean logic to them.
PostLookupFilterGroupImpl(PostLookupFilter[], int, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl: Constructor
postprocess() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
pOutput - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser: distance files of the form label1_dist_pearson_5.txt parse out the metric and degree from the file name.
pow - Variable in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
pow - Variable in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
POWDER - Static variable in class org.apache.ctakes.drugner.elements.FormElement
PP - Class in org.apache.ctakes.typesystem.type.syntax: A prepositional phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.PP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
PP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.PP: Never called.
PP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PP: Internal - constructor used by generator
PP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PP
PP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PP
PP_Type - Class in org.apache.ctakes.typesystem.type.syntax: A prepositional phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.PP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
PP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PP_Type: initialize variables to correspond with Cas Type and Features
pPercent - Static variable in class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
ppt - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
ppv - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
precededByH_O(JCas, Annotation) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
precision() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
precision(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
PrecisionBaselineEventTimeRelationAnnotator - Class in org.apache.ctakes.temporal.ae.baselines
PrecisionBaselineEventTimeRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator
PrecisionTermConsumer - Class in org.apache.ctakes.dictionary.lookup2.consumer: Refine a collection of dictionary terms to only contain the most specific variations: "colon cancer" instead of "cancer", performed by span inclusion / complete containment, not overlap
Author: SPF Affiliation: CHIP-NLP Date: 1/9/14
PrecisionTermConsumer(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer
Predicate - Class in org.apache.ctakes.typesystem.type.textsem: Predicates are typically verbs and may participate in SemanticRoleRelations.
Predicate() - Constructor for class org.apache.ctakes.typesystem.type.textsem.Predicate: Never called.
Predicate(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Predicate: Internal - constructor used by generator
Predicate(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Predicate
Predicate(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Predicate
Predicate_Type - Class in org.apache.ctakes.typesystem.type.textsem: Predicates are typically verbs and may participate in SemanticRoleRelations.
Predicate_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.Predicate_Type: initialize variables to correspond with Cas Type and Features
PredicateArgumentExtractor - Class in org.apache.ctakes.temporal.ae.feature
PredicateArgumentExtractor(JCas) - Constructor for class org.apache.ctakes.temporal.ae.feature.PredicateArgumentExtractor
predict(svm_node[]) - Method in class org.apache.ctakes.coreference.util.AbstractClassifier
predict(svm_node[], TreebankNode) - Method in class org.apache.ctakes.coreference.util.AbstractClassifier
predictedClassId - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
predictedClassId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
predictedOutcomes - Variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
preExecutionTest() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
PREF_TERM_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
PreferDesig - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
PREFERRED_TERM_UNKNOWN - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.Concept
PREFERRED_TEXT_UNKNOWN - Static variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
prefix - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
prefix - Variable in class org.apache.ctakes.core.util.CtakesFileNamer
prefix - Variable in class org.apache.ctakes.ytex.kernel.FileUtil.PrefixFileFilter
PREFIXES - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
prefs - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Stores user preferences
prefsMed - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
preload - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
PreLookupFilter - Interface in org.apache.ctakes.dictionary.lookup.filter
prepare(String, String, Map<String, Object>) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl: run the prepare script if defined.
prepare(String, String) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl: run 'preparation' statements.
prepareCopy() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Clones this object and its attributes, but leave references blank.
prepareQuery(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
prepareScript - Variable in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
prepareScriptStatementDelimiter - Variable in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
prepareSubSection(JCas, JFSIndexRepository, Set) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Given the set of subSectionInds to parse (via SubSectionIndicatorFSM) create SubSectionAnnotation This method created SubsectionAnnotation and sets the header begin, end as well as body begin and end
prepareUniqueFeatureEvalQuery(String, String, String, String, Integer, Double, String, String) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
prepareXMIsFor(List<Integer>) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
prepend(DependencyRegex) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
prepend(DEPNode[]) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
prependOptional(DependencyRegex) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
prependOptional(DEPNode[]) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
PrepositionFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that indicate whether there is a preposition between the two arguments.
PrepositionFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PrepositionFeatureExtractor
preprocess(File) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
preprocess() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
PreprocessAndWriteXmi - Class in org.apache.ctakes.coreference.cc
PreprocessAndWriteXmi() - Constructor for class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi
PreprocessAndWriteXmi.Options - Class in org.apache.ctakes.coreference.cc
PreprocessAndWriteXmi.Options() - Constructor for class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.Options
PreprocessAndWriteXmi.SerializeDocumentToXMI - Class in org.apache.ctakes.coreference.cc
PreprocessAndWriteXmi.SerializeDocumentToXMI() - Constructor for class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.SerializeDocumentToXMI
preprocessDir - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
preprocessForDev - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
preprocessForTest - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
PreProcessor - Interface in org.apache.ctakes.preprocessor
preprocessRootDirectory - Static variable in class org.apache.ctakes.assertion.util.AssertionConst: DON'T CHANGE THESE
prepStmtValArr - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
prepStmtValArrIdx - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
PreserveCertainEventEventRelationsInGold - Class in org.apache.ctakes.temporal.duration: Preserve only those event-event relations whose both event arguments have duration data.
PreserveCertainEventEventRelationsInGold() - Constructor for class org.apache.ctakes.temporal.duration.PreserveCertainEventEventRelationsInGold
PreserveCertainEventsInGold - Class in org.apache.ctakes.temporal.duration: Preserve only those events that have duration data.
PreserveCertainEventsInGold() - Constructor for class org.apache.ctakes.temporal.duration.PreserveCertainEventsInGold
PreserveCertainEventTimeRelationsInGold - Class in org.apache.ctakes.temporal.duration: Preserve only those event-time relations whose event argument has duration data and whose time argument can be normalized using Steve's timex normalizer.
PreserveCertainEventTimeRelationsInGold() - Constructor for class org.apache.ctakes.temporal.duration.PreserveCertainEventTimeRelationsInGold
PreserveUMLSEventEventRelationsInGold - Class in org.apache.ctakes.temporal.duration: Preserve only those event-event relations whose both arguments have covering system event mentions.
PreserveUMLSEventEventRelationsInGold() - Constructor for class org.apache.ctakes.temporal.duration.PreserveUMLSEventEventRelationsInGold
PreserveUMLSEventTimeRelationsInGold - Class in org.apache.ctakes.temporal.duration: Preserve only those event-time relations whose event argument was found by ctakes dictionary lookup (i.e.
PreserveUMLSEventTimeRelationsInGold() - Constructor for class org.apache.ctakes.temporal.duration.PreserveUMLSEventTimeRelationsInGold
preTest(CollectionReader, File, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
Prevents - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
Prevents() - Constructor for class org.apache.ctakes.typesystem.type.relation.Prevents: Never called.
Prevents(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Prevents: Internal - constructor used by generator
Prevents(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Prevents
Prevents_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
Prevents_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Prevents_Type: initialize variables to correspond with Cas Type and Features
PreventsTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
PreventsTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation: Never called.
PreventsTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation: Internal - constructor used by generator
PreventsTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation
PreventsTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
PreventsTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation_Type: initialize variables to correspond with Cas Type and Features
print() - Method in class org.apache.ctakes.coreference.util.ParentPtrTree
printAnnotation - Variable in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
printCommon() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Prints common elements along with their attributes in the two XCAS files to stdout.
printContext(String, IdentifiedAnnotation, int) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
printContext(String, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
printContext - Variable in class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.RelationContextPrinter
printDiff() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Prints elements that are unique to each XCAS file to stdout.
printDiff(XcasFile, XcasFile) - Static method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Prints elements that are unique to each XCAS file to stdout.
printErrors - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
printErrors(JCas, Collection<IdentifiedAnnotation>, Collection<IdentifiedAnnotation>, String, Object, Class<? extends Object>) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
printErrors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
printErrors - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
printErrors - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
PrintFailedTimeNormalizations - Class in org.apache.ctakes.temporal.data.analysis
PrintFailedTimeNormalizations() - Constructor for class org.apache.ctakes.temporal.data.analysis.PrintFailedTimeNormalizations
PrintFailedTimeNormalizations.Options - Interface in org.apache.ctakes.temporal.data.analysis
printFeatures(TreebankNode, List<Feature>) - Static method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
printHelp(Options) - Static method in class org.apache.ctakes.ytex.KernelLauncher
printHelp(Options) - Static method in class org.apache.ctakes.ytex.weka.ImportWekaResults
printHelp(Options) - Static method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
printHTML(Writer) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Writes an HTML summary of the comparison of the two XCAS files.
printHTML(XcasFile, XcasFile, Writer) - Static method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Writes an HTML summary of the comparison of the two specified XCAS files.
PrintInconsistentAnnotations - Class in org.apache.ctakes.temporal.data.analysis
PrintInconsistentAnnotations() - Constructor for class org.apache.ctakes.temporal.data.analysis.PrintInconsistentAnnotations
PrintInconsistentAnnotations.Options - Interface in org.apache.ctakes.temporal.data.analysis
printInConsole(boolean, String) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently: Prints messages and set foreground color in the console according to a given errorFlag.
printInstances - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
printInstances(JCas, Collection<IdentifiedAnnotation>, Collection<IdentifiedAnnotation>, String, Object, Class<? extends Object>, File) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
printLibsvmDataToFile(String) - Method in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData
PrintNormalizedTemporalExpressions - Class in org.apache.ctakes.temporal.data.analysis: Print the time units produced by Steven Bethard's TimeEx normalizer for temporal expressions in the gold standard.
PrintNormalizedTemporalExpressions() - Constructor for class org.apache.ctakes.temporal.data.analysis.PrintNormalizedTemporalExpressions
printOptionsForDebugging(AssertionEvaluation.Options) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
printOverlapping - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
printRelationAnnotations(String, Collection<BinaryTextRelation>) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
printRelations - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase
PrintRelations - Class in org.apache.ctakes.temporal.eval
PrintRelations() - Constructor for class org.apache.ctakes.temporal.eval.PrintRelations
PrintRelations.Options - Interface in org.apache.ctakes.temporal.eval
PrintRelationStatistics - Class in org.apache.ctakes.relationextractor.eval
PrintRelationStatistics() - Constructor for class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics
PrintRelationStatistics.Options - Class in org.apache.ctakes.relationextractor.eval
PrintRelationStatistics.Options() - Constructor for class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics.Options
printResults(String, List) - Static method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile: Prints out the tokenized results, for debug use.
printScore(Map<String, AnnotationStatisticsCompact<String>>, String) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
printSentenceTokens(String, Iterable<String>) - Static method in class org.apache.ctakes.core.cc.SentenceTokensPrinter: Prints the (base) tokens of each sentence on a separate line, separated by spaces, on standard output
printSimilarities(List<ConceptPair>, List<ConceptPairSimilarity>, List<ConceptSimilarityService.SimilarityMetricEnum>, List<SimilarityInfo>, boolean, PrintStream) - Static method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
printToFile() - Static method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
printTree(Node, int) - Static method in class org.apache.ctakes.ytex.kernel.evaluator.TreePrinter
printTrees - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
printUniq(int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Prints elements that are unique to XCAS file i.
printUsage() - Static method in class org.apache.ctakes.postagger.TagDictionaryCreator
printUsageMessage() - Static method in class org.apache.ctakes.ytex.tools.RunCPE
printVectors - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
prob - Variable in class org.apache.ctakes.coreference.ae.MarkableProb
probabilities - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
ProbabilityDistribution - Class in org.apache.ctakes.typesystem.type.util: A brute force probability distribution for discrete variables.
ProbabilityDistribution() - Constructor for class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution: Never called.
ProbabilityDistribution(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution: Internal - constructor used by generator
ProbabilityDistribution(JCas) - Constructor for class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution
ProbabilityDistribution_Type - Class in org.apache.ctakes.typesystem.type.util: A brute force probability distribution for discrete variables.
ProbabilityDistribution_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type: initialize variables to correspond with Cas Type and Features
probabilityOfKeepingADefaultExample - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
probabilityOfKeepingANegativeExample - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
probabilityOfKeepingANegativeExample - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
probabilityOfKeepingANegativeExample - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
probabilityOfKeepingANegativeExample - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
PROBABLE_STATUS - Static variable in class org.apache.ctakes.core.fsm.output.StatusIndicator
PROBABLE_STATUS - Static variable in class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
problemSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
PROC - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
PROC_TUIS - Static variable in class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
Procedure - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Procedures (except that Laboratory procedures are separate).
Procedure() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Procedure: Never called.
Procedure(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Procedure: Internal - constructor used by generator
Procedure(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Procedure
PROCEDURE_TUIS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
Procedure_Type - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Procedures (except that Laboratory procedures are separate).
Procedure_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Procedure_Type: initialize variables to correspond with Cas Type and Features
ProcedureDevice - Class in org.apache.ctakes.typesystem.type.refsem: Corresponds to the UMLS Devices semantic group: medical device and research device.
ProcedureDevice() - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice: Never called.
ProcedureDevice(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice: Internal - constructor used by generator
ProcedureDevice(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice
ProcedureDevice_Type - Class in org.apache.ctakes.typesystem.type.refsem: Corresponds to the UMLS Devices semantic group: medical device and research device.
ProcedureDevice_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type: initialize variables to correspond with Cas Type and Features
ProcedureDeviceModifier - Class in org.apache.ctakes.typesystem.type.textsem: Corresponds to the UMLS Devices semantic group: medical device and research device.
ProcedureDeviceModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier: Never called.
ProcedureDeviceModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier: Internal - constructor used by generator
ProcedureDeviceModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
ProcedureDeviceModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
ProcedureDeviceModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: Corresponds to the UMLS Devices semantic group: medical device and research device.
ProcedureDeviceModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type: initialize variables to correspond with Cas Type and Features
ProcedureMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (Procedure) Event.
ProcedureMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: Never called.
ProcedureMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: Internal - constructor used by generator
ProcedureMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMention
ProcedureMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMention
ProcedureMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (Procedure) Event.
ProcedureMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type: initialize variables to correspond with Cas Type and Features
ProcedureMethod - Class in org.apache.ctakes.typesystem.type.refsem: The way or the equipment used to give or administration something (medication, test).
ProcedureMethod() - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod: Never called.
ProcedureMethod(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod: Internal - constructor used by generator
ProcedureMethod(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod
ProcedureMethod_Type - Class in org.apache.ctakes.typesystem.type.refsem: The way or the equipment used to give or administration something (medication, test).
ProcedureMethod_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type: initialize variables to correspond with Cas Type and Features
ProcedureMethodModifier - Class in org.apache.ctakes.typesystem.type.textsem: The way or the equipment used to give or administration something (medication, test).
ProcedureMethodModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier: Never called.
ProcedureMethodModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier: Internal - constructor used by generator
ProcedureMethodModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier
ProcedureMethodModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier
ProcedureMethodModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: The way or the equipment used to give or administration something (medication, test).
ProcedureMethodModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type: initialize variables to correspond with Cas Type and Features
process(JCas) - Method in class org.apache.ctakes.assertion.attributes.GenericAttributeAnalysisEngine
process(JCas) - Method in class org.apache.ctakes.assertion.attributes.SubjectAttributeAnalysisEngine
process(JCas) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
process(JCas) - Method in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
process(JCas) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
process(JCas) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.OnlyGoldAssertions
process(JCas) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer
process(JCas) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier
process(JCas) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier
process(JCas) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold
process(JCas) - Method in class org.apache.ctakes.assertion.eval.MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas: Copy all annotations of the given types from the corresponding cas that has a gold view to the current cas
process(JCas) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
process(JCas) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
process(JCas) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
process(JCas) - Method in class org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
process(JCas) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: Invokes this annotator's analysis logic.
process(JCas) - Method in class org.apache.ctakes.chunker.ae.Chunker
process(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator: Method invoked by UIMA framework to process a document
process(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations
process(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows
process() - Method in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
process(JCas) - Method in class org.apache.ctakes.constituency.parser.ae.ConstituencyParser
process(JCas) - Method in class org.apache.ctakes.constituency.parser.ae.ParserEvaluationAnnotator
process(JCas) - Method in class org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator
process(JCas) - Method in class org.apache.ctakes.core.ae.CDASegmentAnnotator
process(JCas) - Method in class org.apache.ctakes.core.ae.CopyAnnotator
process(JCas) - Method in class org.apache.ctakes.core.ae.DocumentIdPrinterAnalysisEngine
process(JCas) - Method in class org.apache.ctakes.core.ae.FilterAnnotator: Checks if the annotation is of the type to be retained.
process(JCas) - Method in class org.apache.ctakes.core.ae.NullAnnotator
process(JCas) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator
process(JCas) - Method in class org.apache.ctakes.core.ae.SectionSegmentAnnotator: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.core.ae.SentenceDetector: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
process(JCas) - Method in class org.apache.ctakes.core.ae.SimpleSegmentAnnotator: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.core.ae.SimpleSegmentWithTagsAnnotator: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotator: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB: Entry point for processing.
process(CAS) - Method in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes: Processes the CAS which was populated by the TextAnalysisEngines.
process(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableCreator
process(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
process(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
process(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
process(JCas) - Method in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
process(JCas) - Method in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.SerializeDocumentToXMI
process(JCas) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
process(JCas) - Method in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
process(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator: Entry point for processing.
process(JCas) - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
process(JCas) - Method in class org.apache.ctakes.drugner.ae.CopyDrugAnnotator
process(JCas) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
process(JCas) - Method in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
process(JCas) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator: Invokes this annotator's analysis logic.
process(JCas) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator: Invokes this annotator's analysis logic.
process(JCas) - Method in class org.apache.ctakes.necontexts.ContextAnnotator
process(JCas) - Method in class org.apache.ctakes.postagger.ClearNLPPOSTaggerAE
process(JCas) - Method in class org.apache.ctakes.postagger.POSTagger
process(JCas) - Method in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
process(String) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
process(String) - Method in interface org.apache.ctakes.preprocessor.PreProcessor: Process a document to retrieve meta data about the document.
process(JCas) - Method in class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
process(JCas) - Method in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer.RelationContextPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.RelationContextPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation.OnlyGoldModifiers
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveSmallerEventMentions
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.SHARPXMI.CopyDocumentTextToGoldView
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.SHARPXMI.DocumentIDAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.RelationExtractorPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
process(JCas) - Method in class org.apache.ctakes.sideeffect.ae.PSESentenceAnnotator
process(JCas, ResultSpecification) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceClassifierAnnotator
process(JCas) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator
process(JCas) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
process(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
process(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
process(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
process(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
process(JCas) - Method in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster: Invokes this annotator's analysis logic.
process(JCas) - Method in class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.ClearTKDocumentCreationTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.ClearTKLinkToTHYMELinkAnnotator
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.EventAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.EventToClearTKEventAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.I2B2TemporalXMLReader
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.NEPredicateEventAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
process(JCas) - Method in class org.apache.ctakes.temporal.ae.TemporalRelationRuleAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.TemporalSequenceAnnotator_ImplBase
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.TemporalSequenceAnnotator_ImplBase
process(JCas) - Method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
process(JCas) - Method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
process(JCas, Segment) - Method in class org.apache.ctakes.temporal.ae.TimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.ae.TimexToClearTKTimexAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
process(JCas) - Method in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.EventWriter
process(JCas) - Method in class org.apache.ctakes.temporal.data.analysis.GoldRelationViewer.RelationContextPrinter
process(JCas) - Method in class org.apache.ctakes.temporal.data.analysis.PrintNormalizedTemporalExpressions
process(JCas) - Method in class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.RelationContextPrinter
process(JCas) - Method in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
process(JCas) - Method in class org.apache.ctakes.temporal.duration.EventEventDurationStatistics.AnalyseRelationArgumentDuration
process(JCas) - Method in class org.apache.ctakes.temporal.duration.EventTimeDurationStatistics.AnalyseRelationArgumentDuration
process(JCas) - Method in class org.apache.ctakes.temporal.duration.ExtractDurationsUsingContainsRelation.ProcessRelations
process(JCas) - Method in class org.apache.ctakes.temporal.duration.PreserveCertainEventEventRelationsInGold
process(JCas) - Method in class org.apache.ctakes.temporal.duration.PreserveCertainEventsInGold
process(JCas) - Method in class org.apache.ctakes.temporal.duration.PreserveCertainEventTimeRelationsInGold
process(JCas) - Method in class org.apache.ctakes.temporal.duration.PreserveUMLSEventEventRelationsInGold
process(JCas) - Method in class org.apache.ctakes.temporal.duration.PreserveUMLSEventTimeRelationsInGold
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyFromGold
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.EntityMentionRemover
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.EventMentionRemover
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.TimexAnnotationCorrector
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.UriToDocumentTextAnnotatorCtakes
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader
process(JCas) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIWriter
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddClosure
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddContain2Overlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddFlippedOverlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddTransitiveContainsRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveNonTLINKRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveNonUMLSEvents
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties.ClearEventProperties
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddClosure
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddContain2Overlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddFlippedOverlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddTransitiveContainsRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.CountCloseRelation
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveNonUMLSEvents
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.ClearEventProperties
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddClosure
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddContain2Overlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddFlippedOverlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddTransitiveContainsRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.CountCloseRelation
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.Overlap2Contains
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveEventEventRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveNonUMLSEtEvents
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.AddClosure
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.AddFlippedOverlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.FindLongDisRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.RemoveNonTLINKRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.RemoveNullArgumentRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.RemoveRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddClosure
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddContain2Overlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddFlippedOverlap
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.OverwriteTemporalRelationToSystem
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveEventEventRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes
process(JCas) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations
process(JCas) - Method in class org.apache.ctakes.temporal.eval.RemoveTreeAlignedMentions
process(JCas) - Method in class org.apache.ctakes.temporal.pipelines.EventPrintingPipeline.PrintEventAnnotations
process(JCas) - Method in class org.apache.ctakes.temporal.pipelines.FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
process(String) - Static method in class org.apache.ctakes.utils.xcas_comparison.XcasFile: Creates a new XcasFile object from the specified file.
process(File) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor: Parses the specified file and returns a parsed XcasFile object.
process(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor: Parses the specified file and returns a parsed XcasFile object.
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.DBConsumer: call the documentMapperService to save the document.
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator: Add Segment annotations to the cas.
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
process(JCas) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: Entry point for processing.
processAE(AnalysisEngine, File) - Static method in class org.apache.ctakes.utils.test.TestUtil: This method simply calls #createAnalysisEngineJCas(File, File, String) with the charSetName equal to "UTF-8".
processAE(AnalysisEngine, File, String) - Static method in class org.apache.ctakes.utils.test.TestUtil: This method reads in the text from the text file using the provided character set and then calls #getJCas(File, String)
processAE(AnalysisEngine, String) - Static method in class org.apache.ctakes.utils.test.TestUtil: This method creates a JCas for the provided analysis engine descriptor file and then processes the provided text and returns the JCas.
processCas(JCas, String) - Method in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
processCas(CAS) - Method in class org.apache.ctakes.constituency.parser.uima.co.ParserTreeWriterConsumer
processCas(CAS) - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter
processCas(CAS) - Method in class org.apache.ctakes.core.cc.CasConsumer: Create an xml file from the data in the cas.
processCas(CAS) - Method in class org.apache.ctakes.core.cc.FilesInDirectoryCasConsumer
processCas(CAS) - Method in class org.apache.ctakes.core.cc.HtmlTableCasConsumer
processCas(CAS) - Method in class org.apache.ctakes.core.cc.NormalizedFilesInDirectoryCasConsumer
processCas(CAS) - Method in class org.apache.ctakes.core.cc.SentenceTokensPrinter: Saves the (base) tokens of each sentence on a separate line, separated by spaces
processCas(CAS) - Method in class org.apache.ctakes.core.cc.TokenFreqCasConsumer: Iterates through all of the WordTokenAnnotation's, gets the covered text for each annotation and increments the frequency count for that text.
processCas(CAS) - Method in class org.apache.ctakes.core.cc.TokenOffsetsCasConsumer
processCas(CAS) - Method in class org.apache.ctakes.dependency.parser.DependencyNodeWriter: Create an xml file from the data in the cas.
processCas(CAS) - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
processCas(CAS) - Method in class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
processCas(CAS) - Method in class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
processCas(CAS) - Method in class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
processDem(Markable, List<Markable>, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
processDocument(JCas) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
processDocument(JCas) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
processedStyleMap - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
processedStyleMap - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
processEndPunctSymbol(List<Token>, Token, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
processForEntityType(JCas, int, Class<? extends IdentifiedAnnotation>) - Method in class org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
processLine(String) - Method in class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
processLine(String) - Method in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor.StringToDoublesProcessor
processLine(String) - Method in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor
processLine(String) - Method in class org.apache.ctakes.temporal.duration.Utils.Callback
processNE(Markable, List<Markable>, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
processNELazily(Markable, List<Markable>, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
processPronoun(Markable, LinkedList<Markable>, JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
processRegex(JCas, Annotation, NamedEntityRegex, Pattern) - Method in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator: Search the document / annotation span for with the supplied pattern.
processRow(ResultSet) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.ConceptInstanceMapExtractor
processStartPunctSymbol(List<Token>, Token, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer
processView(JCas) - Method in class org.apache.ctakes.core.cc.CasConsumer: Write a formatted xml file containing data from the view.
processView(JCas) - Method in class org.apache.ctakes.dependency.parser.DependencyNodeWriter: Write a tab-delimited file containing data from the view.
processWindow(JCas, Annotation, Map<RareWordDictionary, CollectionMap<TextSpan, Long, ? extends Collection<Long>>>) - Method in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator: Processes a window of annotations for dictionary terms
processWindow(JCas, Annotation, Map<RareWordDictionary, CollectionMap<TextSpan, Long, ? extends Collection<Long>>>) - Method in interface org.apache.ctakes.dictionary.lookup2.ae.WindowProcessor: Processes a window of annotations for dictionary terms
processXmlFile(JCas, File) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
PRODIST - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
ProductKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: compute the product of delegate kernels
ProductKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.ProductKernel
projects - Static variable in class org.apache.ctakes.utils.build.BuildPipelinePears
projects - Static variable in class org.apache.ctakes.utils.build.InstallPipelineFromPears
prompt(String) - Static method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
promptForAE() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: copied from AnnotationViewerDialog.
promptForAE() - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: If the current AE filename is not know ask for it.
PRON - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
pron_coref_feats - Static variable in class org.apache.ctakes.coreference.util.FeatureVector
pronFeatSet - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
PronounMarkable - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-coreference/target/jcasgen/typesystem.xml
PronounMarkable() - Constructor for class org.apache.ctakes.coreference.type.PronounMarkable: Never called.
PronounMarkable(int, TOP_Type) - Constructor for class org.apache.ctakes.coreference.type.PronounMarkable: Internal - constructor used by generator
PronounMarkable(JCas) - Constructor for class org.apache.ctakes.coreference.type.PronounMarkable
PronounMarkable(JCas, int, int) - Constructor for class org.apache.ctakes.coreference.type.PronounMarkable
PronounMarkable_Type - Class in org.apache.ctakes.coreference.type: Updated by JCasGen Wed Sep 30 11:05:59 EDT 2015
PronounMarkable_Type(JCas, Type) - Constructor for class org.apache.ctakes.coreference.type.PronounMarkable_Type: initialize variables to correspond with Cas Type and Features
pronOut - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
pronSelFeats - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
pronTreeOut - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
propagateJointDistribution(Map<String, ImputedFeatureEvaluatorImpl.JointDistribution>, ImputedFeatureEvaluatorImpl.Parameters, String, int, ConceptGraph, Map<String, Set<Long>>) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: 'complete' the joint distribution tables wrt a fold (yMargin).
properties - Variable in class org.apache.ctakes.jdl.common.PropertiesFile
PROPERTIES_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser: everything else is implementation-specific and therefore optional and therefore set as a property
PropertiesFile - Class in org.apache.ctakes.jdl.common: Access to a properties file.
PropertiesFile() - Constructor for class org.apache.ctakes.jdl.common.PropertiesFile
PROPERTY_NAMES - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
PROPERTY_NAMES - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
PropFile - Class in org.apache.ctakes.jdl.common: Access to a properties file.
PropFile() - Constructor for class org.apache.ctakes.jdl.common.PropFile
props - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
props - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
PRT - Class in org.apache.ctakes.typesystem.type.syntax: A particle, e.g., "out" in "rule out" Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.PRT Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
PRT() - Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT: Never called.
PRT(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT: Internal - constructor used by generator
PRT(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT
PRT(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT
PRT_Type - Class in org.apache.ctakes.typesystem.type.syntax: A particle, e.g., "out" in "rule out" Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.PRT Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
PRT_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PRT_Type: initialize variables to correspond with Cas Type and Features
pRun - Static variable in class org.apache.ctakes.ytex.kernel.FileUtil
pse - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.SideEffect
PSESentence - Class in org.apache.ctakes.sideeffect.type: sentence(s) that contains potential side effect and causing drug Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-side-effect/target/jcasgen/typesystem.xml
PSESentence() - Constructor for class org.apache.ctakes.sideeffect.type.PSESentence: Never called.
PSESentence(int, TOP_Type) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentence: Internal - constructor used by generator
PSESentence(JCas) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentence
PSESentence(JCas, int, int) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentence
PSESentence_Type - Class in org.apache.ctakes.sideeffect.type: sentence(s) that contains potential side effect and causing drug Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015
PSESentence_Type(JCas, Type) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentence_Type: initialize variables to correspond with Cas Type and Features
PSESentenceAnnotator - Class in org.apache.ctakes.sideeffect.ae: Identify the sentence(s) that contains PSE (signs/symptoms or disease/disorder) and drugs and add them to PSESentence.
PSESentenceAnnotator() - Constructor for class org.apache.ctakes.sideeffect.ae.PSESentenceAnnotator
PSESentenceFeature - Class in org.apache.ctakes.sideeffect.type: Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-side-effect/target/jcasgen/typesystem.xml
PSESentenceFeature() - Constructor for class org.apache.ctakes.sideeffect.type.PSESentenceFeature: Never called.
PSESentenceFeature(int, TOP_Type) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentenceFeature: Internal - constructor used by generator
PSESentenceFeature(JCas) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentenceFeature
PSESentenceFeature(JCas, int, int) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentenceFeature
PSESentenceFeature_Type - Class in org.apache.ctakes.sideeffect.type: Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015
PSESentenceFeature_Type(JCas, Type) - Constructor for class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type: initialize variables to correspond with Cas Type and Features
psv - Static variable in class org.apache.ctakes.ytex.svmlight.SVMLightParser
ptPatt - Static variable in class org.apache.ctakes.utils.tree.SimpleTree
PunctuationFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that capture punctuation marks between the two arguments.
PunctuationFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PunctuationFeatureExtractor
PunctuationToken - Interface in org.apache.ctakes.core.fsm.token
PunctuationToken - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being punctuation rather than a contraction, symbol, newline, word, or number.
PunctuationToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.PunctuationToken: Never called.
PunctuationToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PunctuationToken: Internal - constructor used by generator
PunctuationToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PunctuationToken
PunctuationToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PunctuationToken
PunctuationToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being punctuation rather than a contraction, symbol, newline, word, or number.
PunctuationToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.PunctuationToken_Type: initialize variables to correspond with Cas Type and Features
PunctuationTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
PunctuationTokenAdapter(PunctuationToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.PunctuationTokenAdapter
PunctuationTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter: Adapts a Context Free Tokenizer token into a Context Dependent Tokenizer PunctuationToken.
PunctuationTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.PunctuationTokenAdapter
PunctuationValueCondition - Class in org.apache.ctakes.core.fsm.condition
PunctuationValueCondition(char) - Constructor for class org.apache.ctakes.core.fsm.condition.PunctuationValueCondition
put(K, List<V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
put(K, T) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
put(K, Set<V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
put(K, Set<V>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
put(K, T) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
putAll(Map<? extends K, ? extends List<V>>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
putAll(Map<? extends K, ? extends T>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
putAll(Map<? extends K, ? extends Set<V>>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
putAll(Map<? extends K, ? extends Set<V>>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
putAll(Map<? extends K, ? extends T>) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
putInBin(String) - Static method in class org.apache.ctakes.temporal.duration.Utils: Take the time unit from Bethard noramlizer and return a coarser time unit, i.e.
pvc - Static variable in class org.apache.ctakes.ytex.svmlight.SVMLightParser
pWeight - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser

Q

QUANTITY_24 - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_BIWEEKLY - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_EIGHT - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_ELEVEN - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_EVERY_OTHER_DAY - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_FIVE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_FOUR - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_MONTHLY - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_NINE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_ONE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_PRN - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_SEVEN - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_SIX - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_TEN - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_THREE - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_TWO - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_WEEKLY - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
QUANTITY_YEARLY - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.FrequencyUnitToken
query - Variable in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
query - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
queryArgs - Variable in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
queryGetDocument - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader: the queyr to get a document given a key.
queryGetDocumentKeys - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader: the query to get the document keys set in config file
QueryMappingInfo - Class in org.apache.ctakes.ytex.kernel.tree
QueryMappingInfo() - Constructor for class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
queryParser - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
queryPrepStmt - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
quote(String) - Static method in class org.apache.ctakes.utils.build.BuildPear: Quote the string, using double quotes if the string contains any single quotes, otherwise using single quotes.
quote(String) - Static method in class org.apache.ctakes.utils.build.BuildPipelinePears
quote(String) - Static method in class org.apache.ctakes.utils.build.InstallPearSilently
quote(String) - Static method in class org.apache.ctakes.utils.build.InstallPipelineFromPears

R

R_POS_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
R_POS_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
R_POS_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
R_REL_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
R_REL_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
R_REL_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
R_TOK_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
R_TOK_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
R_TOK_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
ra - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
RadaMetric - Class in org.apache.ctakes.ytex.kernel.metric: 1 - path / (2*maxDepth)
RadaMetric(ConceptSimilarityService, Integer) - Constructor for class org.apache.ctakes.ytex.kernel.metric.RadaMetric
random - Static variable in class org.apache.ctakes.assertion.util.AssertionTreeUtils
random - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
randomizeWords(SimpleTree, boolean) - Method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
RangeAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RangeAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
RangeAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation: Never called.
RangeAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation: Internal - constructor used by generator
RangeAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
RangeAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
RangeAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RangeAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
RangeAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type: initialize variables to correspond with Cas Type and Features
RangeCondition - Class in org.apache.ctakes.core.fsm.condition: Checks whether a token is a RangeToken.
RangeCondition() - Constructor for class org.apache.ctakes.core.fsm.condition.RangeCondition
RangeDosageCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a RangeStrengthToken.
RangeDosageCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.RangeDosageCondition
RangeFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect ranges in the given input of tokens.
RangeFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.RangeFSM: Constructor
RangeStrengthAnnotation - Class in org.apache.ctakes.drugner.type: The range portion of dosages stength determination for the Drug NER profile.
RangeStrengthAnnotation() - Constructor for class org.apache.ctakes.drugner.type.RangeStrengthAnnotation: Never called.
RangeStrengthAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.RangeStrengthAnnotation: Internal - constructor used by generator
RangeStrengthAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.RangeStrengthAnnotation
RangeStrengthAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.RangeStrengthAnnotation
RangeStrengthAnnotation_Type - Class in org.apache.ctakes.drugner.type: The range portion of dosages stength determination for the Drug NER profile.
RangeStrengthAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.RangeStrengthAnnotation_Type: initialize variables to correspond with Cas Type and Features
RangeStrengthCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a RangeStrengthToken.
RangeStrengthCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.RangeStrengthCondition
RangeStrengthFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect range strength tokens in the given input of tokens.
RangeStrengthFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.RangeStrengthFSM: Constructor
RangeStrengthToken - Class in org.apache.ctakes.drugner.fsm.output.util
RangeStrengthToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.RangeStrengthToken
RangeToken - Class in org.apache.ctakes.core.fsm.output
RangeToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.RangeToken
RangeToken - Class in org.apache.ctakes.drugner.fsm.output.util
RangeToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.RangeToken
rank(ImputedFeatureEvaluator.MeasureType, FeatureEvaluation, Map<String, ImputedFeatureEvaluatorImpl.JointDistribution>, double, List<FeatureRank>) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
rank - Variable in class org.apache.ctakes.ytex.kernel.model.FeatureRank
rank(Map<String, Double>, ConceptGraph, int, double, double) - Method in interface org.apache.ctakes.ytex.kernel.pagerank.PageRankService: PageRank for conceptGraph.
rank(Map<String, Double>, ConceptGraph) - Method in interface org.apache.ctakes.ytex.kernel.pagerank.PageRankService: call rank() with default values for iter (30), threshold(1e-4), dampingFactor(0.85)
rank(Map<String, Double>, ConceptGraph, int, double, double) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
rank(Map<String, Double>, ConceptGraph) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
rank2(Map<Integer, Double>, ConceptGraph, int, double, double) - Method in interface org.apache.ctakes.ytex.kernel.pagerank.PageRankService
rank2(Map<Integer, Double>, ConceptGraph, int, double, double) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
rankCutoff - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
rankInternal(Map<Integer, Double>, ConceptGraph, int, double, double) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl
RARE_WORD_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
RareWordDictionary - Interface in org.apache.ctakes.dictionary.lookup2.dictionary: Dictionary used to lookup terms by the most rare word within them Author: SPF Affiliation: CHIP-NLP Date: 11/20/13
RareWordTerm - Class in org.apache.ctakes.dictionary.lookup2.term: Container class for terms in a RareWordDictionary Author: SPF Affiliation: CHIP-NLP Date: 11/18/13
RareWordTerm(String, Long, String, int, int) - Constructor for class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
RareWordTermMapCreator - Class in org.apache.ctakes.dictionary.lookup2.dictionary: Given a collection of RareWordTermMapCreator.CuiTerm Objects, this factory can create a Map of RareWordTerm collections indexed by rare word.
RareWordTermMapCreator() - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
RareWordTermMapCreator.CuiTerm - Class in org.apache.ctakes.dictionary.lookup2.dictionary
RareWordTermMapCreator.CuiTerm(String, String) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
rawText - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
rawTextDirectory - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
RBFKernel - Class in org.apache.ctakes.utils.kernel
RBFKernel(double) - Constructor for class org.apache.ctakes.utils.kernel.RBFKernel
readAndParseAllLines(String) - Static method in class org.apache.ctakes.assertion.cr.NegExCorpusReader
ReadAndPreprocessForAttributeModels - Class in org.apache.ctakes.assertion.train
ReadAndPreprocessForAttributeModels() - Constructor for class org.apache.ctakes.assertion.train.ReadAndPreprocessForAttributeModels
readConceptGraph(String) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
reader - Variable in class org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator
readI2B2Challenge2010(File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readLinesFromFile(String) - Method in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
readLinesFromFile(String) - Method in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
readLinesFromFile(String) - Method in class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
readLinesFromFile(String) - Static method in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData
readMetaKeywordsFromFile(String, List) - Method in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator: Return LinkedHashMap (key:metakeyword, value:set of actual keywords belonging to metakeyword) and assign key in the insertion order (cf) LinkedHashMap.keySet() keeps the order) input file format: metakeyword|keyword|keyword...
readMiPACQ(File, File, File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readNegexTestSet(File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readNonWhiteSpaceLines(String) - Static method in class org.apache.ctakes.assertion.cr.NegExCorpusReader
readObject() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion: Write your own initialization here
readObject() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: Write your own initialization here
readObject() - Method in class org.apache.ctakes.assertion.zoner.types.Heading: Write your own initialization here
readObject() - Method in class org.apache.ctakes.assertion.zoner.types.Subzone: Write your own initialization here
readObject() - Method in class org.apache.ctakes.assertion.zoner.types.Zone: Write your own initialization here
readObject() - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.DemMarkable: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.Markable: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.MarkablePair: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.MarkablePairSet: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.NEMarkable: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.Pair: Write your own initialization here
readObject() - Method in class org.apache.ctakes.coreference.type.PronounMarkable: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.DosagesAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.DurationAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.FormAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.FrequencyAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.RouteAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.StrengthAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.sideeffect.type.PSESentence: Write your own initialization here
readObject() - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: Write your own initialization here
readObject() - Method in class org.apache.ctakes.sideeffect.type.SESentence: Write your own initialization here
readObject() - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: Write your own initialization here
readObject() - Method in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Attribute: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Course: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Date: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Element: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Entity: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Event: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Severity: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.Time: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.Affects: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.Contraindicates: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.DegreeOf: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.Diagnoses: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.Indicates: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.LocationOf: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ManagesTreats: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ManifestationOf: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.Prevents: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.Relation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ResultOf: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.TemporalRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.relation.UMLSRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.ADJP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.ADVP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.CONJP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.ContractionToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.INTJ: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.LST: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.NewlineToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.NP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.O: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.PP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.PRT: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.SBAR: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.SymbolToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.UCP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.VP: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.CourseModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.Markable: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textspan.List: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textspan.Paragraph: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textspan.Segment: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.util.Pair: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.util.Pairs: Write your own initialization here
readObject() - Method in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution: Write your own initialization here
readObject(ObjectInputStream) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel: read parent/children concept ids, not the objects
readObject() - Method in class org.apache.ctakes.ytex.uima.types.Date: Write your own initialization here
readObject() - Method in class org.apache.ctakes.ytex.uima.types.DocKey: Write your own initialization here
readObject() - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: Write your own initialization here
readOnlySharpRelations - Static variable in class org.apache.ctakes.relationextractor.data.Stats
readOrderedLinesFromFile(String) - Method in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
readPredictions(String, int) - Method in class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser: read the predictions
ReadPreprocessTrainTestJudge - Class in org.apache.ctakes.assertion.train
ReadPreprocessTrainTestJudge() - Constructor for class org.apache.ctakes.assertion.train.ReadPreprocessTrainTestJudge
readSharpSeedUmls(File, File, File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readSharpSeedUmlsCem(File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readSharpSeedUmlsCem(File, File, File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readSharpStratifiedUmls(File, File, File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readSharpUmls(File[], File, File, File, <any>) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
readXMI(File) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
rebuildCache(JCas) - Method in class org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor
recalculate() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Calculates the differences or recalculates after the two files are updated.
recall() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
recall(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
RecallBaselineEventEventRelationAnnotator - Class in org.apache.ctakes.temporal.ae.baselines
RecallBaselineEventEventRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventEventRelationAnnotator
RecallBaselineEventTimeRelationAnnotator - Class in org.apache.ctakes.temporal.ae.baselines
RecallBaselineEventTimeRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator
recallModeEvaluation - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
recallModeEvaluation - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
recallModeEvaluation - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
recallModeEvaluation - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
RECORD_DELIM - Static variable in interface org.apache.ctakes.ytex.sparsematrix.InstanceDataExporter
RecordResolutionCasConsumer - Class in org.apache.ctakes.smokingstatus.cc
RecordResolutionCasConsumer() - Constructor for class org.apache.ctakes.smokingstatus.cc.RecordResolutionCasConsumer
RecordSentence - Class in org.apache.ctakes.smokingstatus.i2b2.type: Represents a single sentence from an I2B2 record.
RecordSentence() - Constructor for class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: Never called.
RecordSentence(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: Internal - constructor used by generator
RecordSentence(JCas) - Constructor for class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence
RecordSentence(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence
RecordSentence_Type - Class in org.apache.ctakes.smokingstatus.i2b2.type: Represents a single sentence from an I2B2 record.
RecordSentence_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type: initialize variables to correspond with Cas Type and Features
RECTAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
RECTAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
recursivelyCreateStructure(JCas, TreebankNode, Parse, TopTreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
recursivelyProcessNode(JCas, TreebankNode, Set<TimeMention>, double) - Method in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
REF_PREFIX - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
referenceOutcomes - Variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
references - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
refIntArrays - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
regex - Variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
regex - Variable in class org.apache.ctakes.sideeffect.util.PatternMatch
regex - Static variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution.TemporalDurationExtractor
regex - Variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
regex - Variable in class org.apache.ctakes.ytex.uima.model.SegmentRegex
regexes - Variable in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
regexMap - Variable in class org.apache.ctakes.ytex.uima.annotators.NamedEntityRegexAnnotator
regexMap - Variable in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
regexSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
rel - Variable in class org.apache.ctakes.ytex.umls.model.MRREL
rel_conjunctSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
REL_DISCOVERY_TECH_GOLD_ANNOTATION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
rela - Variable in class org.apache.ctakes.ytex.umls.model.MRREL
Relation - Class in org.apache.ctakes.typesystem.type.relation: A superclass for semantic relationships between Elements.
Relation() - Constructor for class org.apache.ctakes.typesystem.type.relation.Relation: Never called.
Relation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Relation: Internal - constructor used by generator
Relation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Relation
RELATION_CLASSES - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
Relation_Type - Class in org.apache.ctakes.typesystem.type.relation: A superclass for semantic relationships between Elements.
Relation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Relation_Type: initialize variables to correspond with Cas Type and Features
RelationAnnotationViewer - Class in org.apache.ctakes.relationextractor.pipelines: View the annotations obtained by running the relation extractor on clinical notes.
RelationAnnotationViewer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer
RelationAnnotationViewer.Options - Class in org.apache.ctakes.relationextractor.pipelines
RelationAnnotationViewer.Options() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.Options
RelationAnnotationViewer.RelationExtractorPrinter - Class in org.apache.ctakes.relationextractor.pipelines
RelationAnnotationViewer.RelationExtractorPrinter() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.RelationExtractorPrinter
RelationArgument - Class in org.apache.ctakes.typesystem.type.relation: Relations are like lines connecting two or more endpoints.
RelationArgument() - Constructor for class org.apache.ctakes.typesystem.type.relation.RelationArgument: Never called.
RelationArgument(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.RelationArgument: Internal - constructor used by generator
RelationArgument(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.RelationArgument
RelationArgument_Type - Class in org.apache.ctakes.typesystem.type.relation: Relations are like lines connecting two or more endpoints.
RelationArgument_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type: initialize variables to correspond with Cas Type and Features
relationArgumentDistance - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
relationClass - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
relationClass - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
relationClass - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
RelationContextViewerPipeline - Class in org.apache.ctakes.temporal.data.analysis: Print gold standard relations and their context.
RelationContextViewerPipeline() - Constructor for class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline
RelationContextViewerPipeline.Options - Interface in org.apache.ctakes.temporal.data.analysis
RelationContextViewerPipeline.RelationContextPrinter - Class in org.apache.ctakes.temporal.data.analysis: Print gold standard relations and their context.
RelationContextViewerPipeline.RelationContextPrinter() - Constructor for class org.apache.ctakes.temporal.data.analysis.RelationContextViewerPipeline.RelationContextPrinter
RelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae
RelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
RelationExtractorAnnotator.IdentifiedAnnotationPair - Class in org.apache.ctakes.relationextractor.ae
RelationExtractorAnnotator.IdentifiedAnnotationPair(IdentifiedAnnotation, IdentifiedAnnotation) - Constructor for class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
RelationExtractorConsumer - Class in org.apache.ctakes.relationextractor.pipelines: This is a sample relation annotation consumer.
RelationExtractorConsumer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
RelationExtractorEvaluation - Class in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation(File, Class<? extends BinaryTextRelation>, Class<? extends RelationExtractorAnnotator>, ParameterSettings, boolean, boolean, boolean, boolean) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation: An evaluation of a relation extractor.
RelationExtractorEvaluation(File, Class<? extends BinaryTextRelation>, Class<? extends RelationExtractorAnnotator>, ParameterSettings) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
RelationExtractorEvaluation.HashableArguments - Class in org.apache.ctakes.relationextractor.eval: This class is useful for mapping the spans of relation arguments to the relation's category.
RelationExtractorEvaluation.HashableArguments(int, int, int, int) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
RelationExtractorEvaluation.HashableArguments(Annotation, Annotation) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
RelationExtractorEvaluation.HashableArguments(BinaryTextRelation) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
RelationExtractorEvaluation.Options - Interface in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations - Class in org.apache.ctakes.relationextractor.eval: Annotator that removes cTAKES mentions in the system view and copies relations from the gold view to the system view
RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations
RelationExtractorEvaluation.RemoveSmallerEventMentions - Class in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation.RemoveSmallerEventMentions() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveSmallerEventMentions
RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions - Class in org.apache.ctakes.relationextractor.eval: Annotator that removes cTAKES Mentions and Modifiers from the system view, and copies over the manually annotated Mentions and Modifiers from the gold view.
RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions
RelationExtractorPipeline - Class in org.apache.ctakes.relationextractor.pipelines: A simple pipeline that runs relation extraction on all files in a directory and saves the resulting annotations as XMI files.
RelationExtractorPipeline() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline
RelationExtractorPipeline.Options - Class in org.apache.ctakes.relationextractor.pipelines
RelationExtractorPipeline.Options() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline.Options
RelationExtractorPipelineSingleCas - Class in org.apache.ctakes.relationextractor.pipelines: Run relation extraction AE on a single sentence.
RelationExtractorPipelineSingleCas() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipelineSingleCas
RelationExtractorTrain - Class in org.apache.ctakes.relationextractor.pipelines: This class produces production models for the RelationExtractor module.
RelationExtractorTrain() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
RelationExtractorTrain.Options - Interface in org.apache.ctakes.relationextractor.pipelines
RelationFeaturesExtractor<T1,T2> - Interface in org.apache.ctakes.relationextractor.ae.features: Define an interface for people to implement feature extractors.
relationId - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
RelationInfo - Class in org.apache.ctakes.assertion.cr: Information about a relation that includes the info about the relation's arguments.
RelationInfo(String, String, String, String, String) - Constructor for class org.apache.ctakes.assertion.cr.RelationInfo
RelationInfo - Class in org.apache.ctakes.relationextractor.knowtator: Information about a relation that includes the info about the relation's arguments.
RelationInfo(String, String, String, String, String) - Constructor for class org.apache.ctakes.relationextractor.knowtator.RelationInfo
relationType - Variable in class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.RelationContextPrinter
relationTypes - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.Overlap2Contains
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveEventEventRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveEventEventRelations
relationViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations
rels - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
remainTimes - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
remove() - Method in class org.apache.ctakes.core.util.FSListIterator
remove(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
remove(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
remove(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
remove(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
remove(Object) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
removeAnnotations(JCas, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
removeArticleAndDemon(String) - Static method in class org.apache.ctakes.coreference.util.PairAttributeCalculator
removeChild(int) - Method in class org.apache.ctakes.utils.tree.SimpleTree
removeCommas(String) - Method in class org.apache.ctakes.core.fsm.adapters.NumberTokenAdapter
removeCommas(String) - Method in class org.apache.ctakes.core.fsm.token.adapter.NumberTokenAdapter
removeDoctors(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
removeDrugNerTypes(JCas, int[]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Remove most extra annotation types that we created here but not all as downstream annotators might want to use some such as SubSectionAnnotation
removeDuplicatedNEs(JCas) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: Remove duplicated NEs from Index (same type and offset)
removeEnvelopedChunks(List<Chunk>, int) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster: Remove from our local list of chunks the chunks that have been enveloped.
removeExtraneousMentions(JCas) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
removeHistoryOf(JCas) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
removeLeftOfAnnotation(JCas, TreebankNode, Annotation) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
removeList - Variable in class org.apache.ctakes.core.ae.FilterAnnotator
removeParents(HashSet<ConcRel>, HashSet<ConcRel>) - Static method in class org.apache.ctakes.ytex.kernel.model.ConcRel: remove the parents of candidate lcses from the list of parents we were planning on looking at in the next iteration
removeRelations(JCas) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
removeRightOfAnnotation(JCas, TreebankNode, Annotation) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils
removeSingleChild(Element, String, String) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
removeSingleChildText(Element, String, String) - Static method in class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
RemoveTreeAlignedMentions - Class in org.apache.ctakes.temporal.eval
RemoveTreeAlignedMentions() - Constructor for class org.apache.ctakes.temporal.eval.RemoveTreeAlignedMentions
removeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: removes value from a collection mapped with key
removeValue(K, V) - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: removes value from a collection mapped with key
removeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: removes value from a collection mapped with key
removeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: removes value from a collection mapped with key
removeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: removes value from a collection mapped with key
removeValue(K, V) - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: removes value from a collection mapped with key
replace(Object, Object, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
replace(Object, Object, Object) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
replaceChild(TreebankNode, TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
replaceDependencyWordsWithSemanticClasses(SimpleTree, SemanticClasses) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
replaceNonAsciiChars(StringBuffer, char) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor: Replaces any non-ascii characters with the specified char.
replaceNonAsciiChars(StringBuffer, char) - Static method in class org.apache.ctakes.preprocessor.Utility: Replaces any non-ascii characters with the specified char.
replaceWordsWithSemanticClasses(SimpleTree, SemanticClasses) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
reportStats(HashMap<String, Integer>, int) - Static method in class org.apache.ctakes.relationextractor.data.Stats
reset() - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
reset() - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
resetCounts() - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
resetListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
resetListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
resetListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
resetOptions() - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
ResMgr - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
ResolutionAnnotator - Class in org.apache.ctakes.smokingstatus.ae: Resolves the data produced by the KU classifier, negation detection, and PCS classifier into a single smoking status value for the given sentence.
ResolutionAnnotator() - Constructor for class org.apache.ctakes.smokingstatus.ae.ResolutionAnnotator
resolveClassification() - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries: Given all the unique classifications for a given record, resolve it down to a single final classifcation.
resolveEntity(String, String) - Method in class org.apache.ctakes.preprocessor.DTDloader
restorePreferences() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Reset GUI to preferences last saved via DBAnnotationViewerMain.savePreferences().
result - Variable in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor.StringToDoublesProcessor
result - Variable in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor.StringToDoublesProcessor
ResultOf - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
ResultOf() - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOf: Never called.
ResultOf(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOf: Internal - constructor used by generator
ResultOf(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOf
ResultOf_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
ResultOf_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOf_Type: initialize variables to correspond with Cas Type and Features
ResultOfTextRelation - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
ResultOfTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation: Never called.
ResultOfTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation: Internal - constructor used by generator
ResultOfTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation
ResultOfTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
ResultOfTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation_Type: initialize variables to correspond with Cas Type and Features
results - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
resumed() - Method in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
resumed() - Method in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl: Called when the CPM is resumed after a pause.
retainAnnType - Variable in class org.apache.ctakes.core.ae.FilterAnnotator
retainAttrTypeId - Variable in class org.apache.ctakes.core.ae.FilterAnnotator
retainMetaData(String) - Method in class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary: Tells the Dictionary to retain specific bits of metadata for each entry in the Dictionary.
retainMetaData(String) - Method in class org.apache.ctakes.dictionary.lookup.BaseDictionaryImpl: Deprecated.
retainMetaData(String) - Method in interface org.apache.ctakes.dictionary.lookup.Dictionary: Tells the Dictionary to retain specific bits of metadata for each entry in the Dictionary.
returnedClass() - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
returnedClass() - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
reverse() - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
REVERSE_LOOKUP_PROBLEM_TUI - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
REVERSE_LOOKUP_TEST_TUI - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
REVERSE_LOOKUP_TREATMENT_TUI - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
reverseLookup(ConceptType, JCas) - Static method in class org.apache.ctakes.assertion.medfacts.ConceptLookup
RGramMatrixExporter - Interface in org.apache.ctakes.ytex.R
RGramMatrixExporterImpl - Class in org.apache.ctakes.ytex.R
RGramMatrixExporterImpl() - Constructor for class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
RIGHT_SCOPE - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator
rightScopeSize - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
rmDup(JCas, LinkedList<Annotation>) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkableExpander
role - Variable in class org.apache.ctakes.assertion.cr.ArgumentInfo
role - Variable in class org.apache.ctakes.relationextractor.knowtator.ArgumentInfo
role1 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
role1 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
role2 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
role2 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
rollbackConnection() - Method in class org.apache.ctakes.jdl.data.base.JdlConnection: Undoes all changes made in the current transaction and releases any database locks currently held by this Connection object.
RomanNumeralAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
RomanNumeralAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation: Never called.
RomanNumeralAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation: Internal - constructor used by generator
RomanNumeralAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
RomanNumeralAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
RomanNumeralAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
RomanNumeralAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type: initialize variables to correspond with Cas Type and Features
RomanNumeralCondition - Class in org.apache.ctakes.core.fsm.condition: Checks whether a token is a RomanNumeralToken.
RomanNumeralCondition() - Constructor for class org.apache.ctakes.core.fsm.condition.RomanNumeralCondition
RomanNumeralFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect roman numerals in the given input of tokens.
RomanNumeralFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM: Constructor
RomanNumeralFSM.RomanNumeralCondition - Class in org.apache.ctakes.core.fsm.machine
RomanNumeralFSM.RomanNumeralCondition() - Constructor for class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM.RomanNumeralCondition
RomanNumeralToken - Class in org.apache.ctakes.core.fsm.output
RomanNumeralToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.RomanNumeralToken
root - Variable in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
rootConcept - Variable in class org.apache.ctakes.ytex.kernel.metric.LinMetric
roots - Static variable in class org.apache.ctakes.utils.wiki.ApproximateMath
route - Variable in class org.apache.ctakes.drugner.DrugMention: e.g oral Topical Examples include medications applied onto the skin, asthma medications, enema, eye or ear drops, decongestants, vaginal creams.
route - Variable in class org.apache.ctakes.drugner.elements.RouteElement
RouteAnnotation - Class in org.apache.ctakes.drugner.type: The route determination for the Drug NER profile.
RouteAnnotation() - Constructor for class org.apache.ctakes.drugner.type.RouteAnnotation: Never called.
RouteAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.RouteAnnotation: Internal - constructor used by generator
RouteAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.RouteAnnotation
RouteAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.RouteAnnotation
RouteAnnotation_Type - Class in org.apache.ctakes.drugner.type: The route determination for the Drug NER profile.
RouteAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.RouteAnnotation_Type: initialize variables to correspond with Cas Type and Features
RouteCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a RouteToken.
RouteCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.RouteCondition
RouteElement - Class in org.apache.ctakes.drugner.elements
RouteElement() - Constructor for class org.apache.ctakes.drugner.elements.RouteElement
RouteElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.RouteElement
RouteFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect route data in the given input of tokens.
RouteFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.RouteFSM: Constructor
RouteToken - Class in org.apache.ctakes.drugner.fsm.output.elements
RouteToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
row - Variable in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
RowFillerThread - Class in org.apache.ctakes.coreference.treekernel.training
RowFillerThread(ThreadDelegator, Kernel, ArrayList<Double>, int) - Constructor for class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
rowNum - Variable in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
RRFtoWideTab - Class in org.apache.ctakes.ytex.kernel: Convert RRF files to UCS2 tab-delimited format for import into SQL Server.
RRFtoWideTab() - Constructor for class org.apache.ctakes.ytex.kernel.RRFtoWideTab
rs - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
rui - Variable in class org.apache.ctakes.ytex.umls.model.MRREL
rule - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.SideEffect
rule - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
rule - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
run(Kernel) - Method in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
run() - Method in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
run(TreeKernel) - Method in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
run() - Method in class org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.DotPlotter
run() - Method in class org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.DotPlotter
run() - Method in class org.apache.ctakes.utils.build.InstallPearSilently.RunInstallation: Runs the PEAR installation process.
run - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
run - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
RUN_ID - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
RUN_ID - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
RUN_ID - Static variable in class org.apache.ctakes.assertion.train.TestAttributeModels
RunCorpusDiagnostics - Class in org.apache.ctakes.temporal.utils
RunCorpusDiagnostics() - Constructor for class org.apache.ctakes.temporal.utils.RunCorpusDiagnostics
RunCorpusDiagnostics.Options - Interface in org.apache.ctakes.temporal.utils
RunCPE - Class in org.apache.ctakes.ytex.tools: copied form Uima SimpleRunCPE example
RunCPE(String[]) - Constructor for class org.apache.ctakes.ytex.tools.RunCPE: Constructor for the class.
RunCPE.StatusCallbackListenerImpl - Class in org.apache.ctakes.ytex.tools: Callback Listener.
RunCPE.StatusCallbackListenerImpl() - Constructor for class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl
runCVD() - Static method in class org.apache.ctakes.utils.build.InstallPearSilently: This method runs the installed AE in CVD (Gladis).
runEmailTests() - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
RunJudgeAttributeInstances - Class in org.apache.ctakes.assertion.pipelines
RunJudgeAttributeInstances() - Constructor for class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances
RunJudgeAttributeInstances.Options - Class in org.apache.ctakes.assertion.pipelines
RunJudgeAttributeInstances.Options() - Constructor for class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances.Options
runNumberTests() - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
runTimexParser(String) - Static method in class org.apache.ctakes.temporal.duration.Utils: Use Bethard normalizer to map a temporal expression to a time unit.
RXNORM_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
rxNormCode - Variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile

S

s - Variable in class org.apache.ctakes.coreference.eval.helpers.Span
s - Variable in class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator
sab - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
sab - Variable in class org.apache.ctakes.ytex.umls.model.MRREL
sameSegment(List<Sentence>, Segment) - Static method in class org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator
sameTime(JCas, TimeMention, TimeMention) - Static method in class org.apache.ctakes.temporal.ae.TemporalRelationRuleAnnotator
sameTree(TreebankNode, TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
sample() - Method in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.CombineCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.DayNightWordCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.DecimalCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.DecimalRangeCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.DecimalValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.DisjoinCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.HourMinuteCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.IntegerCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.IntegerRangeCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.IntegerValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.NegateCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.NumberCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.PunctuationValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.RangeCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.RomanNumeralCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.SymbolValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.TextSetCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.TextValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.WordSetCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.condition.WordValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.core.fsm.machine.RomanNumeralFSM.RomanNumeralCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.ContainsSetTextValueCondition: Called to check if the conditional meets the criteria defined by this state.
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.DecimalStrengthStatusCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.DosageCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.DrugChangeStatusCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.FormCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.FractionCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.FractionStrengthCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.FrequencyUnitCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.RangeDosageCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.RangeStrengthCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.RouteCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.StrengthCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.StrengthUnitCombinedCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.StrengthUnitCondition
satisfiedBy(Object) - Method in class org.apache.ctakes.drugner.fsm.elements.conditions.TimeCondition
saui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
save(URI) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
save(URI) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
save(URI) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
save(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
save(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
save(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
save(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
save(URI) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
saveAnnoBase(JCas, Set<String>, int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
saveAnnoBaseHib(JCas, Set<String>, Document) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
saveAnnoBindVariables(Type, AnnoMappingInfo, PreparedStatement, int, FeatureStructure, <any>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: bind the variables to the prepared statement
saveAnnoFS(List<DocumentMapperServiceImpl.AnnoFSAttribute>, <any>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: insert composite attributes.
saveAnnoLinks(List<DocumentMapperServiceImpl.AnnoLink>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: save annotation to annotation links (many-to-many relationships)
saveAnnoPrimitive(<any>, Set<Integer>, List<DocumentMapperServiceImpl.AnnoLink>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: save the annotation properties for a given type
saveAnnotation - Variable in class org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator
saveAnnotations(Map<JdbcWriterTemplate.I2b2FieldInfo, Object>, String, String, Iterable<IdentifiedAnnotation>, boolean) - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate
saveAnnotationsHib(JCas, boolean, Set<String>, Document) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
saveClassifierEvaluation(ClassifierEvaluation, Map<Integer, String>, boolean) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
saveClassifierEvaluation(ClassifierEvaluation, Map<Integer, String>, boolean, boolean, Integer) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
saveClassifierEvaluation(ClassifierEvaluation, Map<Integer, String>, boolean) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
saveClassifierEvaluation(ClassifierEvaluation, Map<Integer, String>, boolean, boolean, Integer) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
saveDocKey(Document, DocKey) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: update the document table - set key values from dockey for the give document_id
saveDocument(JCas, String, boolean, boolean, boolean, Set<String>) - Method in interface org.apache.ctakes.ytex.uima.mapper.DocumentMapperService: Save Document and all mapped annotations.
saveDocument(JCas, String, boolean, boolean, boolean, Set<String>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
saveEntities(JCas, int, long, String, Timestamp) - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate
saveFeatureEvaluation(FeatureEvaluation, List<FeatureRank>) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
saveFeatureEvaluation(FeatureEvaluation, List<FeatureRank>) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
saveFeatureEvaluation(Map<String, ImputedFeatureEvaluatorImpl.JointDistribution>, ImputedFeatureEvaluatorImpl.Parameters, String, int, double, String, List<FeatureRank>) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
saveFeatureParentChild(FeatureParentChild) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
saveFeatureParentChild(FeatureParentChild) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
saveFold(CrossValidationFold) - Method in interface org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDao
saveFold(CrossValidationFold) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
saveI2b2Concept(Map<JdbcWriterTemplate.I2b2FieldInfo, Object>, JdbcWriterTemplate.I2b2Concept, Iterable<IdentifiedAnnotation>) - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate
saveIRStats(ClassifierEvaluation, Map<Integer, String>, Integer) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
savePreferences() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: Save user's preferences using Java's Preference API.
saveSentenceTokens(String, String, Iterable<String>) - Static method in class org.apache.ctakes.core.cc.SentenceTokensPrinter: Saves the (base) tokens of each sentence on a separate line, separated by spaces
SaxParser - Class in org.apache.ctakes.jdl.data.xml: To parse SAX.
SaxParser(String) - Constructor for class org.apache.ctakes.jdl.data.xml.SaxParser
saxSucceed() - Method in class org.apache.ctakes.jdl.data.xml.Validation
SBAR - Class in org.apache.ctakes.typesystem.type.syntax: A subordinate clause Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.SBAR Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
SBAR() - Constructor for class org.apache.ctakes.typesystem.type.syntax.SBAR: Never called.
SBAR(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SBAR: Internal - constructor used by generator
SBAR(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SBAR
SBAR(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SBAR
SBAR_Type - Class in org.apache.ctakes.typesystem.type.syntax: A subordinate clause Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.SBAR Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
SBAR_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SBAR_Type: initialize variables to correspond with Cas Type and Features
scaleTime - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
scalingFactor - Variable in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
scanner - Variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: The EndOfSentenceScanner to use when scanning for end of sentence offsets.
SCHEMA_FULL_CHECKING_FEATURE_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Schema full checking feature id (http://apache.org/xml/features/valid...full-checking).
SCHEMA_NONS_LOCATION_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Schema nons location id.
SCHEMA_VALIDATION_FEATURE_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Schema validation feature id (http://apache.org/xml/features/validation/schema).
SchemaUtil - Class in org.apache.ctakes.jdl.data.xml: Utility to manage Schema.
SchemaUtil() - Constructor for class org.apache.ctakes.jdl.data.xml.SchemaUtil
scope - Variable in enum org.apache.ctakes.ytex.kernel.SparseDataExporter.ScopeEnum
SCOPE - Static variable in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: scope property key
SCOPE_FOLD - Static variable in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: fold value for scope
SCOPE_LABEL - Static variable in interface org.apache.ctakes.ytex.kernel.SparseDataFormatter: label value for scope
SCOPE_ORDER_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "ScopeOrder" is a required, multiple, string parameter that specifies the order that the scopes should be processed in.
scopes - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
score(String) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
score(Span, Span) - Static method in class org.apache.ctakes.coreference.eval.helpers.Span
score(String) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
score(String) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
score(String) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
scoreConcept(String, Map<String, Integer>, ConceptSimilarityService.SimilarityMetricEnum, boolean) - Method in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
scui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
SD_MODEL_FILE_PARAM - Static variable in class org.apache.ctakes.core.ae.SentenceDetector
SD_MODEL_FILE_PARAM - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
sdmodel - Variable in class org.apache.ctakes.core.ae.SentenceDetector
sdmodel - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
sdModelPath - Variable in class org.apache.ctakes.core.ae.SentenceDetector
sdui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
search(String) - Method in class org.apache.ctakes.utils.wiki.WikiIndex: Search the index.
searchByCui(String) - Method in interface org.apache.ctakes.ytex.web.search.DocumentSearchService
searchByCui(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
SearchConfigBean - Class in org.apache.ctakes.ytex.web.search: JSF Bean that holds search configuration parameters.
SearchConfigBean() - Constructor for class org.apache.ctakes.ytex.web.search.SearchConfigBean
searchCUI - Variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
searchCUI - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
searchField - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
searchListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
searchListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
searchProperties - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
searchProperties - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
searchProperties - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
searchProperties - Variable in class org.apache.ctakes.ytex.web.search.SearchConfigBean
SearchResult - Class in org.apache.ctakes.utils.wiki
SearchResult(String, float) - Constructor for class org.apache.ctakes.utils.wiki.SearchResult
searchResultList - Variable in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
searchResultList - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
searchTerm - Variable in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
secondKernel - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
secondKernelIndex - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
section_names - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
SECTION_PATTERN - Static variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator
SectionHeaderExtractor - Class in org.apache.ctakes.temporal.ae.feature
SectionHeaderExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.SectionHeaderExtractor
SectionHeaderRelationExtractor - Class in org.apache.ctakes.temporal.ae.feature
SectionHeaderRelationExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor
sectionIDExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
sectionName - Variable in class org.apache.ctakes.core.util.DocumentSection
sections - Variable in class org.apache.ctakes.core.ae.SectionSegmentAnnotator
SECTIONS - Static variable in class org.apache.ctakes.temporal.eval.THYMEData
sections_path - Variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
SectionSegmentAnnotator - Class in org.apache.ctakes.core.ae: Creates a single segment annotation that spans the entire document.
SectionSegmentAnnotator() - Constructor for class org.apache.ctakes.core.ae.SectionSegmentAnnotator
sectionsToIgnore - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
Segment - Class in org.apache.ctakes.typesystem.type.textspan: A section of a clinical text, e.g., Diagnosis, Current Medications, Problem List.
Segment() - Constructor for class org.apache.ctakes.typesystem.type.textspan.Segment: Never called.
Segment(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Segment: Internal - constructor used by generator
Segment(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Segment
Segment(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Segment
Segment_Type - Class in org.apache.ctakes.typesystem.type.textspan: A section of a clinical text, e.g., Diagnosis, Current Medications, Problem List.
Segment_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Segment_Type: initialize variables to correspond with Cas Type and Features
segmentId - Variable in class org.apache.ctakes.core.ae.SectionSegmentAnnotator
segmentId - Variable in class org.apache.ctakes.core.ae.SimpleSegmentAnnotator
segmentId - Variable in class org.apache.ctakes.core.ae.SimpleSegmentWithTagsAnnotator
segmentID - Variable in class org.apache.ctakes.ytex.uima.model.SegmentRegex
SegmentMetaData - Class in org.apache.ctakes.preprocessor: MetaData about a segment.
SegmentMetaData() - Constructor for class org.apache.ctakes.preprocessor.SegmentMetaData
SegmentRegex - Class in org.apache.ctakes.ytex.uima.model: Mapped to ref_segment_regex
SegmentRegex() - Constructor for class org.apache.ctakes.ytex.uima.model.SegmentRegex
SegmentRegexAnnotator - Class in org.apache.ctakes.ytex.uima.annotators: Annotate segments (i.e.
SegmentRegexAnnotator() - Constructor for class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
segmentRegexDao - Variable in class org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator
SegmentRegexDao - Interface in org.apache.ctakes.ytex.uima.dao: Dao to access Segment Boundary Regular Expressions.
SegmentRegexDaoImpl - Class in org.apache.ctakes.ytex.uima.dao
SegmentRegexDaoImpl() - Constructor for class org.apache.ctakes.ytex.uima.dao.SegmentRegexDaoImpl
segmentRegexID - Variable in class org.apache.ctakes.ytex.uima.model.SegmentRegex
SEGMENTS_TO_SKIP - Static variable in class org.apache.ctakes.temporal.eval.THYMEData
SELECT_A - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.DeleteActionImpl
SELECT_A - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
SELECT_A_B - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.DeleteActionImpl
SELECT_B - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.DeleteActionImpl
SELECT_B - Static variable in class org.apache.ctakes.core.ae.OverlapAnnotator.ModifyActionImpl
selectBaseToken(JCas) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
selectDemonAndRelative(JCas) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
selectedFeatureNames - Variable in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
selectedFeatureNames - Variable in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
selectExact(JCas, Class<T>, Segment) - Static method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
SelectiveRelationAnnotationViewer - Class in org.apache.ctakes.relationextractor.pipelines: View relation instances in xmi files.
SelectiveRelationAnnotationViewer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer
SelectiveRelationAnnotationViewer.Options - Class in org.apache.ctakes.relationextractor.pipelines
SelectiveRelationAnnotationViewer.Options() - Constructor for class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.Options
SelectiveRelationAnnotationViewer.RelationExtractorPrinter - Class in org.apache.ctakes.relationextractor.pipelines
SelectiveRelationAnnotationViewer.RelationExtractorPrinter() - Constructor for class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
selectNE(JCas) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
selectPronoun(JCas, HashSet<String>, HashSet<String>, HashSet<String>, Logger) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
selectSentence(JCas) - Static method in class org.apache.ctakes.coreference.util.AnnotationSelector
selectTestItems(List<Integer>, int, int) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
selectTrainItems(List<Integer>, int, int) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
selFeats - Static variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
SemanticArgument - Class in org.apache.ctakes.typesystem.type.textsem: SemanticArguments are used for predicate-argument structures (SemanticRoleRelations).
SemanticArgument() - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: Never called.
SemanticArgument(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: Internal - constructor used by generator
SemanticArgument(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticArgument
SemanticArgument(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticArgument
SemanticArgument_Type - Class in org.apache.ctakes.typesystem.type.textsem: SemanticArguments are used for predicate-argument structures (SemanticRoleRelations).
SemanticArgument_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type: initialize variables to correspond with Cas Type and Features
SemanticClasses - Class in org.apache.ctakes.assertion.util
SemanticClasses(InputStream) - Constructor for class org.apache.ctakes.assertion.util.SemanticClasses
SemanticCleanupTermConsumer - Class in org.apache.ctakes.dictionary.lookup2.consumer: Refine a collection of dictionary terms to only contain the most specific variations: "colon cancer" instead of "cancer", performed by span inclusion / complete containment, not overlap Also a start at wsd by trim of overlapping terms of conflicting but related semantic group.
SemanticCleanupTermConsumer(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer
SemanticRoleRelation - Class in org.apache.ctakes.typesystem.type.textsem: Predicate-argument structure used for semantic role labeling output.
SemanticRoleRelation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: Never called.
SemanticRoleRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: Internal - constructor used by generator
SemanticRoleRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation
SemanticRoleRelation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Predicate-argument structure used for semantic role labeling output.
SemanticRoleRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type: initialize variables to correspond with Cas Type and Features
SemanticSearchBean - Class in org.apache.ctakes.ytex.web.search: JSF Backing Bean for semanticSearch.jspx.
SemanticSearchBean() - Constructor for class org.apache.ctakes.ytex.web.search.SemanticSearchBean
SemanticSimBean - Class in org.apache.ctakes.ytex.web.search
SemanticSimBean() - Constructor for class org.apache.ctakes.ytex.web.search.SemanticSimBean
SemanticSimBean.SimilarityEntry - Class in org.apache.ctakes.ytex.web.search
SemanticSimBean.SimilarityEntry() - Constructor for class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
semanticSimDescriptionMap - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
SemanticSimKernel - Class in org.apache.ctakes.ytex.kernel.evaluator
SemanticSimKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
semanticSimRegistryBean - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
SemanticSimRegistryBean - Class in org.apache.ctakes.ytex.web.search
SemanticSimRegistryBean() - Constructor for class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
semanticSimRegistryBean - Variable in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
SemanticSimServiceBean - Class in org.apache.ctakes.ytex.web.search
SemanticSimServiceBean() - Constructor for class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
semanticSimServiceList - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
semanticSimServiceMap - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
SemanticTypeKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: Before comparing semantic distance, use this kernel to filter by semantic type.
SemanticTypeKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
SemanticUtil - Class in org.apache.ctakes.dictionary.lookup2.util: Utility class to aid in the handling of semantic groups, semantic types, and tuis.
SemanticUtil() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.SemanticUtil
SemiLClassifierEvaluation - Class in org.apache.ctakes.ytex.kernel.model
SemiLClassifierEvaluation() - Constructor for class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
SemiLEvaluationParser - Class in org.apache.ctakes.ytex.semil: Parse semiL output, store in DB.
SemiLEvaluationParser() - Constructor for class org.apache.ctakes.ytex.semil.SemiLEvaluationParser
SemiLFormatterFactory - Class in org.apache.ctakes.ytex.semil: Export data for use with SemiL.
SemiLFormatterFactory() - Constructor for class org.apache.ctakes.ytex.semil.SemiLFormatterFactory
SemiLFormatterFactory.SemiLDataFormatter - Class in org.apache.ctakes.ytex.semil
SemiLFormatterFactory.SemiLDataFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
semilNumberFormat - Variable in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory.SemiLDataFormatter
sems - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionAboveLeftTreeExtractor
sems - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AssertionDependencyTreeExtractor
sems - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
sems - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
sems - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
senBegin - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.PotentialSideEffect
senEnd - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.PotentialSideEffect
SenseDisambiguatorAnnotator - Class in org.apache.ctakes.ytex.uima.annotators: Disambiguate named entities via adapated Lesk algorithm with semantic similarity.
SenseDisambiguatorAnnotator() - Constructor for class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
sensitivity - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
sentDetect(String) - Method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Detect sentences in a String.
sentDist(JCas, Markable, Markable) - Method in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
SENTDIST - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
sentence - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.PotentialSideEffect
Sentence - Class in org.apache.ctakes.typesystem.type.textspan: Sentences may or may not be fully-formed and grammatical.
Sentence() - Constructor for class org.apache.ctakes.typesystem.type.textspan.Sentence: Never called.
Sentence(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Sentence: Internal - constructor used by generator
Sentence(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Sentence
Sentence(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Sentence
SENTENCE_DETECTOR_PATH - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
Sentence_Type - Class in org.apache.ctakes.typesystem.type.textspan: Sentences may or may not be fully-formed and grammatical.
Sentence_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textspan.Sentence_Type: initialize variables to correspond with Cas Type and Features
SentenceAdjuster - Class in org.apache.ctakes.smokingstatus.ae: UIMA annotator that uses some patterns and some rules about those patterns to adjust certain annotations.
SentenceAdjuster() - Constructor for class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
sentenceCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
sentenceCount - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
SentenceDetector - Class in org.apache.ctakes.core.ae: Wraps the OpenNLP sentence detector in a UIMA annotator
SentenceDetector() - Constructor for class org.apache.ctakes.core.ae.SentenceDetector
sentenceDetector - Variable in class org.apache.ctakes.core.ae.SentenceDetector
SentenceDetector - Class in org.apache.ctakes.ytex.uima.annotators: Wraps the OpenNLP sentence detector in a UIMA annotator.
SentenceDetector() - Constructor for class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
sentenceDetector - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
SentenceDetectorCtakes - Class in org.apache.ctakes.core.sentence: A sentence detector for splitting up raw text into sentences.
SentenceDetectorCtakes(MaxentModel, SDContextGenerator, EndOfSentenceScanner) - Constructor for class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Initializes the current instance.
SentenceSpan - Class in org.apache.ctakes.core.sentence: A span of text and its offsets within some larger text
SentenceSpan(int, int, String) - Constructor for class org.apache.ctakes.core.sentence.SentenceSpan
SentenceSpan - Class in org.apache.ctakes.ytex.uima.annotators: A span of text and its offsets within some larger text
SentenceSpan(int, int, String) - Constructor for class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
sentenceText - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
sentenceText - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
SentenceTokensPrinter - Class in org.apache.ctakes.core.cc: Saves the (base) tokens of each sentence on a separate line, separated by spaces
SentenceTokensPrinter() - Constructor for class org.apache.ctakes.core.cc.SentenceTokensPrinter
sentenceToTokenNumberMap - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
sentenceViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.RemoveCrossSentenceRelations
sentenceViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.RemoveCrossSentenceRelations
sentenceViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations
sentenceViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.RemoveCrossSentenceRelations
sentPosDetect(String) - Method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Detect the position of the first words of sentences in a String.
sentProbs - Variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: The list of probabilities associated with each decision.
serializeInstanceTrees(TreeMappingInfo, String) - Method in interface org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilder
serializeInstanceTrees(TreeMappingInfo, String) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
serialVersionUID - Static variable in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
serialVersionUID - Static variable in class org.apache.ctakes.assertion.util.SemanticClasses
serialVersionUID - Static variable in exception org.apache.ctakes.dictionary.lookup.DictionaryException
serialVersionUID - Static variable in exception org.apache.ctakes.dictionary.lookup.filter.FilterException
serialVersionUID - Static variable in class org.apache.ctakes.utils.wiki.ApproximateSimilarity
serialVersionUID - Static variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.metric.LCSPath
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.ConcRel
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.FeatureRank
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.kernel.tree.Node
serialVersionUID - Static variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
serialVersionUID - Static variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog.MyListCellRenderer
serialVersionUID - Static variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.Document
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.DocumentClass
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.SegmentRegex
serialVersionUID - Static variable in class org.apache.ctakes.ytex.uima.model.UimaType
serialVersionUID - Static variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
serialVersionUID - Static variable in class org.apache.ctakes.ytex.umls.model.MRREL
serialVersionUID - Static variable in class org.apache.ctakes.ytex.umls.model.MRSTY
serialVersionUID - Static variable in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
serialVersionUID - Static variable in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
serialVersionUID - Static variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
serialVersionUID - Static variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
serialVersionUID - Static variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
serialVersionUID - Static variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
serialVersionUID - Static variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
SESentence - Class in org.apache.ctakes.sideeffect.type: Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-side-effect/target/jcasgen/typesystem.xml
SESentence() - Constructor for class org.apache.ctakes.sideeffect.type.SESentence: Never called.
SESentence(int, TOP_Type) - Constructor for class org.apache.ctakes.sideeffect.type.SESentence: Internal - constructor used by generator
SESentence(JCas) - Constructor for class org.apache.ctakes.sideeffect.type.SESentence
SESentence(JCas, int, int) - Constructor for class org.apache.ctakes.sideeffect.type.SESentence
SESentence_Type - Class in org.apache.ctakes.sideeffect.type: Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015
SESentence_Type(JCas, Type) - Constructor for class org.apache.ctakes.sideeffect.type.SESentence_Type: initialize variables to correspond with Cas Type and Features
SESentenceClassifierAnnotator - Class in org.apache.ctakes.sideeffect.ae: Classify side effect sentences and add them to SESentence
SESentenceClassifierAnnotator() - Constructor for class org.apache.ctakes.sideeffect.ae.SESentenceClassifierAnnotator
SESentenceFeatureAnnotator - Class in org.apache.ctakes.sideeffect.ae: Extract SE sentence (from PSESentence) features and add them to PSESentenceFeature.
SESentenceFeatureAnnotator() - Constructor for class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator
SESentenceFeatureAnnotator.SideEffect - Class in org.apache.ctakes.sideeffect.ae
SESentenceFeatureAnnotator.SideEffect() - Constructor for class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator.SideEffect
sessionFactory - Variable in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.uima.dao.SegmentRegexDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
sessionFactory - Variable in class org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter
sessionFactory - Variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
SET_ENV_FILE - Static variable in class org.apache.ctakes.utils.build.InstallPearSilently
setAbnormalInterpretation(DegreeOf) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: setter for abnormalInterpretation - sets
setAbnormalInterpretation(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
setAbnormalInterpretation(DegreeOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: setter for abnormalInterpretation - sets
setAbnormalInterpretation(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
setAlgorithm(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setAlleviatingFactor(ElementRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for alleviatingFactor - sets
setAlleviatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setAlleviatingFactor(ElementRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for alleviatingFactor - sets
setAlleviatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setAlleviatingFactor(ManagesTreatsTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for alleviatingFactor - sets
setAlleviatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setAlleviatingFactor(ManagesTreatsTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for alleviatingFactor - sets
setAlleviatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setAnalysisBatch(String) - Method in class org.apache.ctakes.ytex.uima.model.Document
setAnaphor(Markable) - Method in class org.apache.ctakes.coreference.type.MarkablePair: setter for anaphor - sets
setAnaphor(int, int) - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
setAnaphor(Markable) - Method in class org.apache.ctakes.coreference.type.MarkablePairSet: setter for anaphor - sets
setAnaphor(int, int) - Method in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
setAnaphoric_prob(double) - Method in class org.apache.ctakes.coreference.type.Markable: setter for anaphoric_prob - sets
setAnaphoric_prob(int, double) - Method in class org.apache.ctakes.coreference.type.Markable_Type
setAnnoBaseId(int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
setAnnoClassName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setAnnoFieldName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setAnnoMappingInfos(Set<AnnoMappingInfo>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: initialize mapAnnoMappingInfo from the set
setAntecedent(Markable) - Method in class org.apache.ctakes.coreference.type.MarkablePair: setter for antecedent - sets Proposed antecedent
setAntecedent(int, int) - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
setAntecedentList(FSList) - Method in class org.apache.ctakes.coreference.type.MarkablePairSet: setter for antecedentList - sets
setAntecedentList(int, int) - Method in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
setArg1(Element) - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation: setter for arg1 - sets
setArg1(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
setArg1(RelationArgument) - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: setter for arg1 - sets
setArg1(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
setArg1(Element) - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation: setter for arg1 - sets
setArg1(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
setArg2(Attribute) - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation: setter for arg2 - sets
setArg2(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
setArg2(RelationArgument) - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation: setter for arg2 - sets
setArg2(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
setArg2(Element) - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation: setter for arg2 - sets
setArg2(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
setArgument(Annotation) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: setter for argument - sets
setArgument(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
setArgument(SemanticArgument) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: setter for argument - sets
setArgument(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
setAsEvaluation(ASEvaluation) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
setAspect(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for aspect - sets
setAspect(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setAssertionType(String) - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion: setter for assertionType - sets assertion type -- one of present, absent, possible, conditional, hypothetical, or assocated_with_someone_else
setAssertionType(int, String) - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
setAssociatedConcept(Concept) - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion: setter for associatedConcept - sets
setAssociatedConcept(int, int) - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
setAssociatedSignSymptom(ManifestationOf) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for associatedSignSymptom - sets
setAssociatedSignSymptom(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setAssociatedSignSymptom(ManifestationOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for associatedSignSymptom - sets
setAssociatedSignSymptom(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setAttribute(String) - Method in class org.apache.ctakes.typesystem.type.util.Pair: setter for attribute - sets
setAttribute(int, String) - Method in class org.apache.ctakes.typesystem.type.util.Pair_Type
setAttributeKey(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
setAttributeName(String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue: setter for attributeName - sets
setAttributeName(int, String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
setAttributeName(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
setAttributeSelection(AttributeSelection) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
setAttributesFromOriginal(IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator: Copy values from original to mention and add mention to the indexes.
setAttributeStringValue(String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue: setter for attributeStringValue - sets
setAttributeStringValue(int, String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
setAtui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
setAui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setAui(String) - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
setAuthorSpecialty(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for authorSpecialty - sets
setAuthorSpecialty(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setAutoCommit(boolean) - Method in class org.apache.ctakes.jdl.data.base.JdlConnection
setBagOfWordsExporter(WekaBagOfWordsExporter) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
setBatchCount(int) - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter.TableSqlInfo
setBatchSize(int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setBegin(int) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
setBegin(Integer) - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
setBirthDate(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for birthDate - sets
setBirthDate(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setBodyLaterality(BodyLaterality) - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
setBodyLaterality(BodyLaterality) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setBodyLaterality(BodyLaterality) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setBodyLaterality(BodyLaterality) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setBodyLaterality(BodyLateralityModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
setBodyLaterality(BodyLateralityModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setBodyLaterality(BodyLateralityModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setBodyLaterality(BodyLateralityModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for bodyLaterality - sets
setBodyLaterality(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setBodyLocation(LocationOf) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for bodyLocation - sets
setBodyLocation(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setBodyLocation(LocationOf) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for bodyLocation - sets
setBodyLocation(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setBodyLocation(LocationOf) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for bodyLocation - sets
setBodyLocation(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setBodyLocation(LocationOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for bodyLocation - sets
setBodyLocation(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setBodyLocation(LocationOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for bodyLocation - sets
setBodyLocation(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setBodyLocation(LocationOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for bodyLocation - sets
setBodyLocation(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setBodySide(BodySide) - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
setBodySide(BodySide) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setBodySide(BodySide) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setBodySide(BodySide) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setBodySide(BodySideModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
setBodySide(BodySideModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setBodySide(BodySideModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setBodySide(BodySideModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for bodySide - sets
setBodySide(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setCacheKeyGenerator(CacheKeyGenerator) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
setCacheKeyGenerator(CacheKeyGenerator) - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
setCacheManager(CacheManager) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
setCacheManager(CacheManager) - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
setCacheManager(CacheManager) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
setCacheManager(CacheManager) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setCacheName(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CacheKernel
setCacheName(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
setCacheNorm(boolean) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
setCanonicalForm(WordToken, String) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator
setCanonicalForm(String) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: setter for canonicalForm - sets
setCanonicalForm(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
setCapitalization(WordToken, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
setCapitalization(int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: setter for capitalization - sets
setCapitalization(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
setCaps(byte) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Sets the caps state of the token.
setCas(byte[]) - Method in class org.apache.ctakes.ytex.uima.model.Document
setCategory(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for category - sets Type of Event.
setCategory(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setCategory(String) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for category - sets
setCategory(int, String) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setCategory(String) - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier: setter for category - sets
setCategory(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
setChangeStatus(String) - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation: setter for changeStatus - sets Indicates the drug change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.
setChangeStatus(int, String) - Method in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
setChangeStatusBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for changeStatusBegin - sets
setChangeStatusBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setChangeStatusEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for changeStatusEnd - sets
setChangeStatusEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setChildAnnoBaseId(int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
setChildAnnotationId(int) - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
setChildren(FSArray) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for children - sets
setChildren(int, TreebankNode) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: indexed setter for children - sets an indexed value -
setChildren(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setChildren(int, int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setChildren(List<Node>) - Method in class org.apache.ctakes.ytex.kernel.tree.Node
setChildrenArray(int[]) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
setChildUimaTypeId(int) - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
setChunkType(String) - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk: setter for chunkType - sets
setChunkType(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
setClassAuto(Integer) - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
setClasses(SortedSet<String>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setClassGold(Integer) - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
setClassIds(List<Integer>) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
setClassification(String) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: setter for classification - sets Smoking status classification for the given sentence.
setClassification(int, String) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
setClassification(String) - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: setter for classification - sets represents the document level classification that RecordResolutionAnnotator assigns
setClassification(int, String) - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
setClassifierEvaluation(ClassifierEvaluation) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setClassifierEvaluation(ClassifierEvaluation) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setClassifierEvaluationDao(ClassifierEvaluationDao) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
setClassifierEvaluationId(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setClassifierEvaluationIRStatId(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setClassifierInstanceEvaluationId(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
setClassifierInstanceEvaluations(Map<Long, ClassifierInstanceEvaluation>) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setClassifierInstanceProbabilities(Map<Integer, Double>) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityFedaCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
setClassLabel(IdentifiedAnnotation, <any>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
setCode(String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: setter for code - sets
setCode(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
setCode(String) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
setCode(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setCodingScheme(String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: setter for codingScheme - sets
setCodingScheme(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
setCodingScheme(String) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
setColumnMappingInfos(Set<ColumnMappingInfo>) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setColumnName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setCommonNode(ConllDependencyNode) - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
setConcept(ConcRel) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
setConcept1(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
setConcept1(ConceptLookupBean) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setConcept1Path(List<String>) - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
setConcept2(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
setConcept2(ConceptLookupBean) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setConcept2Path(List<String>) - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
setConceptDao(ConceptDao) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
setConceptDao(ConceptDao) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
setConceptDao(ConceptDao) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
setConceptDao(ConceptDao) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
setConceptDao(ConceptDao) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setConceptGraph(String) - Method in class org.apache.ctakes.ytex.ws.SimServiceInfo
setConceptGraphName(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setConceptGraphName(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setConceptId(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
setConceptID(String) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
setConceptId(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
setConceptList(List<ConcRel>) - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
setConceptMap(Map<String, ConcRel>) - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
setConceptPair(ConceptPair) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
setConceptPair(ConceptPair) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
setConceptPairText(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setConceptSearchService(ConceptSearchService) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
setConceptSetName(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setConceptSimilarityService(ConceptSimilarityService) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
setConceptSimilarityService(ConceptSimilarityService) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
setConceptSimilarityService(ConceptSimilarityService) - Method in class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric
setConceptSimilarityService(ConceptSimilarityService) - Method in class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
setConceptSimilarityService(ConceptSimilarityService) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
setConceptText(String) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: setter for conceptText - sets
setConceptText(int, String) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
setConceptType(String) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: setter for conceptType - sets the concept type -- one of problem, treatment, or test
setConceptType(int, String) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
setConditional(boolean) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for conditional - sets
setConditional(int, boolean) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setConditional(boolean) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for conditional - sets Whether the relation is conditional/hypothetical.
setConditional(int, boolean) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setConditional(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for conditional - sets
setConditional(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setConfidence(float) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for confidence - sets The confidence of the annotation.
setConfidence(int, float) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setConfidence(double) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for confidence - sets
setConfidence(int, double) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setConfidence(double) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for confidence - sets
setConfidence(int, double) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setConfidence(float) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for confidence - sets The confidence of the annotation.
setConfidence(int, float) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setConfidenceScoreElement(double, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setConfidenceScoreElement(double, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setConfig(Set<String>, int) - Static method in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
setContent(String) - Method in class org.apache.ctakes.core.util.DocumentSection
setContent(Annotation) - Method in class org.apache.ctakes.coreference.type.Markable: setter for content - sets The markable instance, i.e., a Named Entity, pronoun Token, etc.
setContent(int, int) - Method in class org.apache.ctakes.coreference.type.Markable_Type
setContext(String) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
setContextualAspect(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for contextualAspect - sets
setContextualAspect(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setContextualModality(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for contextualModality - sets
setContextualModality(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setContractionTokenLen(int) - Method in class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
setConverter(Converter) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setCorpusIC(double) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
setCorpusLcs(String) - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
setCorpusLcsIC(Double) - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
setCorpusLcsTerm(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setCorpusName(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
setCorpusName(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setCorpusName(String) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setCorpusName(String) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setCorpusName(String) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setCost(Double) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setCourse(Course) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for course - sets
setCourse(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setCourse(Course) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for course - sets
setCourse(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setCourse(DegreeOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for course - sets
setCourse(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setCourse(DegreeOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for course - sets
setCourse(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setCoveredText(String) - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
setCoveredTextColumn(ColumnMappingInfo) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setCpostag(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for cpostag - sets
setCpostag(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setCrossValidationFoldId(int) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setCrossValidationFoldId(int) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setCuePhrase(String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: setter for cuePhrase - sets cue phrase itself (from lookup list)
setCuePhrase(int, String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
setCuePhraseAssertionFamily(String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: setter for cuePhraseAssertionFamily - sets which assertion family this cue phrase belongs to (negation, uncertainty, or conditional)
setCuePhraseAssertionFamily(int, String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
setCuePhraseCategory(String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: setter for cuePhraseCategory - sets
setCuePhraseCategory(int, String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
setCuePhraseFirstWord(String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: setter for cuePhraseFirstWord - sets first word of cue phrase
setCuePhraseFirstWord(int, String) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
setCui(String) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: setter for cui - sets
setCui(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
setCui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setCui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
setCui1(String) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
setCui2(String) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
setCuiText(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
setCuiTuiQuery(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
setCutoff(double) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
setCvf(int) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setCvf(int) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.InfoContentEvaluatorImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMUtilImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
setDataSource(DataSource) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
setDate(Date) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: setter for date - sets
setDate(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
setDate(String) - Method in class org.apache.ctakes.ytex.uima.types.Date: setter for date - sets ISO 8601 Formatted Timestamp: yyyy-MM-dd'T'HH:mm:ssZ
setDate(int, String) - Method in class org.apache.ctakes.ytex.uima.types.Date_Type
setDateFrom(Date) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setDateTo(Date) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setDateValue(String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue: setter for dateValue - sets
setDateValue(int, String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
setDay(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Date: setter for day - sets
setDay(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
setDbSchema(String) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setDbType(String) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setDeathDate(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for deathDate - sets
setDeathDate(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setDefaultCasViewName(String) - Method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: Sets the name of the CAS View that will be displayed first in the annotation viewer.
setDefaults - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
setDefaults - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
setDegree(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for degree - sets
setDegree(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setDegree(int) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setDegree(Integer) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setDelegateKernel(Kernel) - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
setDelegateKernel(Kernel) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NodeAttributeKernel
setDelegateKernel(Kernel) - Method in class org.apache.ctakes.ytex.kernel.evaluator.NormKernel
setDelegateKernel(Kernel) - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
setDelegateKernels(List<Kernel>) - Method in class org.apache.ctakes.ytex.kernel.evaluator.ProductKernel
setDelegateKernels(List<Kernel>) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SumKernel
setDeltaFlag(LabDeltaFlag) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: setter for deltaFlag - sets
setDeltaFlag(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
setDeltaFlag(LabDeltaFlagModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: setter for deltaFlag - sets
setDeltaFlag(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
setDemographics(Demographics) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: setter for demographics - sets
setDemographics(int, int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
setDependencyNodesFromTabbedText(JCas, ArrayList<String>, StringBuffer, ArrayList<ConllDependencyNode>) - Method in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader: Store the dependency information in ConllDependencyNode-s
setDeprel(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for deprel - sets
setDeprel(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setDepth(int) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
setDepth(short) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
setDepthMax(short) - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
setDescription(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimServiceBean
setDescription(String) - Method in class org.apache.ctakes.ytex.ws.SimServiceInfo
setDialectClassName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setDisambiguated(boolean) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: setter for disambiguated - sets Word Sense disambiguation: if this named entity is assigned multiple ontologyConcepts, then the OntologyConcept with disambiguated=true is the most likely sense
setDisambiguated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
setDiscoveryTechnique(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for discoveryTechnique - sets
setDiscoveryTechnique(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setDiscoveryTechnique(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for discoveryTechnique - sets
setDiscoveryTechnique(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setDiscoveryTechnique(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for discoveryTechnique - sets
setDiscoveryTechnique(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setDistance(String) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setDocLengthMap(Map<Integer, Integer>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setDocResultInstanceImporter(DocumentResultInstanceImporter) - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
setDocText(String) - Method in class org.apache.ctakes.ytex.uima.model.Document
setDocTimeRel(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for docTimeRel - sets
setDocTimeRel(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setDocument(Document) - Method in class org.apache.ctakes.jdl.data.xml.Validation
setDocument(String) - Method in class org.apache.ctakes.jdl.data.xml.Validation
setDocument(Document) - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
setDocument(Document) - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
setDocumentAnnotationID(int) - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
setDocumentAnnotations(List<DocumentAnnotation>) - Method in class org.apache.ctakes.ytex.uima.model.Document
setDocumentClasses(Map<Integer, String>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setDocumentClasses(List<DocumentClass>) - Method in class org.apache.ctakes.ytex.uima.model.Document
setDocumentClassID(int) - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
setDocumentDate(Date) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
setDocumentID(String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID: setter for documentID - sets
setDocumentID(int, String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
setDocumentID(String) - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID: setter for documentID - sets
setDocumentID(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
setDocumentID(Integer) - Method in class org.apache.ctakes.ytex.uima.model.Document
setDocumentID(int) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
setDocumentLocator(Locator) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
setDocumentSearchService(DocumentSearchService) - Method in class org.apache.ctakes.ytex.web.search.FullTextDocumentViewBean
setDocumentSearchService(DocumentSearchService) - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
setDocumentSearchService(DocumentSearchService) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setDocumentStandard(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for documentStandard - sets
setDocumentStandard(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setDocumentTitle(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
setDocumentTypeName(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
setDomain(String) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.FedaFeatureFunction
setDosage(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for dosage - sets Dosage refers to how many of each drug the patient is taking.
setDosage(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setDosageBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for dosageBegin - sets
setDosageBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setDosageElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setDosageElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setDosageEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for dosageEnd - sets
setDosageEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setDrug(IdentifiedAnnotation) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: setter for drug - sets
setDrug(int, int) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
setDrugChangeStatus(String) - Method in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
setDrugChangeStatus(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for drugChangeStatus - sets Status refers to the whether the medication is currently being taken or not.
setDrugChangeStatus(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setDrugChangeStatusElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setDrugChangeStatusElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setDuration(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for duration - sets Duration refers to for how long the patient is expected to take the drug.
setDuration(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setDuration(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for duration - sets
setDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setDuration(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for duration - sets
setDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setDuration(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for duration - sets
setDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setDuration(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for duration - sets
setDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setDuration(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for duration - sets
setDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setDuration(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for duration - sets
setDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setDurationBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for durationBegin - sets
setDurationBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setDurationElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setDurationElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setDurationEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for durationEnd - sets
setDurationEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setEnd(int) - Method in class org.apache.ctakes.core.sentence.SentenceSpan: Set offset of end of this span within the larger text
setEnd(int) - Method in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator.NegSpan
setEnd(int) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
setEnd(int) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan: Set offset of end of this span within the larger text
setEnd(Integer) - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
setEndDate(Date) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for endDate - sets
setEndDate(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setEndDate(Date) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for endDate - sets
setEndDate(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setEndDate(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for endDate - sets
setEndDate(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setEndDateElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setEndDateElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setEndLine(int) - Method in class org.apache.ctakes.core.util.DocumentSection
setEndOffset(int) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Sets the end offset.
setEndTime(Time) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for endTime - sets
setEndTime(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setEndTime(Time) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for endTime - sets
setEndTime(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setEndTime(Time) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for endTime - sets
setEndTime(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setEndTime(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for endTime - sets
setEndTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setEndTime(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for endTime - sets
setEndTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setEndTime(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for endTime - sets
setEndTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setEntity(Entity) - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention: setter for entity - sets
setEntity(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
setEvaluation(double) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
setEvaluationType(String) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setEvent(Event) - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention: setter for event - sets
setEvent(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
setExacerbatingFactor(ElementRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for exacerbatingFactor - sets
setExacerbatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setExacerbatingFactor(ElementRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for exacerbatingFactor - sets
setExacerbatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setExacerbatingFactor(ComplicatesDisruptsTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for exacerbatingFactor - sets
setExacerbatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setExacerbatingFactor(ComplicatesDisruptsTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for exacerbatingFactor - sets
setExacerbatingFactor(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setExperiment(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setExperiment(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setExperiment(String) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setExportType(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setExternalId(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: setter for externalId - sets
setExternalId(int, int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
setExtractEventEvent(boolean) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
setExtractEventTime(boolean) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
setF1(double) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setFeats(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for feats - sets
setFeats(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setFeature(TOP) - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS: setter for feature - sets
setFeature(int, int) - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
setFeature(String) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
setFeatureEval(FeatureEvaluation) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
setFeatureEvaluationId(int) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setFeatureName(String) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
setFeatureParentChildId(int) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
setFeatureRankChild(FeatureRank) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
setFeatureRankId(int) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
setFeatureRankParent(FeatureRank) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureParentChild
setFeatures(StringArray) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: setter for features - sets
setFeatures(int, String) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: indexed setter for features - sets an indexed value -
setFeatures(int, int) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
setFeatures(int, int, String) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
setFeatureSetName(String) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setFieldInfoValue(Map<AbstractJdbcWriter.FieldInfo, Object>, AbstractJdbcWriter.FieldInfo, Object) - Static method in class org.apache.ctakes.core.cc.AbstractJdbcWriter: This is a safety method to set values of fieldInfoMaps instead of doing a direct .put in the map.
setFirstName(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for firstName - sets
setFirstName(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setFirstNameSoundex(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for firstNameSoundex - sets
setFirstNameSoundex(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setFn(int) - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
setFn(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setFocusText(String) - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: setter for FocusText - sets
setFocusText(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
setFold(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setFold(int) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setFoldGenerator(FoldGenerator) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
setFoldId(int) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setFoldId(int) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setForm(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for form - sets Form refers to the physical appearance of the drug.
setForm(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setForm(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for form - sets
setForm(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setFormBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for formBegin - sets
setFormBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFormElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setFormElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setFormEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for formEnd - sets
setFormEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFormMethod(int) - Method in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
setFp(int) - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
setFp(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setFrags(Collection<String>) - Method in class org.apache.ctakes.coreference.util.SvmVectorCreator
setFrameSet(String) - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate: setter for frameSet - sets
setFrameSet(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
setFrequency(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for frequency - sets Frequency refers to how often the patient needs to take the drug.
setFrequency(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFrequencyBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for frequencyBegin - sets
setFrequencyBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFrequencyElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setFrequencyElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setFrequencyEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for frequencyEnd - sets
setFrequencyEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFrequencyUnit(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for frequencyUnit - sets
setFrequencyUnit(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFrequencyUnitElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setFrequencyUnitElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setFs(FeatureStructure) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
setFstem(String) - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
setFuBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for fuBegin - sets
setFuBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFuEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for fuEnd - sets
setFuEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setFword(String) - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
setFword(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
setGamma(double) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setGamma(Double) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setGender(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for gender - sets
setGender(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setGeneralizeLeaf(boolean) - Method in class org.apache.ctakes.utils.tree.SimpleTree
setGeneric(boolean) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for generic - sets
setGeneric(int, boolean) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setGeneric(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for generic - sets
setGeneric(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setHead(ConllDependencyNode) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for head - sets
setHead(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setHeadIndex(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for headIndex - sets The head index tracks the index into the word tokens which is the syntactic head of a phrase.
setHeadIndex(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setHistoryOf(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for historyOf - sets
setHistoryOf(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setHistoryOf(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for historyOf - sets
setHistoryOf(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setI2B2Output(String) - Method in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
setId(int) - Method in class org.apache.ctakes.coreference.type.Markable: setter for id - sets
setId(int, int) - Method in class org.apache.ctakes.coreference.type.Markable_Type
setId(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for id - sets
setId(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setId(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for id - sets
setId(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setId(int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: setter for id - sets
setId(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
setId(int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for id - sets The token's position in the sentence.
setId(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setId(int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation: setter for id - sets
setId(int, int) - Method in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
setId(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for id - sets
setId(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setId(String) - Method in class org.apache.ctakes.typesystem.type.textspan.List: setter for id - sets
setId(int, String) - Method in class org.apache.ctakes.typesystem.type.textspan.List_Type
setId(String) - Method in class org.apache.ctakes.typesystem.type.textspan.Segment: setter for id - sets
setId(int, String) - Method in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
setIdfMap(Map<String, Integer>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setIndex(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: setter for index - sets The index of this node in the top node's list of terminals.
setIndex(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
setIndex(Integer) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoFSAttribute
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
setIndicated(boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier: setter for indicated - sets
setIndicated(int, boolean) - Method in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
setInfoContentEvaluator(InfoContentEvaluator) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
setInputFile(String) - Method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
setInstanceDataExporter(InstanceDataExporter) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
setInstanceDataExporter(InstanceDataExporter) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
setInstanceId(long) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
setInstanceId(int) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
setInstanceId(long) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
setInstanceId(long) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
setInstanceID(long) - Method in class org.apache.ctakes.ytex.uima.model.Document
setInstanceId1(long) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
setInstanceId2(long) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
setInstanceIDField(String) - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
setInstanceIDQuery(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setInstanceIds(Set<CrossValidationFoldInstance>) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setInstanceIds(SortedSet<Long>) - Method in class org.apache.ctakes.ytex.kernel.SparseData
setInstanceKernel(Kernel) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setInstanceKey(String) - Method in class org.apache.ctakes.ytex.uima.model.Document
setInstanceNominalWords(Map<Integer, SortedMap<String, String>>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setInstanceNominalWords(Map<Long, SortedMap<String, String>>) - Method in class org.apache.ctakes.ytex.kernel.SparseData
setInstanceNumericWords(Map<Integer, SortedMap<String, Double>>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setInstanceNumericWords(Map<Long, SortedMap<String, Double>>) - Method in class org.apache.ctakes.ytex.kernel.SparseData
setInstanceQueryMappingInfo(QueryMappingInfo) - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
setInstanceTreeBuilder(InstanceTreeBuilder) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setIntakeMethod(String) - Method in class org.apache.ctakes.drugner.type.RouteAnnotation: setter for intakeMethod - sets Means by which the drug was taken.
setIntakeMethod(int, String) - Method in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
setIntrinsicIC(double) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptInfo
setIntrinsicIC(boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.LinMetric
setIntrinsicICMax(double) - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
setIntrinsicInfoContent(double) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
setIntrinsicInfoContentEvaluator(IntrinsicInfoContentEvaluator) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
setIntrinsicLcs(String) - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
setIntrinsicLcsIC(Double) - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
setIntrinsicLcsTerm(String) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setionsToIgnore - Variable in class org.apache.ctakes.sideeffect.ae.PSESentenceAnnotator
setionsToIgnore - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
setIrClass(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setIrClassId(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setIsInteger(boolean) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token
setIspref(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setItems(FSList) - Method in class org.apache.ctakes.typesystem.type.textspan.List: setter for items - sets
setItems(int, int) - Method in class org.apache.ctakes.typesystem.type.textspan.List_Type
setJcas(JCas) - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
setJcas(JCas) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
setJcas(JCas) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
setJxpath(String) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setKernel(Integer) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setKernelEvaluationDao(KernelEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setKernelEvaluationDao(KernelEvaluationDao) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
setKernelEvaluationDao(KernelEvaluationDao) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
setKernelEvaluationDao(KernelEvaluationDao) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
setKernelEvaluationDao(KernelEvaluationDao) - Method in class org.apache.ctakes.ytex.weka.GramMatrixExporterImpl: Deprecated.
setKernelEvaluationId(int) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setKernelEvaluationId(int) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.kernel.FoldGeneratorImpl
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.R.RGramMatrixExporterImpl
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.semil.SemiLFormatterFactory
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
setKernelUtil(KernelUtil) - Method in class org.apache.ctakes.ytex.weka.WekaFormatterFactory
setKey(String) - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma: setter for key - sets
setKey(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
setKey(String) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: setter for key - sets
setKey(int, String) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
setKeyNameToLowerCase(boolean) - Method in class org.apache.ctakes.ytex.uima.DBCollectionReader
setKeyValuePairs(FSArray) - Method in class org.apache.ctakes.ytex.uima.types.DocKey: setter for keyValuePairs - sets
setKeyValuePairs(int, KeyValuePair) - Method in class org.apache.ctakes.ytex.uima.types.DocKey: indexed setter for keyValuePairs - sets an indexed value -
setKeyValuePairs(int, int) - Method in class org.apache.ctakes.ytex.uima.types.DocKey_Type
setKeyValuePairs(int, int, int) - Method in class org.apache.ctakes.ytex.uima.types.DocKey_Type
setLabel(String) - Method in class org.apache.ctakes.assertion.zoner.types.Heading: setter for label - sets
setLabel(int, String) - Method in class org.apache.ctakes.assertion.zoner.types.Heading_Type
setLabel(String) - Method in class org.apache.ctakes.assertion.zoner.types.Subzone: setter for label - sets
setLabel(int, String) - Method in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
setLabel(String) - Method in class org.apache.ctakes.assertion.zoner.types.Zone: setter for label - sets
setLabel(int, String) - Method in class org.apache.ctakes.assertion.zoner.types.Zone_Type
setLabel(boolean) - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: setter for label - sets
setLabel(int, boolean) - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
setLabel(boolean) - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS: setter for label - sets
setLabel(int, boolean) - Method in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
setLabel(boolean) - Method in class org.apache.ctakes.coreference.type.MarkablePair: setter for label - sets Is this pair coreferent?
setLabel(int, boolean) - Method in class org.apache.ctakes.coreference.type.MarkablePair_Type
setLabel(String) - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification: setter for label - sets
setLabel(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
setLabel(String) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: setter for label - sets
setLabel(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
setLabel(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setLabel(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
setLabel(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setLabel(String) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setLabel(String) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setLabel(String) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setLabelToClassMap(SortedMap<String, SortedSet<String>>) - Method in class org.apache.ctakes.ytex.kernel.InstanceData
setLabelToInstanceMap(SortedMap<String, SortedMap<Integer, SortedMap<Integer, SortedMap<Boolean, SortedMap<Long, String>>>>>) - Method in class org.apache.ctakes.ytex.kernel.InstanceData
setLabValue(LabValue) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: setter for labValue - sets
setLabValue(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
setLabValue(ResultOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: setter for labValue - sets
setLabValue(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
setLambda(double) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setLastName(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for lastName - sets
setLastName(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setLastNameSoundex(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for lastNameSoundex - sets
setLastNameSoundex(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setLat(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setLcs(String) - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
setLcsCache(Cache) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setLcsDist(Integer) - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
setLcsImputedType(String) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setLcsPathMap(Map<String, String>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setLcsPaths(List<LCSPath>) - Method in class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
setLeaf(boolean) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for leaf - sets
setLeaf(int, boolean) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setLeafCount(int) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
setLemma(WordToken, String, JCas) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator
setLemma(BaseToken, String, JCas) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
setLemma(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for lemma - sets
setLemma(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setLemmaEntries(FSList) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: setter for lemmaEntries - sets
setLemmaEntries(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
setLF() - Static method in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog: set default look and feel
setLibsvmUtil(LibSVMUtil) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
setLimitToRegex(boolean) - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
setLogging(Level, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
setLui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setMap(File, Map<String, String>, Map<String, Set<String>>) - Method in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator: set keyDrugMap and sideEffectMap -- skip line starting with "//"
setMapAnnoMappingInfo(Map<String, AnnoMappingInfo>) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setMapIndexWeight(Map<Integer, Double>) - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
setMatches(ValueChangeEvent) - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean: Utility method for building the match list given the current value of the SelectInputText component.
setMatches(ValueChangeEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean: Utility method for building the match list given the current value of the SelectInputText component.
setMaxSizeList(int) - Static method in class org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities: Set the maximum list size to be returned from a lucene index
setMedicationAbrs - Static variable in class org.apache.ctakes.ytex.uima.annotators.MetaMapToCTakesAnnotator
setMedicationAllergy(MedicationAllergyModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationAllergy - sets
setMedicationAllergy(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationDosage(MedicationDosage) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationDosage - sets
setMedicationDosage(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationDosage(MedicationDosage) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationDosage - sets
setMedicationDosage(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationDosage(MedicationDosageModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationDosage - sets
setMedicationDosage(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationDuration(MedicationDuration) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationDuration - sets
setMedicationDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationDuration(MedicationDuration) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationDuration - sets
setMedicationDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationDuration(MedicationDurationModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationDuration - sets
setMedicationDuration(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationForm(MedicationForm) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationForm - sets
setMedicationForm(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationForm(MedicationForm) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationForm - sets
setMedicationForm(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationForm(MedicationFormModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationForm - sets
setMedicationForm(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationFrequency(MedicationFrequency) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationFrequency - sets
setMedicationFrequency(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationFrequency(MedicationFrequency) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationFrequency - sets
setMedicationFrequency(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationFrequency(MedicationFrequencyModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationFrequency - sets
setMedicationFrequency(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationRoute(MedicationRoute) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationRoute - sets
setMedicationRoute(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationRoute(MedicationRoute) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationRoute - sets
setMedicationRoute(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationRoute(MedicationRouteModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationRoute - sets
setMedicationRoute(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationStatusChange(MedicationStatusChange) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationStatusChange - sets
setMedicationStatusChange(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationStatusChange(MedicationStatusChange) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationStatusChange - sets
setMedicationStatusChange(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationStatusChange(MedicationStatusChangeModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationStatusChange - sets
setMedicationStatusChange(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMedicationStrength(MedicationStrength) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for medicationStrength - sets
setMedicationStrength(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setMedicationStrength(MedicationStrength) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for medicationStrength - sets
setMedicationStrength(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setMedicationStrength(MedicationStrengthModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for medicationStrength - sets
setMedicationStrength(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setMembers(FSList) - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation: setter for members - sets A super-type for relationships between multiple spans of text.
setMembers(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
setMentions(FSArray) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for mentions - sets
setMentions(int, IdentifiedAnnotation) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: indexed setter for mentions - sets an indexed value -
setMentions(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setMentions(int, int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setMethod(ProcedureMethod) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for method - sets
setMethod(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setMethod(ProcedureMethodModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for method - sets
setMethod(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setMethodName(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.MethodCachingInterceptor
setMetricNames(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
setMetrics(List<ConceptSimilarityService.SimilarityMetricEnum>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setMetricSelectCorpusIC(String[]) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setMetricSelectIntrinsicIC(String[]) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setMetricSelectTaxonomy(String[]) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setMiddleName(String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics: setter for middleName - sets
setMiddleName(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
setMode(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
setModel(byte[]) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setMonth(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Date: setter for month - sets
setMonth(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
setMu(double) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setName(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setName(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setNamedEntityRegexID(int) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
setNameToFormatterMap(Map<String, SparseDataFormatterFactory>) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
setNameToParserMap(Map<String, ClassifierEvaluationParser>) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationImporter
setNegationStatus(Boolean) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setNodeIndex(int) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
setNodeQueryMappingInfos(List<QueryMappingInfo>) - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
setNodeTags(StringArray) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for nodeTags - sets
setNodeTags(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: indexed setter for nodeTags - sets an indexed value -
setNodeTags(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setNodeTags(int, int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setNodeType(String) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for nodeType - sets
setNodeType(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setNodeType(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
setNodeType(String) - Method in class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
setNodeTypes(List<NodeMappingInfo>) - Method in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
setNodeValue(String) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for nodeValue - sets
setNodeValue(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setNominalValue(String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue: setter for nominalValue - sets
setNominalValue(int, String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
setNominalWordValueMap(SortedMap<String, SortedSet<String>>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setNominalWordValueMap(SortedMap<String, SortedSet<String>>) - Method in class org.apache.ctakes.ytex.kernel.SparseData
setNorm(Double) - Method in class org.apache.ctakes.ytex.kernel.tree.Node
setNormalizedForm(BaseToken, String) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
setNormalizedForm(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Time: setter for normalizedForm - sets
setNormalizedForm(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Time_Type
setNormalizedForm(String) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: setter for normalizedForm - sets
setNormalizedForm(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
setNormalizedForm(Attribute) - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier: setter for normalizedForm - sets
setNormalizedForm(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
setNormalizedLaplacian(boolean) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setNoteSubTypeCode(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for noteSubTypeCode - sets
setNoteSubTypeCode(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setNoteTypeCode(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for noteTypeCode - sets
setNoteTypeCode(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setNpv(double) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setNumber(String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue: setter for number - sets
setNumber(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
setNumber(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: setter for number - sets
setNumber(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
setNumber(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: setter for number - sets
setNumber(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
setNumericValue(String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue: setter for numericValue - sets
setNumericValue(int, String) - Method in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
setNumericWords(SortedSet<String>) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setNumericWords(SortedSet<String>) - Method in class org.apache.ctakes.ytex.kernel.SparseData
setNumPosition(byte) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Sets the position of a number inside a Token.
setNumPosition(WordToken, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
setNumPosition(int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: setter for numPosition - sets
setNumPosition(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
setNumType(NumToken, String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
setNumType(int) - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken: setter for numType - sets
setNumType(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
setObjects(ArrayList<?>) - Static method in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
setOid(String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: setter for oid - sets
setOid(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
setOid(String) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
setOntologyConcept(OntologyConcept) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for ontologyConcept - sets
setOntologyConcept(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setOntologyConceptArr(FSArray) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for ontologyConceptArr - sets
setOntologyConceptArr(int, OntologyConcept) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: indexed setter for ontologyConceptArr - sets an indexed value -
setOntologyConceptArr(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setOntologyConceptArr(int, int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setOptions(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setOrdinalInterpretation(DegreeOf) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: setter for ordinalInterpretation - sets
setOrdinalInterpretation(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
setOrdinalInterpretation(DegreeOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: setter for ordinalInterpretation - sets
setOrdinalInterpretation(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
setOriginalEntityExternalId(int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept: setter for originalEntityExternalId - sets
setOriginalEntityExternalId(int, int) - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
setOriginalText(FSArray) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for originalText - sets The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation.
setOriginalText(int, TOP) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: indexed setter for originalText - sets an indexed value - The covered text of the span or the disjoint spans that resulted in the creation of this IdentifiedAnnotation.
setOriginalText(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setOriginalText(int, int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setOui(String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: setter for oui - sets holds the rxnorm unique identifier for a given drug mention.
setOui(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
setOutputFile(String) - Method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus
setP1(TOP) - Method in class org.apache.ctakes.coreference.type.Pair: setter for p1 - sets
setP1(int, int) - Method in class org.apache.ctakes.coreference.type.Pair_Type
setP2(TOP) - Method in class org.apache.ctakes.coreference.type.Pair: setter for p2 - sets
setP2(int, int) - Method in class org.apache.ctakes.coreference.type.Pair_Type
setPageRankService(PageRankService) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setPairs(FSArray) - Method in class org.apache.ctakes.typesystem.type.util.Pairs: setter for pairs - sets
setPairs(int, Pair) - Method in class org.apache.ctakes.typesystem.type.util.Pairs: indexed setter for pairs - sets an indexed value -
setPairs(int, int) - Method in class org.apache.ctakes.typesystem.type.util.Pairs_Type
setPairs(int, int, int) - Method in class org.apache.ctakes.typesystem.type.util.Pairs_Type
setParam1(double) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setParam1(Double) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setParam1(double) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setParam1(double) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setParam2(String) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setParam2(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setParam2(String) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureEvaluation
setParam2(String) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluation
setParent(TreebankNode) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode: setter for parent - sets
setParent(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
setParentAnnoBaseId(int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.AnnoLink
setParentAnnotationId(int) - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
setParentsArray(int[]) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
setParentSectionId(String) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: setter for parentSectionId - sets The section in which the subsection was found.
setParentSectionId(int, String) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
setParentUimaTypeId(int) - Method in class org.apache.ctakes.ytex.uima.model.AnnotationContainmentLink
setParticipatesIn(FSList) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: setter for participatesIn - sets
setParticipatesIn(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
setPartOfSpeech(String) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: setter for partOfSpeech - sets
setPartOfSpeech(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
setPatientID(long) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: setter for patientID - sets
setPatientID(int, long) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
setPatientId(Integer) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setPattern(Pattern) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
setPdeprel(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for pdeprel - sets
setPdeprel(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setPercentLabeled(double) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setPeriod(float) - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation: setter for period - sets The periodic unit used, e.g day, month, hour, etc.
setPeriod(int, float) - Method in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
setPermanence(String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for permanence - sets
setPermanence(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setPhead(ConllDependencyNode) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for phead - sets
setPhead(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setPolarity(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for polarity - sets
setPolarity(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setPolarity(int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties: setter for polarity - sets
setPolarity(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
setPolarity(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for polarity - sets
setPolarity(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setPolarity(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for polarity - sets
setPolarity(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setPostag(String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode: setter for postag - sets
setPostag(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
setPosTag(String) - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma: setter for posTag - sets
setPosTag(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
setPow(double) - Method in class org.apache.ctakes.ytex.kernel.evaluator.ConvolutionKernel
setPow(int) - Method in class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
setPpv(double) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setPredicate(Predicate) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation: setter for predicate - sets
setPredicate(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
setPredictedClassId(int) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
setPredictedClassId(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
setPreferredText(String) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: setter for preferredText - sets preferredText is the preferred term.
setPreferredText(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
setPreferredText(String) - Method in class org.apache.ctakes.typesystem.type.textspan.Segment: setter for preferredText - sets preferredText is the normalized/resolved section name.
setPreferredText(int, String) - Method in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
setPreload(boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setPrepareScript(String) - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
setPrepareScriptStatementDelimiter(String) - Method in class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
setPrepStmtValues(PreparedStatement, List<String>) - Method in class org.apache.ctakes.core.cr.JdbcCollectionReader: Helper method that sets the prepared statement values.
setPrimaryAssociatedCodeElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setPrimaryAssociatedCodeElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setProbabilities(double[]) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
setProcedureDevice(ProcedureDevice) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for procedureDevice - sets
setProcedureDevice(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setProcedureDevice(ProcedureDeviceModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for procedureDevice - sets
setProcedureDevice(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setProperties(Properties) - Method in class org.apache.ctakes.jdl.common.PropertiesFile
setProperties(EventProperties) - Method in class org.apache.ctakes.typesystem.type.refsem.Event: setter for properties - sets
setProperties(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Event_Type
setProviderID(LongArray) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: setter for providerID - sets
setProviderID(int, long) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: indexed setter for providerID - sets an indexed value -
setProviderID(int, int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
setProviderID(int, int, long) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
setPseSen(PSESentence) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature: setter for pseSen - sets
setPseSen(int, int) - Method in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
setQuery(String) - Method in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
setQueryArgs(Map<String, Object>) - Method in class org.apache.ctakes.ytex.kernel.tree.QueryMappingInfo
setRank(int) - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
setRankCutoff(Integer) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel
setReason(FSArray) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for reason - sets
setReason(int, TOP) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: indexed setter for reason - sets an indexed value -
setReason(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setReason(int, int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setRecordID(String) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: setter for recordID - sets ID of record that this sentence belongs to.
setRecordID(int, String) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
setRecordID(String) - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: setter for recordID - sets Represents the document record id
setRecordID(int, String) - Method in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
setRecordTextBegin(int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: setter for recordTextBegin - sets Begin offset of the sentence relative to the entire record text.
setRecordTextBegin(int, int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
setRecordTextEnd(int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence: setter for recordTextEnd - sets End offset of the sentence relative to the entire record text.
setRecordTextEnd(int, int) - Method in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
setReferenceRangeNarrative(LabReferenceRange) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab: setter for referenceRangeNarrative - sets
setReferenceRangeNarrative(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
setReferenceRangeNarrative(LabReferenceRangeModifier) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention: setter for referenceRangeNarrative - sets
setReferenceRangeNarrative(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
setRegex(String) - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
setRegex(String) - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
setRel(String) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
setRela(String) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
setRelation(SemanticRoleRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument: setter for relation - sets
setRelation(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
setRelations(FSList) - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate: setter for relations - sets
setRelations(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
setRelativeTemporalContext(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setRelativeTemporalContext(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setRelativeTemporalContext(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setRelativeTemporalContext(TemporalRelation) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setRelativeTemporalContext(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setRelativeTemporalContext(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setRelativeTemporalContext(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setRelativeTemporalContext(TemporalTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for relativeTemporalContext - sets
setRelativeTemporalContext(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setResults(List<ClassifierEvaluationResult>) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResults
setRole(String) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument: setter for role - sets
setRole(int, String) - Method in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
setRoot(String) - Method in class org.apache.ctakes.ytex.kernel.model.ConceptGraph
setRoute(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for route - sets Medication route refers to the way that a drug is introduced into the body.
setRoute(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setRouteBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for routeBegin - sets
setRouteBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setRouteElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setRouteElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setRouteEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for routeEnd - sets
setRouteEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setRow(ArrayList<Double>, int) - Method in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
setRui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
setRule(String) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
setRun(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluation
setRun(int) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setSab(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setSab(String) - Method in class org.apache.ctakes.ytex.umls.model.MRREL
setSaui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setSchema(Schema) - Method in class org.apache.ctakes.jdl.data.xml.Validation
setSchema(String) - Method in class org.apache.ctakes.jdl.data.xml.Validation
setScope(String) - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation: setter for Scope - sets
setScope(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
setScore(double) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept: setter for score - sets Word Sense disambiguation: if this named entity is assigned multiple ontologyConcepts, the score represents how similar this sense is to surrounding senses (higher scores = more likely to be the correct sense)
setScore(int, double) - Method in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
setScui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setSdui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setSearchCUI(ConceptFirstWord) - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
setSearchCUI(ConceptFirstWord) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setSearchProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
setSearchProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
setSearchProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
setSearchProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.SearchConfigBean
setSearchResultList(List<Map<String, Object>>) - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
setSearchResultList(List<DocumentSearchResult>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setSearchTerm(String) - Method in class org.apache.ctakes.ytex.web.search.FullTextSearchBean
setSecondaryAssociatedCodeElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setSecondaryAssociatedCodeElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setSectionName(String) - Method in class org.apache.ctakes.core.util.DocumentSection
setSegmentID(String) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for segmentID - sets
setSegmentID(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setSegmentId(String) - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence: setter for segmentId - sets
setSegmentId(int, String) - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
setSegmentID(String) - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
setSegmentRegexID(int) - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
setSemanticSimRegistryBean(SemanticSimRegistryBean) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setSemanticSimRegistryBean(SemanticSimRegistryBean) - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
setSemanticSimServiceList(List<SemanticSimServiceBean>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimRegistryBean
setSensitivity(double) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setSentence(SESentence) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: setter for sentence - sets sentence containing side effect
setSentence(int, int) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
setSentenceID(String) - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation: setter for sentenceID - sets
setSentenceID(int, String) - Method in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
setSentenceID(String) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for sentenceID - sets contains the sentence id of the sentence that contains the NE's text span
setSentenceID(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setSentenceNumber(int) - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence: setter for sentenceNumber - sets
setSentenceNumber(int, int) - Method in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
setSentenceText(String) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.kernel.dao.ClassifierEvaluationDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.uima.dao.DocumentDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.uima.dao.NamedEntityRegexDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.uima.dao.SegmentRegexDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.weka.DocumentResultInstanceImporter
setSessionFactory(SessionFactory) - Method in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
setSeverity(String) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for severity - sets
setSeverity(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setSeverity(DegreeOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for severity - sets
setSeverity(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setSeverity(DegreeOfTextRelation) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for severity - sets
setSeverity(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setSideEffect(IdentifiedAnnotation) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: setter for sideEffect - sets side effect mention in NamedEntity
setSideEffect(int, int) - Method in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
setSimilarities(List<Double>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
setSimilarity(double) - Method in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
setSimilarityInfo(SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
setSimilarityList(List<SemanticSimBean.SimilarityEntry>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setSimilarityMap(Map<ConceptSimilarityService.SimilarityMetricEnum, Double>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setSimilarityMap(Map<ConceptSimilarityService.SimilarityMetricEnum, Double>) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
setSimilarityMetricMap(Map<ConceptSimilarityService.SimilarityMetricEnum, SimilarityMetric>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setSimInfo(SimilarityInfo) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
setSize(int) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setSkipTrain(boolean) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
setSkipTrainComponents(boolean) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
setSoftLabel(boolean) - Method in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
setSourceApplication(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceApplication - sets
setSourceApplication(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSourceData(SourceData) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata: setter for sourceData - sets
setSourceData(int, int) - Method in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
setSourceEncounterId(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceEncounterId - sets
setSourceEncounterId(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSourceInstanceId(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceInstanceId - sets
setSourceInstanceId(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSourceInstitution(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceInstitution - sets
setSourceInstitution(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSourceOriginalDate(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceOriginalDate - sets
setSourceOriginalDate(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSourceRevisionDate(String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceRevisionDate - sets
setSourceRevisionDate(int, String) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSourceRevisionNbr(int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData: setter for sourceRevisionNbr - sets
setSourceRevisionNbr(int, int) - Method in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
setSparseDataExporter(SparseDataExporter) - Method in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
setSpecificity(double) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setSplitName(String) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
setSql(String) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setSqlType(int) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setSrcXml(String) - Method in class org.apache.ctakes.jdl.data.xml.DomParser
setSrcXml(String) - Method in class org.apache.ctakes.jdl.data.xml.SaxParser
setSrl(int) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setStart(int) - Method in class org.apache.ctakes.core.sentence.SentenceSpan: Set offset of start of this span within the larger text
setStart(int) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
setStart(int) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan: Set offset of start of this span within the larger text
setStartDate(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for startDate - sets
setStartDate(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setStartDate(Date) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication: setter for startDate - sets
setStartDate(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
setStartDate(Date) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention: setter for startDate - sets
setStartDate(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
setStartDate(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention: setter for startDate - sets
setStartDate(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
setStartDateElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setStartDateElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setStartLine(int) - Method in class org.apache.ctakes.core.util.DocumentSection
setStartOffset(int) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Sets the start offset.
setStartTime(Time) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder: setter for startTime - sets
setStartTime(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
setStartTime(Time) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure: setter for startTime - sets
setStartTime(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
setStartTime(Time) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom: setter for startTime - sets
setStartTime(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
setStartTime(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention: setter for startTime - sets
setStartTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
setStartTime(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention: setter for startTime - sets
setStartTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
setStartTime(TimeMention) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: setter for startTime - sets
setStartTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
setStatus(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for status - sets
setStatus(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setStatus(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: setter for status - sets Status of 'possible', 'history of', or 'family history of'.
setStatus(int, int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
setStemmedStr(String) - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
setStn(String) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
setStopWordsList(HashSet<String>) - Method in class org.apache.ctakes.coreference.util.AttributeCalculator
setStr(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setStrength(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for strength - sets
setStrength(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setStrengthBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for strengthBegin - sets
setStrengthBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setStrengthElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setStrengthElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setStrengthEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for strengthEnd - sets
setStrengthEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setStrengthUnit(String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for strengthUnit - sets
setStrengthUnit(int, String) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setStrengthUnitElement(String, int, int) - Method in class org.apache.ctakes.drugner.DrugMention
setStrengthUnitElement(String, int, int) - Method in interface org.apache.ctakes.drugner.DrugModel
setStt(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setSty(String) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
setSuBegin(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for suBegin - sets
setSuBegin(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setSubject(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for subject - sets
setSubject(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setSubject(String) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for subject - sets
setSubject(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setSubSectionBodyBegin(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: setter for subSectionBodyBegin - sets Sub-section body begin offset.
setSubSectionBodyBegin(int, int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
setSubSectionBodyEnd(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: setter for subSectionBodyEnd - sets Sub-section body end offset.
setSubSectionBodyEnd(int, int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
setSubSectionHeaderBegin(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: setter for subSectionHeaderBegin - sets Begin offset of subSection header
setSubSectionHeaderBegin(int, int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
setSubSectionHeaderEnd(int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation: setter for subSectionHeaderEnd - sets Ending offset of subsection header
setSubSectionHeaderEnd(int, int) - Method in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
setSubsumerCount(int) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
setSuEnd(int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation: setter for suEnd - sets
setSuEnd(int, int) - Method in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
setSuggestion(String) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken: setter for suggestion - sets
setSuggestion(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
setSui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setSupportVectors(Integer) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setSuppress(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setTableName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setTableName(String) - Method in class org.apache.ctakes.ytex.uima.model.UimaType
setTag(String) - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
setTargetClassId(int) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
setTargetClassId(Integer) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
setTargetClassName(String) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
setTargetTypeName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
setTask(String) - Method in class org.apache.ctakes.ytex.uima.model.DocumentClass
setTerminals(FSArray) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: setter for terminals - sets Stores the terminal nodes of the parse tree.
setTerminals(int, TerminalTreebankNode) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: indexed setter for terminals - sets an indexed value - Stores the terminal nodes of the parse tree.
setTerminals(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
setTerminals(int, int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
setText(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token
setText(String) - Method in class org.apache.ctakes.core.sentence.SentenceSpan
setText(String) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData
setText(String) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
setText(String) - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
setTfIdf(boolean) - Method in class org.apache.ctakes.ytex.kernel.BagOfWordsData
setTime(Time) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: setter for time - sets
setTime(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
setTimeClass(String) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention: setter for timeClass - sets DATE, DURATION, QUANTIFIER, PREPOSTEXP, etc.
setTimeClass(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
setTn(int) - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
setTn(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setTokenIndex(int) - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: setter for tokenIndex - sets The tokenIndex of a terminal is n, where the terminal is the nth token in a sentence.
setTokenIndex(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
setTokenizedStr(String) - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
setTokenNumber(int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken: setter for tokenNumber - sets
setTokenNumber(int, int) - Method in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
setTp(int) - Method in class org.apache.ctakes.ytex.kernel.IRMetrics
setTp(int) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setTrain(boolean) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
setTrain(boolean) - Method in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
setTrainFileToDomain(Map<String, String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
setTransactionManager(PlatformTransactionManager) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setTree(String) - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree: setter for tree - sets
setTree(int, String) - Method in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
setTreebankParse(String) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: setter for treebankParse - sets A bracketed sentence string representing the parse tree.
setTreebankParse(int, String) - Method in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
setTreeMappingInfo(TreeMappingInfo) - Method in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
setTs(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setTty(String) - Method in class org.apache.ctakes.ytex.umls.model.MRCONSO
setTui(String) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: setter for tui - sets
setTui(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
setTui(String) - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
setTxTemplateNew(TransactionTemplate) - Method in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
setType(byte) - Method in class org.apache.ctakes.core.nlp.tokenizer.Token: Sets the type of the token.
setType(String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Sets the type name of this annotation.
setType(String) - Method in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
setType(String) - Method in class org.apache.ctakes.ytex.kernel.tree.Node
setTypeID(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for typeID - sets The type of named entity (e.g.
setTypeID(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setTypesToIgnore - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
setUimaDocId(JCas, Document, String, String) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: get the document id from the specified type and feature.
setUimaType(UimaType) - Method in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
setUimaTypeId(int) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setUimaTypeID(int) - Method in class org.apache.ctakes.ytex.uima.model.UimaType
setUimaTypeIdColumnName(String) - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
setUimaTypeName(String) - Method in class org.apache.ctakes.ytex.uima.model.UimaType
setUmlsDao(UMLSDao) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
setUmlsFirstWordService(ConceptSearchService) - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
setUmlsFirstWordService(ConceptSearchService) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
setUncertainty(int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element: setter for uncertainty - sets
setUncertainty(int, int) - Method in class org.apache.ctakes.typesystem.type.refsem.Element_Type
setUncertainty(int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation: setter for uncertainty - sets
setUncertainty(int, int) - Method in class org.apache.ctakes.typesystem.type.relation.Relation_Type
setUncertainty(int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation: setter for uncertainty - sets
setUncertainty(int, int) - Method in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
setUnit(String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue: setter for unit - sets
setUnit(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
setUnit(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency: setter for unit - sets The periodic unit used, e.g day, month, hour, etc.
setUnit(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
setUnit(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength: setter for unit - sets the unit of measurement
setUnit(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
SetupAuiFirstWord - Class in org.apache.ctakes.ytex.tools: setup umls_aui_fword table
SetupAuiFirstWord() - Constructor for class org.apache.ctakes.ytex.tools.SetupAuiFirstWord: Initialize tokenizer using the hyphen map from "tokenizer/hyphenated.txt".
setupAuiFirstWord() - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
setValue(TOP) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
setValue(TOP) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeatureFromFeature
setValue(TOP) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedRelationFeature
setValue(TOP) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
setValue(TOP) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeatureFromFeature
setValue(TOP) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
setValue(String) - Method in class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Course: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Course_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange: setter for value - sets Indicates the change status of 'stop', 'start', 'increase', 'decrease', or 'noChange'.
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Severity: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
setValue(String) - Method in class org.apache.ctakes.typesystem.type.util.Pair: setter for value - sets
setValue(int, String) - Method in class org.apache.ctakes.typesystem.type.util.Pair_Type
setValue(Map<String, Serializable>) - Method in class org.apache.ctakes.ytex.kernel.tree.Node
setValueFrom(Map<String, ? extends TOP>) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader.DelayedFeature
setValueFrom(Map<String, ? extends TOP>) - Method in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
setValueLong(long) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: setter for valueLong - sets
setValueLong(int, long) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
SetValuePostLookupFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter: A filter that uses a value to filter against a MetaDataHit.
SetValuePostLookupFilterImpl(String, int, int, boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.SetValuePostLookupFilterImpl
setValues(Set<String>) - Method in class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
setValues(PreparedStatement, int, T) - Method in interface org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.ChunkPreparedStatementSetter
setValueString(String) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair: setter for valueString - sets
setValueString(int, String) - Method in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
setVcdim(Double) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setWeight(String) - Method in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
setWordTokenLen(int) - Method in class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
setYear(String) - Method in class org.apache.ctakes.typesystem.type.refsem.Date: setter for year - sets
setYear(int, String) - Method in class org.apache.ctakes.typesystem.type.refsem.Date_Type
setYtexProperties(Properties) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
setYtexProperties(Properties) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
setYtexProperties(Properties) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
setYtexProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
setYtexProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
setYtexProperties(Properties) - Method in class org.apache.ctakes.ytex.web.search.DocumentViewBean
SEUtil - Class in org.apache.ctakes.sideeffect.util: Utility methods used in the project
SEUtil() - Constructor for class org.apache.ctakes.sideeffect.util.SEUtil
Severity - Class in org.apache.ctakes.typesystem.type.refsem: An explicitly-mentioned indication of the seriousness of a condition.
Severity() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Severity: Never called.
Severity(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Severity: Internal - constructor used by generator
Severity(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Severity
Severity_Type - Class in org.apache.ctakes.typesystem.type.refsem: An explicitly-mentioned indication of the seriousness of a condition.
Severity_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Severity_Type: initialize variables to correspond with Cas Type and Features
SeverityModifier - Class in org.apache.ctakes.typesystem.type.textsem: An explicitly-mentioned indication of the seriousness of a condition.
SeverityModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.SeverityModifier: Never called.
SeverityModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SeverityModifier: Internal - constructor used by generator
SeverityModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SeverityModifier
SeverityModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SeverityModifier
SeverityModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: An explicitly-mentioned indication of the seriousness of a condition.
SeverityModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type: initialize variables to correspond with Cas Type and Features
SGTFormatterFactory - Class in org.apache.ctakes.ytex.svmlight: For each scope, create a data.txt file.
SGTFormatterFactory() - Constructor for class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory
SGTFormatterFactory.SGTFormatter - Class in org.apache.ctakes.ytex.svmlight
SGTFormatterFactory.SGTFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.svmlight.SGTFormatterFactory.SGTFormatter
shallowCopy() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Clones this object, its attributes, and reference keys.
SHAMPOO - Static variable in class org.apache.ctakes.drugner.elements.FormElement
shareAllXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
shareDevXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
shareTestXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
shareTrainXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
SHARP_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_I2B2_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_I2B2_MIPACQ_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_I2B2_MIPACQ_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_I2B2_MIPACQ_NEGEX_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_I2B2_MIPACQ_NEGEX_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_I2B2_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_I2B2_NEGEX_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_I2B2_NEGEX_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_MIPACQ_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_MIPACQ_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_MIPACQ_NEGEX_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_MIPACQ_NEGEX_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_NEGEX_FEDA - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
SHARP_NEGEX_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_SEED_CORPUS - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
SHARP_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
SHARP_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTests
SHARP_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
SHARP_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
sharpAllXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
SharpCorpusSplit - Class in org.apache.ctakes.assertion.pipelines
SharpCorpusSplit() - Constructor for class org.apache.ctakes.assertion.pipelines.SharpCorpusSplit
SharpCorpusSplit.Subcorpus - Enum in org.apache.ctakes.assertion.pipelines
SharpCorpusSplit.Subcorpus() - Constructor for enum org.apache.ctakes.assertion.pipelines.SharpCorpusSplit.Subcorpus
sharpDevXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
SHARPKnowtatorXMLDefaults - Class in org.apache.ctakes.core.util: A helper class that centralizes methods to assign all the default values from the SHARP corpus annotation guidelines.
SHARPKnowtatorXMLDefaults() - Constructor for class org.apache.ctakes.core.util.SHARPKnowtatorXMLDefaults
SHARPKnowtatorXMLReader - Class in org.apache.ctakes.core.ae
SHARPKnowtatorXMLReader() - Constructor for class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
SHARPKnowtatorXMLReader.DelayedFeature - Class in org.apache.ctakes.core.ae
SHARPKnowtatorXMLReader.DelayedFeature(Annotation, String, KnowtatorAnnotation) - Constructor for class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeature
SHARPKnowtatorXMLReader.DelayedFeatureFromFeature - Class in org.apache.ctakes.core.ae
SHARPKnowtatorXMLReader.DelayedFeatureFromFeature(Annotation, String, KnowtatorAnnotation) - Constructor for class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedFeatureFromFeature
SHARPKnowtatorXMLReader.DelayedRelation - Class in org.apache.ctakes.core.ae
SHARPKnowtatorXMLReader.DelayedRelation() - Constructor for class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
SHARPKnowtatorXMLReader.DelayedRelationFeature - Class in org.apache.ctakes.core.ae
SHARPKnowtatorXMLReader.DelayedRelationFeature(Annotation, String, KnowtatorAnnotation, Class<? extends BinaryTextRelation>, Annotation, Class<? extends Annotation>, Annotation, Class<? extends Annotation>) - Constructor for class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelationFeature
sharpRelationsAll - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsHighPriority - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsLowPriority - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsSelected - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpTestXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpTrainXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
SHARPXMI - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI() - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI
SHARPXMI.CopyDocumentTextToGoldView - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI.CopyDocumentTextToGoldView() - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI.CopyDocumentTextToGoldView
SHARPXMI.DocumentIDAnnotator - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI.DocumentIDAnnotator() - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI.DocumentIDAnnotator
SHARPXMI.EvaluateOn - Enum in org.apache.ctakes.relationextractor.eval
SHARPXMI.EvaluateOn() - Constructor for enum org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluateOn
SHARPXMI.Evaluation_ImplBase - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI.Evaluation_ImplBase(File) - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI.Evaluation_ImplBase
SHARPXMI.EvaluationOptions - Interface in org.apache.ctakes.relationextractor.eval
SHARPXMI.Options - Interface in org.apache.ctakes.relationextractor.eval
shortType() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Returns a short description of this XcasAnnotation's type, specifically, the last segment as separated by dots.
SideEffectAnnotation - Class in org.apache.ctakes.sideeffect.type: Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-side-effect/target/jcasgen/typesystem.xml
SideEffectAnnotation() - Constructor for class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: Never called.
SideEffectAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.sideeffect.type.SideEffectAnnotation: Internal - constructor used by generator
SideEffectAnnotation(JCas) - Constructor for class org.apache.ctakes.sideeffect.type.SideEffectAnnotation
SideEffectAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.sideeffect.type.SideEffectAnnotation
SideEffectAnnotation_Type - Class in org.apache.ctakes.sideeffect.type: Updated by JCasGen Wed Sep 30 11:06:01 EDT 2015
SideEffectAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type: initialize variables to correspond with Cas Type and Features
SideEffectAnnotator - Class in org.apache.ctakes.sideeffect.ae: Rule-based side effect extraction.
SideEffectAnnotator() - Constructor for class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
SideEffectAnnotator.PotentialSideEffect - Class in org.apache.ctakes.sideeffect.ae
SideEffectAnnotator.PotentialSideEffect() - Constructor for class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.PotentialSideEffect
SideEffectAnnotator.SideEffect - Class in org.apache.ctakes.sideeffect.ae
SideEffectAnnotator.SideEffect() - Constructor for class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.SideEffect
SideEffectCasConsumer - Class in org.apache.ctakes.sideeffect.cc
SideEffectCasConsumer() - Constructor for class org.apache.ctakes.sideeffect.cc.SideEffectCasConsumer
sideEffectMap - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
SideEffectSentenceCasConsumer - Class in org.apache.ctakes.sideeffect.cc
SideEffectSentenceCasConsumer() - Constructor for class org.apache.ctakes.sideeffect.cc.SideEffectSentenceCasConsumer
sideEffectWord - Variable in class org.apache.ctakes.sideeffect.ae.SideEffectAnnotator
SignSymptom - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Sign or Symtom.
SignSymptom() - Constructor for class org.apache.ctakes.typesystem.type.refsem.SignSymptom: Never called.
SignSymptom(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.SignSymptom: Internal - constructor used by generator
SignSymptom(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.SignSymptom
SignSymptom_Type - Class in org.apache.ctakes.typesystem.type.refsem: This is an Event from the UMLS semantic group of Sign or Symtom.
SignSymptom_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type: initialize variables to correspond with Cas Type and Features
SignSymptomMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (SignSymptom) Event.
SignSymptomMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: Never called.
SignSymptomMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention: Internal - constructor used by generator
SignSymptomMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
SignSymptomMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
SignSymptomMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string that refers to a (SignSymptom) Event.
SignSymptomMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type: initialize variables to correspond with Cas Type and Features
sim(Parse, Parse) - Method in class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
sim(svm_node[], svm_node[]) - Method in class org.apache.ctakes.utils.kernel.PolyKernel
sim(String, String, ConceptGraph, int, double, double) - Method in interface org.apache.ctakes.ytex.kernel.pagerank.PageRankService
sim(String, String, ConceptGraph, int, double, double) - Method in class org.apache.ctakes.ytex.kernel.pagerank.PageRankServiceImpl: compute similarity using personalized page rank, as documented in Exploring Knowledge Bases for Similarity
sim1 - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
sim2 - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
similarities - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
similarities(String, ConceptPair[], String[], boolean) - Method in interface org.apache.ctakes.ytex.ws.ConceptSimilarityWebService: compute similarity for a list of concept pairs
similarities(String, ConceptPair[], String[], boolean) - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
similarity - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
similarity(List<ConceptSimilarityService.SimilarityMetricEnum>, String, String, Map<String, Double>, boolean) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: compute similarity for a pair of concepts
similarity(List<ConceptPair>, List<ConceptSimilarityService.SimilarityMetricEnum>, Map<String, Double>, boolean) - Method in interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService: compute similarity for a list of concept pairs
similarity(List<ConceptPair>, List<ConceptSimilarityService.SimilarityMetricEnum>, Map<String, Double>, boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
similarity(List<ConceptSimilarityService.SimilarityMetricEnum>, String, String, Map<String, Double>, boolean) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.IntrinsicLCHMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.IntrinsicPathMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.IntrinsicRadaMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.JaccardMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.LCHMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.LinMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.PageRankMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.PathMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.RadaMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in interface org.apache.ctakes.ytex.kernel.metric.SimilarityMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.SokalSneathMetric
similarity(String, String, Map<String, Double>, SimilarityInfo) - Method in class org.apache.ctakes.ytex.kernel.metric.WuPalmerMetric
similarity - Variable in class org.apache.ctakes.ytex.kernel.model.KernelEvaluationInstance
similarity(String, String, String, String, String) - Method in interface org.apache.ctakes.ytex.ws.ConceptSimilarityRestService
similarity(String, String, String, String, String) - Method in class org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl
similarityInfo - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity
SimilarityInfo - Class in org.apache.ctakes.ytex.kernel.metric: Data structure to hold information on the lcs's, paths, and final selected LCS for a similarity measure.
SimilarityInfo() - Constructor for class org.apache.ctakes.ytex.kernel.metric.SimilarityInfo
similarityList - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean: when doing similarity for multiple concept pairs
similarityMap - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean.SimilarityEntry
similarityMap - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean
SimilarityMetric - Interface in org.apache.ctakes.ytex.kernel.metric
similarityMetricMap - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
simInfo - Variable in class org.apache.ctakes.ytex.web.search.SemanticSimBean: when doing similarity for a single concept pair
simListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean: handle submit
simMultiListen(ActionEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
SIMPLE_SEGMENT - Static variable in class org.apache.ctakes.core.ae.CDASegmentAnnotator
SIMPLE_SEGMENTER_PATH - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
simpleJdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
simpleJdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
simpleJdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
simpleJdbcTemplate - Variable in class org.apache.ctakes.ytex.kernel.tree.InstanceTreeBuilderImpl
simpleJdbcTemplate - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
SimpleSegmentAnnotator - Class in org.apache.ctakes.core.ae: Creates a single segment annotation that spans the entire document.
SimpleSegmentAnnotator() - Constructor for class org.apache.ctakes.core.ae.SimpleSegmentAnnotator
SimpleSegmentWithTagsAnnotator - Class in org.apache.ctakes.core.ae: Creates a single segment annotation that spans the entire document.
SimpleSegmentWithTagsAnnotator() - Constructor for class org.apache.ctakes.core.ae.SimpleSegmentWithTagsAnnotator
SimpleTree - Class in org.apache.ctakes.utils.tree
SimpleTree(String) - Constructor for class org.apache.ctakes.utils.tree.SimpleTree
SimpleTree(String, SimpleTree) - Constructor for class org.apache.ctakes.utils.tree.SimpleTree
SimpleTree(String, SimpleTree, boolean) - Constructor for class org.apache.ctakes.utils.tree.SimpleTree
simplifyGCG(SimpleTree) - Static method in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
simplifyGCG(SimpleTree) - Static method in class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor
SimServiceInfo - Class in org.apache.ctakes.ytex.ws
SimServiceInfo() - Constructor for class org.apache.ctakes.ytex.ws.SimServiceInfo
SimServiceInfo(String, String) - Constructor for class org.apache.ctakes.ytex.ws.SimServiceInfo
simSvc - Variable in class org.apache.ctakes.ytex.kernel.metric.BaseSimilarityMetric
SimSvcContextHolder - Class in org.apache.ctakes.ytex.kernel
SimSvcContextHolder() - Constructor for class org.apache.ctakes.ytex.kernel.SimSvcContextHolder
SingleDocumentProcessorCtakes - Class in org.apache.ctakes.assertion.medfacts.i2b2.api
SingleDocumentProcessorCtakes() - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
Singleton - Class in org.apache.ctakes.jdl.common: Singleton example.
Singleton() - Constructor for class org.apache.ctakes.jdl.common.Singleton
size - Variable in class org.apache.ctakes.core.cpe.CmdLineCpeRunner.MyStatusCallbackListener
size() - Method in class org.apache.ctakes.coreference.eval.helpers.Span
size - Variable in class org.apache.ctakes.coreference.util.ParentPtrTree
size() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
size() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
size() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
size() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
size() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
size() - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
size - Variable in class org.apache.ctakes.utils.distsem.WordVector
size() - Method in class org.apache.ctakes.utils.distsem.WordVector
size() - Method in class org.apache.ctakes.utils.struct.CounterTreeMap
size - Variable in class org.apache.ctakes.ytex.tools.RunCPE.StatusCallbackListenerImpl
size - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
skipReadingValuesJustReadText - Variable in class org.apache.ctakes.assertion.cr.NegExCorpusReader
skipSegmentIDs - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
skipSegmentsArray - Variable in class org.apache.ctakes.core.ae.SentenceDetector
skipSegmentsArray - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
skipSegmentsSet - Variable in class org.apache.ctakes.core.ae.SentenceDetector
skipSegmentsSet - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
skipSegmentsSet - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
skipSegmentsSet - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
skipSegmentsSet - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
skipSegmentsSet - Variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
skipSegmentsSet - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
skipTrain - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
skipTrainComponents - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
slot - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.IdAndSlot
SmokerNamedEntityAnnotation - Class in org.apache.ctakes.smokingstatus.type: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
SmokerNamedEntityAnnotation() - Constructor for class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation: Never called.
SmokerNamedEntityAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation: Internal - constructor used by generator
SmokerNamedEntityAnnotation(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation
SmokerNamedEntityAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation
SmokerNamedEntityAnnotation_Type - Class in org.apache.ctakes.smokingstatus.type: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
SmokerNamedEntityAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation_Type: initialize variables to correspond with Cas Type and Features
SmokerNamedEntityLookupConsumerImpl - Class in org.apache.ctakes.smokingstatus.lookup.ae: copied from edu.may.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl in the "Dictionary Lookup" project to use "SmokerNamedEntityAnnotation" instead of NamedEntityAnnotation
SmokerNamedEntityLookupConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.smokingstatus.lookup.ae.SmokerNamedEntityLookupConsumerImpl
SmokingDocumentClassification - Class in org.apache.ctakes.smokingstatus.type: Represents classification related to the document Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
SmokingDocumentClassification() - Constructor for class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: Never called.
SmokingDocumentClassification(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification: Internal - constructor used by generator
SmokingDocumentClassification(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification
SmokingDocumentClassification(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification
SmokingDocumentClassification_Type - Class in org.apache.ctakes.smokingstatus.type: Represents classification related to the document Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
SmokingDocumentClassification_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type: initialize variables to correspond with Cas Type and Features
smokingWords - Variable in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
smoothingCount - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
smoothingCount - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
smoothingCount - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
smoothingCount - Variable in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
smoteNeighborNumber - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
smoteNeighborNumber - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
smoteNumOfNeighbors - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
smoteNumOfNeighbors - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
SMOTEplus - Class in org.apache.ctakes.temporal.utils: A simple implementation of SMOTE algorithm.
SMOTEplus(int) - Constructor for class org.apache.ctakes.temporal.utils.SMOTEplus
SNOMED_CODE_LIST_CONFIG_PARM - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
SNOMED_MAPPING_PRP_KEY - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
SNOMED_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
snomedLikeCodesIndex - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
SOAP - Static variable in class org.apache.ctakes.drugner.elements.FormElement
softLabel - Variable in class org.apache.ctakes.ytex.kernel.model.SemiLClassifierEvaluation
SokalSneathMetric - Class in org.apache.ctakes.ytex.kernel.metric: Sokal and Sneath metric as in eqn 18 from http://dx.doi.org/10.1016/j.jbi.2011.03.013
SokalSneathMetric(ConceptSimilarityService) - Constructor for class org.apache.ctakes.ytex.kernel.metric.SokalSneathMetric
SOLUTION - Static variable in class org.apache.ctakes.drugner.elements.FormElement
sort(Markable, LinkedList<Markable>, JCas) - Static method in class org.apache.ctakes.coreference.util.HobbsTreeNavigator
sortAnnotations(Object[]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: Sort annotations by begin offset
sortedSetToString(SortedSet<String>) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
SortedSetUserType - Class in org.apache.ctakes.ytex.kernel.dao
SortedSetUserType() - Constructor for class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
sortFeatureRankList(List<FeatureRank>, Comparator<FeatureRank>) - Static method in class org.apache.ctakes.ytex.kernel.model.FeatureRank: sort the features, set the rank correspondingly.
sortSignatureElements(JCas, int, int, int, int[], int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator: The range defined by the begin and end is searched all discovered drugs, newline locations and related drug signature elements.
sortSubSectionInd(Object[]) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
source - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
SourceData - Class in org.apache.ctakes.typesystem.type.structured: Information about the caregiving setting for the clinical document.
SourceData() - Constructor for class org.apache.ctakes.typesystem.type.structured.SourceData: Never called.
SourceData(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.SourceData: Internal - constructor used by generator
SourceData(JCas) - Constructor for class org.apache.ctakes.typesystem.type.structured.SourceData
SourceData_Type - Class in org.apache.ctakes.typesystem.type.structured: Information about the caregiving setting for the clinical document.
SourceData_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.structured.SourceData_Type: initialize variables to correspond with Cas Type and Features
sourceFile - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
SourceMetadataUtil - Class in org.apache.ctakes.core.util: Utility class with convenience methods for a few commonly-used JCas Metadata types that are begged of the source
SourceMetadataUtil() - Constructor for class org.apache.ctakes.core.util.SourceMetadataUtil
sp - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
Span - Class in org.apache.ctakes.assertion.cr: Represents span of a named entity
Span(int, int) - Constructor for class org.apache.ctakes.assertion.cr.Span
Span - Class in org.apache.ctakes.coreference.eval.helpers
Span() - Constructor for class org.apache.ctakes.coreference.eval.helpers.Span
Span(int[]) - Constructor for class org.apache.ctakes.coreference.eval.helpers.Span
Span(String) - Constructor for class org.apache.ctakes.coreference.eval.helpers.Span
span - Variable in class org.apache.ctakes.preprocessor.SegmentMetaData
Span - Class in org.apache.ctakes.relationextractor.knowtator: Represents span of a named entity
Span(int, int) - Constructor for class org.apache.ctakes.relationextractor.knowtator.Span
SPAN_END_LABEL - Static variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate
SPAN_LIMIT - Static variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
SPAN_START_LABEL - Static variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate
SpanAlignment - Class in org.apache.ctakes.coreference.eval.helpers
SpanAlignment(Span[], Span[]) - Constructor for class org.apache.ctakes.coreference.eval.helpers.SpanAlignment
SpannedRareWordTerm - Class in org.apache.ctakes.dictionary.lookup2.term: A RareWordTerm tied to a text span Author: SPF Affiliation: CHIP-NLP Date: 11/18/13
SpannedRareWordTerm(RareWordTerm, int, int) - Constructor for class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
SpannedRareWordTerm(RareWordTerm, TextSpan) - Constructor for class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
spannedText - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The text spanned by this annnotation (null if not associated with a span of text).
SpanOffsetComparator - Class in org.apache.ctakes.coreference.eval.helpers
SpanOffsetComparator() - Constructor for class org.apache.ctakes.coreference.eval.helpers.SpanOffsetComparator
spans - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The character offsets of this annotation (empty if not associated with a span of text).
SparseData - Class in org.apache.ctakes.ytex.kernel: Data structure populated by SparseDataExporter that has all the instance attributes needed for exporting to various formats.
SparseData() - Constructor for class org.apache.ctakes.ytex.kernel.SparseData
SparseDataExporter - Interface in org.apache.ctakes.ytex.kernel
sparseDataExporter - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
SparseDataExporter.ScopeEnum - Enum in org.apache.ctakes.ytex.kernel
SparseDataExporter.ScopeEnum(String) - Constructor for enum org.apache.ctakes.ytex.kernel.SparseDataExporter.ScopeEnum
SparseDataExporterImpl - Class in org.apache.ctakes.ytex.kernel
SparseDataExporterImpl() - Constructor for class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
SparseDataFormatter - Interface in org.apache.ctakes.ytex.kernel: stateful class called by the sparseDataExporter to export sparse data in a specific format.
SparseDataFormatterFactory - Interface in org.apache.ctakes.ytex.kernel
SparseMatrixFormatterFactory - Class in org.apache.ctakes.ytex.sparsematrix: export sparse data matrix to data.txt.
SparseMatrixFormatterFactory() - Constructor for class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory
SparseMatrixFormatterFactory.SparseMatrixDataFormatter - Class in org.apache.ctakes.ytex.sparsematrix
SparseMatrixFormatterFactory.SparseMatrixDataFormatter(InstanceDataExporter, KernelUtil) - Constructor for class org.apache.ctakes.ytex.sparsematrix.SparseMatrixFormatterFactory.SparseMatrixDataFormatter
SpecialAnnotationRelationExtractor - Class in org.apache.ctakes.temporal.ae.feature
SpecialAnnotationRelationExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.SpecialAnnotationRelationExtractor
specialWd - Variable in class org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor
specificity - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
SPLIT - Static variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes: Constant indicates a sentence split.
split(CharSequence) - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
split() - Method in class org.apache.ctakes.relationextractor.data.Splitter
SPLIT_PATTERN - Static variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change split sentences on these patterns
splitAtLineBreaksAndTrim(String) - Method in class org.apache.ctakes.core.sentence.SentenceSpan: Trim any leading or trailing whitespace.
splitAtLineBreaksAndTrim(String) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan: Trim any leading or trailing whitespace.
splitAtPeriodAndTrim(Pattern, Pattern, Pattern) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan: vng added
splitChildren(String) - Static method in class org.apache.ctakes.utils.tree.SimpleTree
splitName - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
splitName - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFold
splitName - Variable in class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter
splitPattern - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector: vng change
splitSeed(File) - Static method in class org.apache.ctakes.assertion.pipelines.SharpCorpusSplit
splitStratified(int) - Static method in class org.apache.ctakes.assertion.pipelines.SharpCorpusSplit
splitStratified(File) - Static method in class org.apache.ctakes.assertion.pipelines.SharpCorpusSplit
splitSubspans(List<SentenceSpan>, Pattern) - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan: vng added
Splitter - Class in org.apache.ctakes.relationextractor.data: Randomly split a set of files in a directory into three sets: train, dev, and test.
Splitter(double, double) - Constructor for class org.apache.ctakes.relationextractor.data.Splitter: Specify percentages of the split.
Splitter(int, int, int) - Constructor for class org.apache.ctakes.relationextractor.data.Splitter: Specify the size of each set.
SPRAY - Static variable in class org.apache.ctakes.drugner.elements.FormElement
sql - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
sqlType - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
sqlTypes() - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
sqlTypes() - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
srcClass - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
srcClassName - Variable in class org.apache.ctakes.core.ae.CopyAnnotator
srcConn - Variable in class org.apache.ctakes.jdl.AppJdl
srcData - Variable in class org.apache.ctakes.jdl.AppJdl
srcLoad - Variable in class org.apache.ctakes.jdl.AppJdl
srcToDocument(String) - Static method in class org.apache.ctakes.jdl.data.xml.DomUtil
srcToSchema(String) - Static method in class org.apache.ctakes.jdl.data.xml.SchemaUtil
srcXml - Variable in class org.apache.ctakes.jdl.data.xml.DomParser
srcXml - Variable in class org.apache.ctakes.jdl.data.xml.SaxParser
srcXml - Variable in class org.apache.ctakes.jdl.data.xml.Validation
srl - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
SRL_NAME - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
srlabeler - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
SRLFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
SRLFeatureExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SRLFeatureExtractor
srlModelUri - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
srlPredUri - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
SRLRelationFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
SRLRelationFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor
srlRoleUri - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE
SRLUtility - Class in org.apache.ctakes.dependency.parser.util
SRLUtility() - Constructor for class org.apache.ctakes.dependency.parser.util.SRLUtility
standardAnalyzer - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
StanfordDependency - Class in org.apache.ctakes.typesystem.type.syntax: Stanford dependencies provide a representation of grammatical relations between words in a sentence.
StanfordDependency() - Constructor for class org.apache.ctakes.typesystem.type.syntax.StanfordDependency: Never called.
StanfordDependency(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.StanfordDependency: Internal - constructor used by generator
StanfordDependency(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.StanfordDependency
StanfordDependency_Type - Class in org.apache.ctakes.typesystem.type.syntax: Stanford dependencies provide a representation of grammatical relations between words in a sentence.
StanfordDependency_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.StanfordDependency_Type: initialize variables to correspond with Cas Type and Features
start - Variable in class org.apache.ctakes.assertion.cr.Span
start - Variable in class org.apache.ctakes.core.sentence.SentenceSpan
start - Variable in class org.apache.ctakes.coreference.treekernel.training.RowFillerThread
START - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
start - Variable in class org.apache.ctakes.preprocessor.IntegerRange
start - Variable in class org.apache.ctakes.relationextractor.knowtator.Span
start - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
start - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
START_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
startDate - Variable in class org.apache.ctakes.drugner.DrugMention: If there is a specific date in the note associated with the drug mention, the specific date.
StartDateElement - Class in org.apache.ctakes.drugner.elements
StartDateElement() - Constructor for class org.apache.ctakes.drugner.elements.StartDateElement
StartDateElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.StartDateElement
startDocument() - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
startElement(String, String, String, Attributes) - Method in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
startElement(String, String, String, Attributes) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
startLine - Variable in class org.apache.ctakes.core.util.DocumentSection
startMatch(String, String) - Static method in class org.apache.ctakes.coreference.util.TextMatch
startOffset - Variable in class org.apache.ctakes.preprocessor.Annotation
startsWithWithoutBeingFollowedByLetter(String, String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
Stats - Class in org.apache.ctakes.relationextractor.data: Calculate relation frequencies in a data set that consists of XML files exported from Knowtator.
Stats() - Constructor for class org.apache.ctakes.relationextractor.data.Stats
stats - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
stats - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
status - Variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
statusChangePhraseGenerator(JCas, int, int, boolean, Iterator, Iterator, List, String[], DrugMentionAnnotation, List, int) - Method in class org.apache.ctakes.drugner.ae.DrugMentionAnnotator
StatusContextAnalyzer - Class in org.apache.ctakes.necontexts.status
StatusContextAnalyzer() - Constructor for class org.apache.ctakes.necontexts.status.StatusContextAnalyzer
StatusContextHitConsumer - Class in org.apache.ctakes.necontexts.status
StatusContextHitConsumer() - Constructor for class org.apache.ctakes.necontexts.status.StatusContextHitConsumer
StatusIndicator - Class in org.apache.ctakes.core.fsm.output
StatusIndicator(int, int, int) - Constructor for class org.apache.ctakes.core.fsm.output.StatusIndicator
StatusIndicatorFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect indications of
family history of
history of
possible/probable/likely
StatusIndicatorFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.StatusIndicatorFSM: Constructor
StatusIndicatorFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect ???
StatusIndicatorFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.StatusIndicatorFSM: Constructor
StemmedLookupAnnotationToJCasAdapter - Class in org.apache.ctakes.ytex.uima.lookup.ae: allow dictionary lookup with stemmed words
StemmedLookupAnnotationToJCasAdapter(Annotation) - Constructor for class org.apache.ctakes.ytex.uima.lookup.ae.StemmedLookupAnnotationToJCasAdapter
stemmedStr - Variable in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
stemToken(Token) - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
stn - Variable in class org.apache.ctakes.ytex.umls.model.MRSTY
STOP - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
STOP_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
stopwords - Variable in class org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
stopwords - Variable in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
stopwords - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
stopwords - Static variable in class org.apache.ctakes.coreference.util.AttributeCalculator
stopwords - Variable in class org.apache.ctakes.coreference.util.SvmVectorCreator
stopWords - Variable in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
stopwords - Variable in class org.apache.ctakes.smokingstatus.MLutil.GenerateTrainingData
store(String, String) - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel: Loads text from a file.
storeAnnotationsToList(JFSIndexRepository, int) - Method in class org.apache.ctakes.core.ae.OverlapAnnotator: create a list of the annotations of the given type
storeAnnotationVersion(JCas) - Method in class org.apache.ctakes.clinicalpipeline.ae.ExtractionPrepAnnotator: Stores annotation version as a property JCas object.
storeAnnotationVersion(JCas) - Method in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel: Stores annotation version as a property JCas object.
storeAsInterval - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
storeAssignedClasses(String) - Method in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
storeChildConcepts(List<FeatureRank>, ImputedFeatureEvaluatorImpl.Parameters, String, int, ConceptGraph, boolean) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: save the children of the 'top' parent concepts.
storeInstanceMap(ApplicationContext, String, CommandLine) - Static method in class org.apache.ctakes.ytex.KernelLauncher
storeIntrinsicIC(String, int, Map<String, IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo>, short[], ConceptGraph) - Method in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl
storeKernel(KernelEvaluation, long, long, double) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao
storeKernel(KernelEvaluation, long, long, double) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
storeKernelEval(KernelEvaluation) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao: store the kernel evaluation if it doesn't exist, else return the existing one
storeKernelEval(KernelEvaluation) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
storeNorm(KernelEvaluation, long, double) - Method in interface org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDao
storeNorm(KernelEvaluation, long, double) - Method in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
storeProbabilities - Variable in class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl.ClassifierEvaluationInstanceImporter
storeResults(File, Properties, SVMClassifierEvaluation) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMParser: store the parsed classifier evaluation
storeResults(File, Properties, SVMClassifierEvaluation) - Method in class org.apache.ctakes.ytex.svmlight.SVMLightParser: store semi supervised results.
storeSemiSupervised(Properties, ClassifierEvaluation, <any>) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
str - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
strDescriptorFile - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: the descriptor file.
strength - Variable in class org.apache.ctakes.drugner.DrugMention
strength - Variable in class org.apache.ctakes.drugner.elements.StrengthElement
StrengthAnnotation - Class in org.apache.ctakes.drugner.type: Holds the value representing the unit of the drug dosage.
StrengthAnnotation() - Constructor for class org.apache.ctakes.drugner.type.StrengthAnnotation: Never called.
StrengthAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.StrengthAnnotation: Internal - constructor used by generator
StrengthAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.StrengthAnnotation
StrengthAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.StrengthAnnotation
StrengthAnnotation_Type - Class in org.apache.ctakes.drugner.type: Holds the value representing the unit of the drug dosage.
StrengthAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.StrengthAnnotation_Type: initialize variables to correspond with Cas Type and Features
StrengthCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a StrengthToken.
StrengthCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.StrengthCondition
StrengthElement - Class in org.apache.ctakes.drugner.elements
StrengthElement() - Constructor for class org.apache.ctakes.drugner.elements.StrengthElement
StrengthElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.StrengthElement
StrengthFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect dosages in the given input of tokens.
StrengthFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.StrengthFSM: Constructor
StrengthToken - Class in org.apache.ctakes.drugner.fsm.output.elements
StrengthToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.StrengthToken
strengthUnit - Variable in class org.apache.ctakes.drugner.DrugMention: Span the drug form, if available.
strengthUnit - Variable in class org.apache.ctakes.drugner.elements.StrengthUnitElement
StrengthUnitAnnotation - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-drug-ner/target/jcasgen/typesystem.xml
StrengthUnitAnnotation() - Constructor for class org.apache.ctakes.drugner.type.StrengthUnitAnnotation: Never called.
StrengthUnitAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.StrengthUnitAnnotation: Internal - constructor used by generator
StrengthUnitAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.StrengthUnitAnnotation
StrengthUnitAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.StrengthUnitAnnotation
StrengthUnitAnnotation_Type - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015
StrengthUnitAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.StrengthUnitAnnotation_Type: initialize variables to correspond with Cas Type and Features
StrengthUnitCombinedCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a StrengthToken.
StrengthUnitCombinedCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.StrengthUnitCombinedCondition
StrengthUnitCombinedToken - Class in org.apache.ctakes.drugner.fsm.output.elements
StrengthUnitCombinedToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitCombinedToken
StrengthUnitCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a StrengthToken.
StrengthUnitCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.StrengthUnitCondition
StrengthUnitElement - Class in org.apache.ctakes.drugner.elements
StrengthUnitElement() - Constructor for class org.apache.ctakes.drugner.elements.StrengthUnitElement
StrengthUnitElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.StrengthUnitElement
StrengthUnitFSM - Class in org.apache.ctakes.drugner.fsm.machines.elements: Uses one or more finite state machines to detect dosages in the given input of tokens.
StrengthUnitFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.elements.StrengthUnitFSM: Constructor
StrengthUnitToken - Class in org.apache.ctakes.drugner.fsm.output.elements
StrengthUnitToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.StrengthUnitToken
STRING_ESCAPE - Static variable in interface org.apache.ctakes.ytex.sparsematrix.InstanceDataExporter
STRING_TYPE - Static variable in interface org.apache.ctakes.dictionary.lookup.MetaDataHitConst
stringArrayToString(String[]) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
StringArrayUserType - Class in org.apache.ctakes.ytex.kernel.dao
StringArrayUserType() - Constructor for class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
StringAttributeValue - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
StringAttributeValue() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue: Never called.
StringAttributeValue(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue: Internal - constructor used by generator
StringAttributeValue(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue
StringAttributeValue(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue
StringAttributeValue_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
StringAttributeValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type: initialize variables to correspond with Cas Type and Features
StringIntegerMapResource - Interface in org.apache.ctakes.core.resource: Resource that defines a map between a String (KEY) and Integer.
StringIntegerMapResourceImpl - Class in org.apache.ctakes.core.resource: Implementation for StringIntegerMapResource interface.
StringIntegerMapResourceImpl() - Constructor for class org.apache.ctakes.core.resource.StringIntegerMapResourceImpl
StringMapResource - Interface in org.apache.ctakes.core.resource: Resource that defines a map between a String (KEY) and Integer.
StringMapResourceImpl - Class in org.apache.ctakes.core.resource: Implementation for StringIntegerMapResource interface.
StringMapResourceImpl() - Constructor for class org.apache.ctakes.core.resource.StringMapResourceImpl
StringPreLookupFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter
StringPreLookupFilterImpl(Set<String>) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.StringPreLookupFilterImpl
stringSlots - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The string-valued annotation attributes
StringsResource - Interface in org.apache.ctakes.core.resource: A Resource interface for getting an array of strings.
StringTable - Class in org.apache.ctakes.dictionary.lookup.strtable
StringTable(String[]) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTable
StringTableDictionaryImpl - Class in org.apache.ctakes.dictionary.lookup.strtable
StringTableDictionaryImpl(StringTable, String) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableDictionaryImpl
StringTableFactory - Class in org.apache.ctakes.dictionary.lookup.strtable
StringTableFactory() - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableFactory
StringTableRow - Class in org.apache.ctakes.dictionary.lookup.strtable
StringTableRow() - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow
StringTableRowMetaDataHitImpl - Class in org.apache.ctakes.dictionary.lookup.strtable
StringTableRowMetaDataHitImpl(StringTableRow) - Constructor for class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl
stringToSortedSet(String) - Method in class org.apache.ctakes.ytex.kernel.dao.SortedSetUserType
stringToSortedSet(String) - Method in class org.apache.ctakes.ytex.kernel.dao.StringArrayUserType
stringTypes - Static variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
stripSuffix(String) - Static method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
strToDocument(String) - Static method in class org.apache.ctakes.jdl.data.xml.DomUtil
strToSchema(String) - Static method in class org.apache.ctakes.jdl.data.xml.SchemaUtil
structureFinder - Variable in class org.apache.ctakes.core.ae.SectionSegmentAnnotator
stt - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
sty - Variable in class org.apache.ctakes.ytex.umls.model.MRSTY
styleMapEditor - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
styleMapFile - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain: style map initialized with descriptor
styleMapFile - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
subChunkLabels - Variable in class org.apache.ctakes.temporal.ae.feature.ChunkingExtractor
subcorpus - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
SUBCUTANEOUS - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
SUBCUTANEOUS - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
subdirs - Variable in class org.apache.ctakes.temporal.ae.THYMETreebankReader
SUBJECT_KNOWTATOR_TO_UIMA_MAP - Static variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
SUBJECT_KNOWTATOR_TO_UIMA_MAP - Static variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
SubjectAttributeAnalysisEngine - Class in org.apache.ctakes.assertion.attributes: This class provides a basic subject attribute extraction technique based on dependency parses.
SubjectAttributeAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.attributes.SubjectAttributeAnalysisEngine
SubjectAttributeClassifier - Class in org.apache.ctakes.assertion.attributes.subject
SubjectAttributeClassifier() - Constructor for class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
SubjectCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
SubjectCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
SubjectFeaturesExtractor - Class in org.apache.ctakes.assertion.attributes.features: SubjectFeaturesExtractor Ports the features and classification decisions of the first version (logic) of the subject tool
SubjectFeaturesExtractor() - Constructor for class org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor
SubjectModifier - Class in org.apache.ctakes.typesystem.type.textsem: The person the observation is on, i.e., a Person mention.
SubjectModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.SubjectModifier: Never called.
SubjectModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SubjectModifier: Internal - constructor used by generator
SubjectModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SubjectModifier
SubjectModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SubjectModifier
SubjectModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: The person the observation is on, i.e., a Person mention.
SubjectModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type: initialize variables to correspond with Cas Type and Features
SubSectionAnnotation - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-drug-ner/target/jcasgen/typesystem.xml
SubSectionAnnotation() - Constructor for class org.apache.ctakes.drugner.type.SubSectionAnnotation: Never called.
SubSectionAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.SubSectionAnnotation: Internal - constructor used by generator
SubSectionAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.SubSectionAnnotation
SubSectionAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.SubSectionAnnotation
SubSectionAnnotation_Type - Class in org.apache.ctakes.drugner.type: Updated by JCasGen Wed Sep 30 11:06:00 EDT 2015
SubSectionAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type: initialize variables to correspond with Cas Type and Features
SubSectionIndicator - Class in org.apache.ctakes.drugner.fsm.output.util
SubSectionIndicator(int, int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.SubSectionIndicator
SubSectionIndicatorFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect sub-sections in the given input of tokens.
SubSectionIndicatorFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.SubSectionIndicatorFSM: Constructor
SUBSUMED_ANNOT - Static variable in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
SUBSUMED_ANNOT - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
SUBSUMED_CHUNK - Static variable in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
SUBSUMED_CHUNK - Static variable in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
subsumerCount - Variable in class org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl.IntrinsicICInfo
Subzone - Class in org.apache.ctakes.assertion.zoner.types: Updated by JCasGen Wed Sep 30 11:06:06 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-assertion-zoner/target/jcasgen/typesystem.xml
Subzone() - Constructor for class org.apache.ctakes.assertion.zoner.types.Subzone: Never called.
Subzone(int, TOP_Type) - Constructor for class org.apache.ctakes.assertion.zoner.types.Subzone: Internal - constructor used by generator
Subzone(JCas) - Constructor for class org.apache.ctakes.assertion.zoner.types.Subzone
Subzone(JCas, int, int) - Constructor for class org.apache.ctakes.assertion.zoner.types.Subzone
Subzone_Type - Class in org.apache.ctakes.assertion.zoner.types: Updated by JCasGen Wed Sep 30 11:06:06 EDT 2015
Subzone_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.zoner.types.Subzone_Type: initialize variables to correspond with Cas Type and Features
succeed(Source) - Method in class org.apache.ctakes.jdl.data.xml.Validation
succeed() - Method in class org.apache.ctakes.jdl.data.xml.Validation
suffix - Variable in class org.apache.ctakes.core.util.CtakesFileNamer
suffix - Variable in class org.apache.ctakes.ytex.kernel.FileUtil.SuffixFileFilter
SUFFIX_IMPUTED - Static variable in interface org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator
SUFFIX_IMPUTED_FILTERED - Static variable in interface org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator
SUFFIX_PROP - Static variable in interface org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator
SUFFIXES - Static variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator
SuffixFrequencyFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect frequency suffix data in the given input of tokens.
SuffixFrequencyFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.SuffixFrequencyFSM: Constructor
SuffixFrequencyToken - Class in org.apache.ctakes.drugner.fsm.output.util
SuffixFrequencyToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.SuffixFrequencyToken
SuffixStrengthAnnotation - Class in org.apache.ctakes.drugner.type: The suffix portion of dosage strength determination for the Drug NER profile.
SuffixStrengthAnnotation() - Constructor for class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation: Never called.
SuffixStrengthAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation: Internal - constructor used by generator
SuffixStrengthAnnotation(JCas) - Constructor for class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation
SuffixStrengthAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation
SuffixStrengthAnnotation_Type - Class in org.apache.ctakes.drugner.type: The suffix portion of dosage strength determination for the Drug NER profile.
SuffixStrengthAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation_Type: initialize variables to correspond with Cas Type and Features
SuffixStrengthFSM - Class in org.apache.ctakes.drugner.fsm.machines.util: Uses one or more finite state machines to detect strength suffix information adjoined to dosage data in the given input of tokens.
SuffixStrengthFSM() - Constructor for class org.apache.ctakes.drugner.fsm.machines.util.SuffixStrengthFSM: Constructor
SuffixStrengthToken - Class in org.apache.ctakes.drugner.fsm.output.util
SuffixStrengthToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.util.SuffixStrengthToken
sui - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
sum(Collection<Integer>) - Static method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
SUM - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.DrugChangeStatusToken
sum(Collection<Integer>) - Static method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
SumKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: apply all the delegate kernels to the objects, sum them up
SumKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.SumKernel
SUMMATION_STATUS - Static variable in class org.apache.ctakes.drugner.elements.DrugChangeStatusElement
supportVectors - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
SUPPOSITORY - Static variable in class org.apache.ctakes.drugner.elements.FormElement
suppress - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
SurroundingExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
SurroundingExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SurroundingExtractor
SVM_KERNELS - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
SVMClassifierEvaluation - Class in org.apache.ctakes.ytex.kernel.model
SVMClassifierEvaluation() - Constructor for class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
svmCls - Variable in class org.apache.ctakes.coreference.util.AbstractClassifier
svmCost - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
svmGamma - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
svmKernel - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
svmKernelIndex - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
SVMLightFormatterFactory - Class in org.apache.ctakes.ytex.svmlight: export for svmlight.
SVMLightFormatterFactory() - Constructor for class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory
SVMLightFormatterFactory.SVMLightFormatter - Class in org.apache.ctakes.ytex.svmlight
SVMLightFormatterFactory.SVMLightFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.svmlight.SVMLightFormatterFactory.SVMLightFormatter
SVMLightParser - Class in org.apache.ctakes.ytex.svmlight: same as libsvm with following changes: parse output.txt - contains vcdim and number support vectors <
SVMLightParser() - Constructor for class org.apache.ctakes.ytex.svmlight.SVMLightParser
SvmlinEvaluationParser - Class in org.apache.ctakes.ytex.kernel
SvmlinEvaluationParser() - Constructor for class org.apache.ctakes.ytex.kernel.SvmlinEvaluationParser
SVMLinFormatterFactory - Class in org.apache.ctakes.ytex.kernel: for each train/test pair create the following files: [prefix]class.txt - as in semil: instance id \t train/test flag \t target class id
SVMLinFormatterFactory() - Constructor for class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory
SVMLinFormatterFactory.SVMLinDataFormatter - Class in org.apache.ctakes.ytex.kernel
SVMLinFormatterFactory.SVMLinDataFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.kernel.SVMLinFormatterFactory.SVMLinDataFormatter
SvmUtils - Class in org.apache.ctakes.coreference.util
SvmUtils() - Constructor for class org.apache.ctakes.coreference.util.SvmUtils
SvmVectorCreator - Class in org.apache.ctakes.coreference.util
SvmVectorCreator(HashSet<String>) - Constructor for class org.apache.ctakes.coreference.util.SvmVectorCreator
SymbolToken - Interface in org.apache.ctakes.core.fsm.token
SymbolToken - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a symbol rather than a punctuation, contraction, newline, word, or number.
SymbolToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.SymbolToken: Never called.
SymbolToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SymbolToken: Internal - constructor used by generator
SymbolToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SymbolToken
SymbolToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SymbolToken
SymbolToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a symbol rather than a punctuation, contraction, newline, word, or number.
SymbolToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.SymbolToken_Type: initialize variables to correspond with Cas Type and Features
SymbolTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
SymbolTokenAdapter(SymbolToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.SymbolTokenAdapter
SymbolValueCondition - Class in org.apache.ctakes.core.fsm.condition
SymbolValueCondition(char) - Constructor for class org.apache.ctakes.core.fsm.condition.SymbolValueCondition
SymmetricPairCacheKeyGenerator - Class in org.apache.ctakes.ytex.kernel.evaluator: cache key for a method that takes 2 arguments, and is symmetric - the order of the arguments doesn't matter.
SymmetricPairCacheKeyGenerator() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.SymmetricPairCacheKeyGenerator
SyntacticParentFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
SyntacticParentFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.SyntacticParentFeatureExtractor
SyntaticSingleTreeExtractor - Class in org.apache.ctakes.temporal.ae.feature.treekernel: Given a focused annotation, get the whole sentence-level parse tree that cover this annotation.
SyntaticSingleTreeExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.treekernel.SyntaticSingleTreeExtractor
SyntaxAttributeCalculator - Class in org.apache.ctakes.coreference.util
SyntaxAttributeCalculator(JCas, Markable, Markable) - Constructor for class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
SyntaxAttributeCalculator(JCas, Markable, Markable, WikiIndex) - Constructor for class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
syntheticInsts - Variable in class org.apache.ctakes.temporal.utils.SMOTEplus
SYRINGE - Static variable in class org.apache.ctakes.drugner.elements.FormElement
SYRUP - Static variable in class org.apache.ctakes.drugner.elements.FormElement
sysId2AlignId - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
sysRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
sysRelationCount - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
sysSpan2id - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
sysSpans - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler
SYSTEM_VIEW_NAME - Static variable in class org.apache.ctakes.temporal.duration.PreserveUMLSEventTimeRelationsInGold
systemViewName - Static variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
systemViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.CountCloseRelation
systemViewName - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.CountCloseRelation

T

t - Variable in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
t1 - Variable in class org.apache.ctakes.utils.wiki.Cache
t2 - Variable in class org.apache.ctakes.utils.wiki.Cache
tableName - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
tableName - Variable in class org.apache.ctakes.ytex.uima.model.UimaType
TABLET - Static variable in class org.apache.ctakes.drugner.elements.FormElement
taeDescriptorFileSelector - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
taeSpecifierStep1 - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
taeSpecifierStep2 - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
taeStep1 - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
taeStep2 - Variable in class org.apache.ctakes.smokingstatus.ae.ClassifiableEntries
tag - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
TagDictionaryCreator - Class in org.apache.ctakes.postagger: From a Part of Speech (POS) corpus in OpenNLP format, create a tagDictionary
Outputs the dictionary to the specified file
TagDictionaryCreator() - Constructor for class org.apache.ctakes.postagger.TagDictionaryCreator
tagger - Variable in class org.apache.ctakes.postagger.POSTagger
tail() - Method in class org.apache.ctakes.coreference.eval.helpers.Span
target - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
targetClass - Static variable in class org.apache.ctakes.temporal.duration.EventDurationDistribution
targetClassId - Variable in class org.apache.ctakes.ytex.kernel.ClassifierEvaluationResult
targetClassId - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierInstanceEvaluation
targetClassName - Variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
targetRelationType - Static variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
targetType - Variable in class org.apache.ctakes.assertion.medfacts.CasIndexer
targetType - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
targetTypeName - Variable in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator
targetTypeName - Variable in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
task - Variable in class org.apache.ctakes.ytex.uima.model.DocumentClass
TEMP_CROSSSENT - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
tempDir - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
TEMPET_CROSSSENT - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
templateFile - Variable in class org.apache.ctakes.core.ae.SectionSegmentAnnotator
TemplateFillerAnnotator - Class in org.apache.ctakes.template.filler.ae
TemplateFillerAnnotator() - Constructor for class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
TemporalAttributeFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
TemporalAttributeFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor
TemporalAttributeForMixEventTimeExtractor - Class in org.apache.ctakes.temporal.ae.feature
TemporalAttributeForMixEventTimeExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TemporalAttributeForMixEventTimeExtractor
TemporalEntityAnnotator_ImplBase - Class in org.apache.ctakes.temporal.ae
TemporalEntityAnnotator_ImplBase() - Constructor for class org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
TemporalExtractionPipeline_ImplBase - Class in org.apache.ctakes.temporal.pipelines
TemporalExtractionPipeline_ImplBase() - Constructor for class org.apache.ctakes.temporal.pipelines.TemporalExtractionPipeline_ImplBase
TemporalExtractionPipeline_ImplBase.Options - Interface in org.apache.ctakes.temporal.pipelines
TemporalFTExtractor - Class in org.apache.ctakes.temporal.ae.feature.treekernel
TemporalFTExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalFTExtractor
temporality - Variable in class org.apache.ctakes.assertion.cr.NegExAnnotation
TemporalPathExtractor - Class in org.apache.ctakes.temporal.ae.feature.treekernel
TemporalPathExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPathExtractor
TemporalPETExtractor - Class in org.apache.ctakes.temporal.ae.feature.treekernel
TemporalPETExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor
TemporalPETFlatExtractor - Class in org.apache.ctakes.temporal.ae.feature
TemporalPETFlatExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
TemporalRelation - Class in org.apache.ctakes.typesystem.type.relation: Based on ISO TimeML's TLINK.
TemporalRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalRelation: Never called.
TemporalRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalRelation: Internal - constructor used by generator
TemporalRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalRelation
TemporalRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: Based on ISO TimeML's TLINK.
TemporalRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalRelation_Type: initialize variables to correspond with Cas Type and Features
TemporalRelationRuleAnnotator - Class in org.apache.ctakes.temporal.ae
TemporalRelationRuleAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.TemporalRelationRuleAnnotator
TemporalSequenceAnnotator_ImplBase - Class in org.apache.ctakes.temporal.ae
TemporalSequenceAnnotator_ImplBase() - Constructor for class org.apache.ctakes.temporal.ae.TemporalSequenceAnnotator_ImplBase
TemporalTextRelation - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
TemporalTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation: Never called.
TemporalTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation: Internal - constructor used by generator
TemporalTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation
TemporalTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A UMLS relation between clinical elements.
TemporalTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation_Type: initialize variables to correspond with Cas Type and Features
TermConsumer - Interface in org.apache.ctakes.dictionary.lookup2.consumer: Stores terms in the cas Author: SPF Affiliation: CHIP-NLP Date: 12/5/13
TerminalTreebankNode - Class in org.apache.ctakes.typesystem.type.syntax: A Penn Treebank Node; as a terminal, there is an associated word, and the index of the word is a feature.
TerminalTreebankNode() - Constructor for class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: Never called.
TerminalTreebankNode(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode: Internal - constructor used by generator
TerminalTreebankNode(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode
TerminalTreebankNode(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode
TerminalTreebankNode_Type - Class in org.apache.ctakes.typesystem.type.syntax: A Penn Treebank Node; as a terminal, there is an associated word, and the index of the word is a feature.
TerminalTreebankNode_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type: initialize variables to correspond with Cas Type and Features
termVals - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
test(CollectionReader, File) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
test(HyphenTextModifierImpl, String) - Static method in class org.apache.ctakes.core.ci.HyphenTextModifierImpl
Test - Class in org.apache.ctakes.coreference.eval.helpers
Test() - Constructor for class org.apache.ctakes.coreference.eval.helpers.Test
test(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
test(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventRelations
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
test(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
test_getLengthIfNextApostIsMiddleOfContraction() - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB
TEST_REMAINDERS - Static variable in class org.apache.ctakes.temporal.eval.THYMEData
TestAttributeModels - Class in org.apache.ctakes.assertion.train: For each assertion attribute (polarity, conditional, etc), run against the test directories for that attribute, using models that are under the models-dir.
TestAttributeModels() - Constructor for class org.apache.ctakes.assertion.train.TestAttributeModels
testClassifier(AnalysisEngineDescription, String, String, String, String, String...) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
testConfigParam(UimaContext, String, String, Object) - Static method in class org.apache.ctakes.utils.test.TestUtil
testConfigParam(UimaContext, String, String, Object, Integer) - Static method in class org.apache.ctakes.utils.test.TestUtil
TestCosineSimilarity - Class in org.apache.ctakes.utils.wiki
TestCosineSimilarity() - Constructor for class org.apache.ctakes.utils.wiki.TestCosineSimilarity
testDirectories - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
testDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
TestDriver - Class in org.apache.ctakes.preprocessor.test
TestDriver() - Constructor for class org.apache.ctakes.preprocessor.test.TestDriver
TESTLOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
testMaxent() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
testOnCTakes - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
testOnly - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
testSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
testsForEmailAddress - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
testsForNumbers - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
testSize - Variable in class org.apache.ctakes.relationextractor.data.Splitter
TestUtil - Class in org.apache.ctakes.utils.test
TestUtil() - Constructor for class org.apache.ctakes.utils.test.TestUtil
text - Variable in class org.apache.ctakes.core.sentence.SentenceSpan
text - Variable in class org.apache.ctakes.sideeffect.ae.SESentenceFeatureAnnotator.SideEffect
text - Variable in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
text - Variable in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
TEXT_MFS_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
TEXT_MFS_PRP_KEY - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
textDirectory - Variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
textDirectory - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
textDoublesMap - Variable in class org.apache.ctakes.temporal.ae.feature.CoveredTextToValuesExtractor
textDoublesMap - Variable in class org.apache.ctakes.temporal.ae.feature.IdentifiedAnnotationFeatureExtractor
TextMatch - Class in org.apache.ctakes.coreference.util
TextMatch() - Constructor for class org.apache.ctakes.coreference.util.TextMatch
TextMentionElement - Class in org.apache.ctakes.drugner.elements
TextMentionElement() - Constructor for class org.apache.ctakes.drugner.elements.TextMentionElement
TextMentionElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.TextMentionElement
TextModification - Class in org.apache.ctakes.core.ci: Value object class that describes a modification of document text.
TextModification(int, int, int, int, String) - Constructor for class org.apache.ctakes.core.ci.TextModification
TextModifier - Interface in org.apache.ctakes.core.ci: Defines a generic interface for modifying text.
TextReader - Class in org.apache.ctakes.core.cr: UIMA CollectionReader that reads in CASes from XMI files.
TextReader() - Constructor for class org.apache.ctakes.core.cr.TextReader
textRoot - Variable in class org.apache.ctakes.coreference.cc.PreprocessAndWriteXmi.Options
TextSetCondition - Class in org.apache.ctakes.core.fsm.condition
TextSetCondition(Set<String>, boolean) - Constructor for class org.apache.ctakes.core.fsm.condition.TextSetCondition
TextSpan - Interface in org.apache.ctakes.dictionary.lookup2.textspan: Author: SPF Affiliation: CHIP-NLP Date: 1/29/14
textSpans - Variable in class org.apache.ctakes.preprocessor.SegmentMetaData
textToDistribution - Variable in class org.apache.ctakes.temporal.duration.Utils.Callback
TextToken - Interface in org.apache.ctakes.core.fsm.token
TextTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
TextTokenAdapter(Annotation) - Constructor for class org.apache.ctakes.core.fsm.adapters.TextTokenAdapter
TextValueCondition - Class in org.apache.ctakes.core.fsm.condition
TextValueCondition(String, boolean) - Constructor for class org.apache.ctakes.core.fsm.condition.TextValueCondition
tf(int) - Method in class org.apache.ctakes.utils.wiki.ApproximateSimilarity
tfIdf - Variable in class org.apache.ctakes.ytex.kernel.BagOfWordsData: should we perform tf-idf normalization?
ThreadDelegator - Interface in org.apache.ctakes.coreference.util
threadDone(RowFillerThread) - Method in class org.apache.ctakes.coreference.treekernel.training.LinearKernelMatrixWriter
threadDone(RowFillerThread) - Method in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
threadDone(RowFillerThread) - Method in interface org.apache.ctakes.coreference.util.ThreadDelegator
ThreadedDictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae: Date: 12/18/12
ThreadedDictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
ThreadedDictionaryLookupAnnotator.LookupDataStore - Class in org.apache.ctakes.dictionary.lookup.ae: Storage for a LookupSpec and all of its unique LookupHits
ThreadedDictionaryLookupAnnotator.LookupDataStore(LookupSpec, Collection<LookupHit>) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupDataStore
ThreadedDictionaryLookupAnnotator.LookupHitKey - Class in org.apache.ctakes.dictionary.lookup.ae: Using a String as a HashMap Key can be slow as the hashCode is computed per character with each call - ditto for equals
ThreadedDictionaryLookupAnnotator.LookupHitKey(LookupHit) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupHitKey
ThreadedUmlsDictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae: UIMA annotator that identified entities based on lookup.
ThreadedUmlsDictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
threadStarted() - Method in class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
THYMEAnaforaXMLReader - Class in org.apache.ctakes.temporal.ae
THYMEAnaforaXMLReader() - Constructor for class org.apache.ctakes.temporal.ae.THYMEAnaforaXMLReader
THYMEData - Class in org.apache.ctakes.temporal.eval: A class for splitting the THYME data into appropriate sets for evaluation.
THYMEData() - Constructor for class org.apache.ctakes.temporal.eval.THYMEData
THYMEKnowtatorXMLReader - Class in org.apache.ctakes.temporal.ae
THYMEKnowtatorXMLReader() - Constructor for class org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader
THYMEKnowtatorXMLReader.Options - Interface in org.apache.ctakes.temporal.ae
THYMETreebankReader - Class in org.apache.ctakes.temporal.ae
THYMETreebankReader() - Constructor for class org.apache.ctakes.temporal.ae.THYMETreebankReader
THYMETreebankReader.TOKEN_TYPE - Enum in org.apache.ctakes.temporal.ae
THYMETreebankReader.TOKEN_TYPE() - Constructor for enum org.apache.ctakes.temporal.ae.THYMETreebankReader.TOKEN_TYPE
Time - Class in org.apache.ctakes.typesystem.type.refsem: A normalized form for Time annotations.
Time() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Time: Never called.
Time(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Time: Internal - constructor used by generator
Time(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Time
TIME_ADMISSION - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
TIME_CLASS_DATE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST
TIME_DISCHARGE - Static variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
Time_Type - Class in org.apache.ctakes.typesystem.type.refsem: A normalized form for Time annotations.
Time_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Time_Type: initialize variables to correspond with Cas Type and Features
TimeAnnotation - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.TimeAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
TimeAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation: Never called.
TimeAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation: Internal - constructor used by generator
TimeAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
TimeAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
TimeAnnotation_Type - Class in org.apache.ctakes.typesystem.type.textsem: Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.TimeAnnotation Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
TimeAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type: initialize variables to correspond with Cas Type and Features
TimeAnnotator - Class in org.apache.ctakes.temporal.ae
TimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.TimeAnnotator
timeChunking - Variable in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
timeChunking - Variable in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
timeChunking - Variable in class org.apache.ctakes.temporal.ae.MetaTimeAnnotator
timeChunking - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
TimeCondition - Class in org.apache.ctakes.drugner.fsm.elements.conditions: Checks whether a token is a TimeToken.
TimeCondition() - Constructor for class org.apache.ctakes.drugner.fsm.elements.conditions.TimeCondition
TimeExtractionPipeline - Class in org.apache.ctakes.temporal.pipelines: Given a temporal expression extraction model, run the time expression extractor on files in a directory of notes.
TimeExtractionPipeline() - Constructor for class org.apache.ctakes.temporal.pipelines.TimeExtractionPipeline
TimeExtractionPipeline.TimexOptions - Interface in org.apache.ctakes.temporal.pipelines
TimeFSM - Class in org.apache.ctakes.core.fsm.machine: Uses one or more finite state machines to detect times in the given input of tokens.
TimeFSM() - Constructor for class org.apache.ctakes.core.fsm.machine.TimeFSM: Constructor
TimeMention - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to a Time (i.e., TIMEX3).
TimeMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeMention: Never called.
TimeMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeMention: Internal - constructor used by generator
TimeMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeMention
TimeMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeMention
TimeMention_Type - Class in org.apache.ctakes.typesystem.type.textsem: A text string (IdentifiedAnnotation) that refers to a Time (i.e., TIMEX3).
TimeMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type: initialize variables to correspond with Cas Type and Features
TimeRelationConstants - Interface in org.apache.ctakes.temporal.utils: Author: SPF Affiliation: CHIP-NLP Date: 4/17/13
TimeToken - Class in org.apache.ctakes.core.fsm.output
TimeToken(int, int) - Constructor for class org.apache.ctakes.core.fsm.output.TimeToken
timewd - Variable in class org.apache.ctakes.temporal.ae.feature.TimeXExtractor
TimeWordTypeExtractor<T extends Annotation> - Class in org.apache.ctakes.temporal.ae.feature
TimeWordTypeExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor
TimexAdmissionTimeAnnotator - Class in org.apache.ctakes.temporal.ae
TimexAdmissionTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
TimexDischargeTimeAnnotator - Class in org.apache.ctakes.temporal.ae
TimexDischargeTimeAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
timeXExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
timeXExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
timeXExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
TimeXExtractor - Class in org.apache.ctakes.temporal.ae.feature
TimeXExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TimeXExtractor
timeXExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
timeXExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
TimeXPropertyRelationFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature: Check is an timex argument is in the begining/end of a sentence
TimeXPropertyRelationFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TimeXPropertyRelationFeaturesExtractor
TimeXRelationFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature: extract the nearby nearest time, date information for any event
TimeXRelationFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor
TimexToClearTKTimexAnnotator - Class in org.apache.ctakes.temporal.ae
TimexToClearTKTimexAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.TimexToClearTKTimexAnnotator
TimexTreeAlignmentStatistics - Class in org.apache.ctakes.temporal.data.analysis
TimexTreeAlignmentStatistics() - Constructor for class org.apache.ctakes.temporal.data.analysis.TimexTreeAlignmentStatistics
TimexTreeAlignmentStatistics.Options - Interface in org.apache.ctakes.temporal.data.analysis
timexView - Variable in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
timexView - Variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
timexView - Variable in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
timexView - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
TimidBaselineEventTimeRelationAnnotator - Class in org.apache.ctakes.temporal.ae.baselines
TimidBaselineEventTimeRelationAnnotator() - Constructor for class org.apache.ctakes.temporal.ae.baselines.TimidBaselineEventTimeRelationAnnotator
tkWeight - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
tl_mapAnnoMappingInfo - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
tl_mapFieldInfo - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: map of annotation to fields that need to be mapped
tlAnalysisBatchDateFormat - Static variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: date format for analysis batch.
tlConfig - Static variable in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
tlDateFormat - Variable in class org.apache.ctakes.ytex.uima.annotators.DateAnnotator
tlDateFormat - Variable in class org.apache.ctakes.ytex.uima.mapper.ISO8601Converter
TlinkType - Enum in org.apache.ctakes.temporal.utils: Enumeration of the three temporal relation types used in THYME (before, overlap, contains) and their reciprocals (after, overlap, contained_by) Begins-on and Ends-on added 4-11-2013
TlinkType(int) - Constructor for enum org.apache.ctakes.temporal.utils.TlinkType
TLinkTypeArray2 - Class in org.apache.ctakes.temporal.utils: Author: SPF Affiliation: CHIP-NLP Date: 6/18/13
TLinkTypeArray2(List<BinaryTextRelation>, AnnotationIdCollection) - Constructor for class org.apache.ctakes.temporal.utils.TLinkTypeArray2
TlinkTypeSet - Class in org.apache.ctakes.temporal.utils: Author: SPF Affiliation: CHIP-NLP Date: 4/17/13
TlinkTypeSet() - Constructor for class org.apache.ctakes.temporal.utils.TlinkTypeSet
tm - Variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
TML_ABC_ARRAY - Static variable in enum org.apache.ctakes.temporal.utils.TlinkType
tn - Variable in class org.apache.ctakes.ytex.kernel.IRMetrics
tn - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
toFeatureStructures(JCas, List<Class<?>>) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
TOKDIST - Static variable in class org.apache.ctakes.coreference.util.CorefConsts
Token - Class in org.apache.ctakes.core.nlp.tokenizer: Object that represents a generic token.
Token(int, int) - Constructor for class org.apache.ctakes.core.nlp.tokenizer.Token: Constructor
TOKEN_CAP_ALL - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_CAP_FIRST_ONLY - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_CAP_MIXED - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_CAP_NONE - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_POS_FIRST - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_POS_LAST - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_POS_MIDDLE - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_POS_NONE - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_TYPE_DECIMAL - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_TYPE_INTEGER - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
TOKEN_NUM_TYPE_UNKNOWN - Static variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
tokenArgumentMap - Variable in class org.apache.ctakes.temporal.ae.feature.PredicateArgumentExtractor
tokenBeginEndTreeSet - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
tokenCleartkExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
tokenContext - Variable in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor: First word of the mention, last word of the mention, all words of the mention as a bag, the preceding 3 words, the following 3 words
tokenContext - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor: First word of the mention, last word of the mention, all words of the mention as a bag, the preceding 3 words, the following 3 words
tokenContext - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor: First word of the mention, last word of the mention, all words of the mention as a bag, the preceding 3 words, the following 3 words
tokenContext - Variable in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor: First word of the mention, last word of the mention, all words of the mention as a bag, the preceding 3 words, the following 3 words
tokenContextFeatureExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
TokenConverter - Class in org.apache.ctakes.core.ae: Utilities methods for converting between Java Tokenizer objects and their equivalent JCas objects.
TokenConverter() - Constructor for class org.apache.ctakes.core.ae.TokenConverter
TokenConverter - Class in org.apache.ctakes.core.fsm.token.adapter
TokenConverter() - Constructor for class org.apache.ctakes.core.fsm.token.adapter.TokenConverter
tokenCount - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
tokenCount - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
tokenCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
tokenCounts - Variable in class org.apache.ctakes.smokingstatus.ae.PcsClassifierAnnotator_libsvm
tokenFeatureExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAnnotator
tokenFeatureExtractors - Variable in class org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
tokenFeatureExtractors - Variable in class org.apache.ctakes.temporal.ae.CRFTimeAnnotator
tokenFeatureExtractors - Variable in class org.apache.ctakes.temporal.ae.TimeAnnotator
TokenFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
TokenFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor
TokenFreqCasConsumer - Class in org.apache.ctakes.core.cc: This class creates a file that contains the frequencies of the word tokens found in a set in a text collection.
TokenFreqCasConsumer() - Constructor for class org.apache.ctakes.core.cc.TokenFreqCasConsumer
tokenize(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Tokenizes a string of text and outputs a list of Token objects.
tokenize(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: Tokenize a string that is assumed to be the entire document (or at least to start at 0)
tokenizeAndSort(String) - Method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Tokenizes a string of text and outputs a list of Token objects in sorted order.
tokenizedStr - Variable in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
tokenizer - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotator
tokenizer - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
Tokenizer - Class in org.apache.ctakes.core.nlp.tokenizer: A class used to break natural text into tokens.
Tokenizer() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Constructor
Tokenizer(Map<String, Integer>, int) - Constructor for class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Constructor
tokenizer - Static variable in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
tokenizer - Variable in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord
TOKENIZER_PATH - Static variable in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
TokenizerAnnotator - Class in org.apache.ctakes.core.ae: UIMA annotator that uses the Tokenizer module.
TokenizerAnnotator() - Constructor for class org.apache.ctakes.core.ae.TokenizerAnnotator
TokenizerAnnotatorPTB - Class in org.apache.ctakes.core.ae: UIMA annotator that tokenizes based on Penn Treebank rules.
TokenizerAnnotatorPTB() - Constructor for class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
TokenizerHelper - Class in org.apache.ctakes.core.nlp.tokenizer
TokenizerHelper() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper
TokenizerPTB - Class in org.apache.ctakes.core.nlp.tokenizer: A class used to break natural text into tokens following PTB rules.
TokenizerPTB() - Constructor for class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: Constructor
tokenizeStr(String, String) - Method in class org.apache.ctakes.ytex.tools.SetupAuiFirstWord: tokenize the umls concept.
tokenizeTextSegment(JCas, String, int, boolean) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB: Tokenize text that starts at offset offsetAdjustment within the complete text
tokenLengthCheckingForHyphenatedTerms(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.HyphenatedPTB: There is the fixed list of hyphenated words to not be split (hyphenatedWordsLookup) And here are some made-up examples of words using affixes to keep together chronic-itis 1 suffix mega-huge 1 prefix e-game-fest 1 prefix and 1 suffix salon-o-torium 1 suffix that contains 2 hyphens urban-esque-wise 2 suffixes
tokenLengthCheckingForSingleQuoteWordsToKeepTogether(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB: for a word like 80's or P'yongyang or James' or Sean's or 80's-like or 80's-esque (or can't or haven't, which are to be split) determine whether the singlequote(apostrophe) needs to be kept with the surrounding letters/numbers and what to do about hyphenated afterwards if there is a hyphen after....
TokenMatchUtil - Class in org.apache.ctakes.dictionary.lookup2.util: Utility class with methods for matching tokens to valid terms
Author: SPF Affiliation: CHIP-NLP Date: 2/25/14
TokenMatchUtil() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.TokenMatchUtil
TokenOffsetsCasConsumer - Class in org.apache.ctakes.core.cc: For each CAS a local file with the offsets of the BaseToken annotations is written to a directory specifed by a parameter.
TokenOffsetsCasConsumer() - Constructor for class org.apache.ctakes.core.cc.TokenOffsetsCasConsumer
tokenOutputFile - Variable in class org.apache.ctakes.temporal.data.analysis.EventContextAnalysisPipeline.EventAndTokenContextWriter
tokenPOS - Variable in class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor: All part-of-speech tags of the mention as a bag
tokenPredicateMap - Variable in class org.apache.ctakes.temporal.ae.feature.PredicateArgumentExtractor
TokenPropertyFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
TokenPropertyFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.TokenPropertyFeaturesExtractor
tokensBetween - Variable in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor: First word, last word, and all words between the mentions
tokensBetween - Variable in class org.apache.ctakes.temporal.ae.feature.MultiTokenFeaturesExtractor: First word, last word, and all words between the mentions
tokensBetween - Variable in class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor: First word, last word, and all words between the mentions
tokensBetween - Variable in class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor: First word, last word, and all words between the mentions
toLines(List<FeatureStructure>) - Static method in class org.apache.ctakes.temporal.data.analysis.CompareFeatureStructures
TOPICAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
TOPICAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
TopTreebankNode - Class in org.apache.ctakes.typesystem.type.syntax: A Penn Treebank Node; as the top node, this stores the whole subsumed sentence's parse tree as a string.
TopTreebankNode() - Constructor for class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: Never called.
TopTreebankNode(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode: Internal - constructor used by generator
TopTreebankNode(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode
TopTreebankNode(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode
TopTreebankNode_Type - Class in org.apache.ctakes.typesystem.type.syntax: A Penn Treebank Node; as the top node, this stores the whole subsumed sentence's parse tree as a string.
TopTreebankNode_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type: initialize variables to correspond with Cas Type and Features
toSimMap(ConceptPairSimilarity) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean
toSimpleMap() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap: Copy of this object as a simple (java.util.Collection) map of Collection
toSimpleMap() - Method in interface org.apache.ctakes.dictionary.lookup2.util.collection.CollectionMap: Copy of this object as a simple (java.util.Collection) map of Collection
toSimpleMap() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap: Copy of this object as a simple (java.util.Collection) map of Collection
toSimpleMap() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap: Copy of this object as a simple (java.util.Collection) map of Collection
toSimpleMap() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap: Copy of this object as a simple (java.util.Collection) map of Collection
toSimpleMap() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap: Copy of this object as a simple (java.util.Collection) map of Collection
toString() - Method in class org.apache.ctakes.assertion.cr.NegExAnnotation
toString() - Method in class org.apache.ctakes.assertion.cr.RelationInfo
toString() - Method in class org.apache.ctakes.assertion.cr.Span
toString() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact.Span
toString() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
toString() - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
toString() - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation.Span
toString() - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation
toString() - Method in class org.apache.ctakes.core.nlp.tokenizer.Token
toString() - Method in class org.apache.ctakes.core.sentence.SentenceSpan
toString() - Method in class org.apache.ctakes.coreference.eval.helpers.Span
toString() - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
toString() - Method in class org.apache.ctakes.dependency.parser.util.DependencyRegex
toString() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
toString() - Method in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
toString() - Method in class org.apache.ctakes.relationextractor.eval.ParameterSettings
toString() - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
toString() - Method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
toString() - Method in class org.apache.ctakes.relationextractor.knowtator.Span
toString() - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings
toString() - Method in class org.apache.ctakes.temporal.utils.TlinkTypeSet
toString() - Method in class org.apache.ctakes.utils.tree.SimpleTree
toString() - Method in class org.apache.ctakes.utils.wiki.SearchResult
toString() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
toString() - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: print out joint distribution table
toString() - Method in class org.apache.ctakes.ytex.kernel.IRMetrics: return tab delimited ir metrics:
tp fp tn fn precision recall f1
toString() - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptPair
toString() - Method in class org.apache.ctakes.ytex.kernel.metric.LCSPath
toString() - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel
toString() - Method in class org.apache.ctakes.ytex.kernel.model.FeatureRank
toString() - Method in class org.apache.ctakes.ytex.kernel.model.ObjPair
toString() - Method in class org.apache.ctakes.ytex.kernel.tree.Node
toString() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexRule
toString() - Method in class org.apache.ctakes.ytex.uima.annotators.NegexAnnotator.NegexToken
toString() - Method in class org.apache.ctakes.ytex.uima.annotators.SentenceSpan
toString() - Method in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
toString() - Method in class org.apache.ctakes.ytex.uima.mapper.ColumnMappingInfo
toString() - Method in class org.apache.ctakes.ytex.uima.model.Document
toString() - Method in class org.apache.ctakes.ytex.uima.model.NamedEntityRegex
toString() - Method in class org.apache.ctakes.ytex.uima.model.SegmentRegex
toString() - Method in class org.apache.ctakes.ytex.uima.model.UimaType
toString() - Method in class org.apache.ctakes.ytex.umls.model.MRREL
toString() - Method in class org.apache.ctakes.ytex.umls.model.MRSTY
toString() - Method in class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
toString() - Method in class org.apache.ctakes.ytex.web.search.ConceptFirstWord
toString() - Method in class org.apache.ctakes.ytex.web.search.DocumentSearchResult
toSyntaxString() - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
TOTAL_SKIP_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator: specifies the number of total tokens that can be skipped
totalNumFiles - Variable in class org.apache.ctakes.core.cr.FilesInDirectoryCollectionCyclicalReads
totalRowCount - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
totalSize - Variable in class org.apache.ctakes.relationextractor.data.Splitter
totalSVPattern - Static variable in class org.apache.ctakes.ytex.libsvm.LibSVMParser
toTripleString() - Method in class org.apache.ctakes.dependency.parser.util.DependencyPath
toTsv() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
toXMIFile(SHARPXMI.Options, File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
toXMIFiles(SHARPXMI.Options, List<File>) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
toYNString(Boolean) - Static method in class org.apache.ctakes.ytex.uima.model.BooleanUtil
tp - Variable in class org.apache.ctakes.ytex.kernel.IRMetrics
tp - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
train(Iterable<<any>>) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
train(Iterable<<any>>) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
train(CollectionReader, File) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
train(String, <any>, boolean, Dictionary) - Static method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
train(String, <any>, boolean, Dictionary, int, int) - Static method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
train(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
train(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
train(Iterable<<any>>) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection
train(Iterable<<any>>) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
train(Iterable<<any>>) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection
train(Iterable<<any>>) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventProperties
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventProperties
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
train(CollectionReader, File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
train - Variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser.InstanceClassInfo
train - Variable in class org.apache.ctakes.ytex.kernel.model.CrossValidationFoldInstance
TRAIN_REMAINDERS - Static variable in class org.apache.ctakes.temporal.eval.THYMEData
trainAndPackage(String, File, String[]) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKEventSpans
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfClearTKTimeSpans
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfEventSpans
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfMetaTimeExpressionExtractor
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfNEPredicateEventSpans
trainAndPackage(File) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
trainAndRetrainAndTest(List<Integer>, List<Integer>) - Method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
TrainAssertionModel - Class in org.apache.ctakes.assertion.medfacts.cleartk
TrainAssertionModel() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
TrainAttributeModels - Class in org.apache.ctakes.assertion.train: For each assertion attribute (polarity, conditional, etc), train a model using the data in the training directories for that attribute, and store the model under the models-dir Note that this uses constants within AssertionConst for the directory names.
TrainAttributeModels() - Constructor for class org.apache.ctakes.assertion.train.TrainAttributeModels
trainDevCutoff - Static variable in class org.apache.ctakes.temporal.eval.I2B2Data
trainDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
trainDirectory - Variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation.Options
trainDirectory - Variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
trainDirectory - Variable in class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics.Options
trainGrid - Static variable in class org.apache.ctakes.assertion.train.PolarityDomainAdaptationTrain
TRAINING_MODE_PARAM - Static variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
trainingArguments - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
trainingArguments - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
trainingArguments - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans
trainingDirectories - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
trainingMode - Variable in class org.apache.ctakes.dependency.parser.cr.DependencyFileCollectionReader
TRAINLOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
trainOnly - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
trainRelationExtractor(File, String, List<File>, Class<? extends BinaryTextRelation>, File) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
trainSize - Variable in class org.apache.ctakes.relationextractor.data.Splitter
transactionManager - Variable in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
transactionManager - Variable in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
transactionManager - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
transactionManager - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
transactionManager - Variable in class org.apache.ctakes.ytex.kernel.KernelUtilImpl
transactionManager - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
transactionManager - Variable in class org.apache.ctakes.ytex.libsvm.LibSVMGramMatrixExporterImpl
transactionManager - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
TRANSDERMAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
TRANSDERMAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
transform(<any>) - Method in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
transform(List<Feature>) - Method in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
transform(<any>) - Method in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
transform(List<Feature>) - Method in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection
TRANSMUCOSAL - Static variable in class org.apache.ctakes.drugner.elements.RouteElement
TRANSMUCOSAL - Static variable in class org.apache.ctakes.drugner.fsm.output.elements.RouteToken
traverseTreeForDPath(SimpleTree) - Method in class org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor
treatmentSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
tree2str(TreebankNode) - Static method in class org.apache.ctakes.constituency.parser.util.TreeUtils
TREEBANK_DIRECTORY - Static variable in class org.apache.ctakes.temporal.ae.THYMETreebankReader
treebankDirectory - Variable in class org.apache.ctakes.temporal.ae.THYMETreebankReader
treebankDirectory - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
TreebankNode - Class in org.apache.ctakes.typesystem.type.syntax: A Penn Treebank-style tree node.
TreebankNode() - Constructor for class org.apache.ctakes.typesystem.type.syntax.TreebankNode: Never called.
TreebankNode(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TreebankNode: Internal - constructor used by generator
TreebankNode(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TreebankNode
TreebankNode(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TreebankNode
TreebankNode_Type - Class in org.apache.ctakes.typesystem.type.syntax: A Penn Treebank-style tree node.
TreebankNode_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type: initialize variables to correspond with Cas Type and Features
TreeExtractor - Class in org.apache.ctakes.constituency.parser.treekernel
TreeExtractor() - Constructor for class org.apache.ctakes.constituency.parser.treekernel.TreeExtractor
TreeFeatureConsumer - Class in org.apache.ctakes.relationextractor.pipelines
TreeFeatureConsumer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
TreeFragmentFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
TreeFragmentFeatureExtractor(String, String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
TreeFragmentFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
TreeFragmentFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.TreeFragmentFeatureExtractor
treeFrags - Variable in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
treeFrags - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
TreeHeightBaseline - Class in org.apache.ctakes.temporal.ae.baselines
TreeHeightBaseline() - Constructor for class org.apache.ctakes.temporal.ae.baselines.TreeHeightBaseline
TreeKernel - Class in org.apache.ctakes.constituency.parser.treekernel
TreeKernel() - Constructor for class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
TreeKernel(boolean) - Constructor for class org.apache.ctakes.constituency.parser.treekernel.TreeKernel
TreeKernelTrainer - Class in org.apache.ctakes.coreference.treekernel.training
TreeKernelTrainer(String, String) - Constructor for class org.apache.ctakes.coreference.treekernel.training.TreeKernelTrainer
treeMappingInfo - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
TreeMappingInfo - Class in org.apache.ctakes.ytex.kernel.tree
TreeMappingInfo() - Constructor for class org.apache.ctakes.ytex.kernel.tree.TreeMappingInfo
TreePrinter - Class in org.apache.ctakes.ytex.kernel.evaluator
TreePrinter() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.TreePrinter
trees - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
TreeUtils - Class in org.apache.ctakes.constituency.parser.util
TreeUtils() - Constructor for class org.apache.ctakes.constituency.parser.util.TreeUtils
TRIPLE_DELIM - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
TRUE_STRING - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
TRUE_STRING - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
TruncateCollectionFilterImpl - Class in org.apache.ctakes.dictionary.lookup.filter: Truncates objects in the collection.
TruncateCollectionFilterImpl(Comparator<MetaDataHit>, int) - Constructor for class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl: Constructor
truncateString(String, int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
TruthValue - Class in org.apache.ctakes.smokingstatus.util
TruthValue() - Constructor for class org.apache.ctakes.smokingstatus.util.TruthValue
ts - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
tty - Variable in class org.apache.ctakes.ytex.umls.model.MRCONSO
TUI - Static variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
tui - Variable in class org.apache.ctakes.ytex.umls.model.MRSTY
TUI_MF_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
TUI_TABLE - Static variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
tuiCheck(Object, Object) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
TuiCodeUtil - Class in org.apache.ctakes.dictionary.lookup2.util: Author: SPF Affiliation: CHIP-NLP Date: 9/5/2014
TuiCodeUtil() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil
tuiList - Variable in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
tuiList - Variable in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl
tuiListToBitset(Set<String>, SortedMap<String, Integer>) - Method in class org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl: convert the list of tuis into a bitset
tuiToMainSui(BitSet) - Method in class org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel
txNew - Variable in class org.apache.ctakes.ytex.kernel.AbstractBagOfWordsExporter
txTemplate - Variable in class org.apache.ctakes.ytex.kernel.dao.KernelEvaluationDaoImpl
txTemplate - Variable in class org.apache.ctakes.ytex.kernel.evaluator.CorpusKernelEvaluatorImpl
txTemplate - Variable in class org.apache.ctakes.ytex.uima.DBCollectionReader
txTemplateNew - Variable in class org.apache.ctakes.ytex.kernel.SparseDataExporterImpl
type - Static variable in class org.apache.ctakes.assertion.medfacts.types.Assertion
type - Static variable in class org.apache.ctakes.assertion.medfacts.types.Concept
type - Static variable in class org.apache.ctakes.assertion.zoner.types.Heading
type - Static variable in class org.apache.ctakes.assertion.zoner.types.Subzone
type - Static variable in class org.apache.ctakes.assertion.zoner.types.Zone
type - Static variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree
type - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
type - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation: The type (or "class") of annotation
type - Static variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS
type - Static variable in class org.apache.ctakes.coreference.type.DemMarkable
type - Static variable in class org.apache.ctakes.coreference.type.Markable
type - Static variable in class org.apache.ctakes.coreference.type.MarkablePair
type - Static variable in class org.apache.ctakes.coreference.type.MarkablePairSet
type - Static variable in class org.apache.ctakes.coreference.type.NEMarkable
type - Static variable in class org.apache.ctakes.coreference.type.Pair
type - Static variable in class org.apache.ctakes.coreference.type.PronounMarkable
type - Static variable in class org.apache.ctakes.drugner.type.ChunkAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.DosagesAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.DurationAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.FormAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.FrequencyAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.RouteAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.StrengthAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation
type - Static variable in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation
type - Static variable in class org.apache.ctakes.sideeffect.type.PSESentence
type - Static variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature
type - Static variable in class org.apache.ctakes.sideeffect.type.SESentence
type - Static variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation
type - Static variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence
type - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
type - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue
type - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID
type - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue
type - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue
type - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue
type - Static variable in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation
type - Static variable in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation
type - Static variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification
type - Static variable in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Attribute
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodySide
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Course
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Date
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Element
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Entity
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Event
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Lab
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabValue
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Medication
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Procedure
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Severity
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.Time
type - Static variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept
type - Static variable in class org.apache.ctakes.typesystem.type.relation.Affects
type - Static variable in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout
type - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.Contraindicates
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOf
type - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.Diagnoses
type - Static variable in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.Indicates
type - Static variable in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor
type - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOf
type - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreats
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOf
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.Prevents
type - Static variable in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.Relation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOf
type - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation
type - Static variable in class org.apache.ctakes.typesystem.type.relation.UMLSRelation
type - Static variable in class org.apache.ctakes.typesystem.type.structured.Demographics
type - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification
type - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentID
type - Static variable in class org.apache.ctakes.typesystem.type.structured.Metadata
type - Static variable in class org.apache.ctakes.typesystem.type.structured.SourceData
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADJP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADVP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.Chunk
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.CONJP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.ContractionToken
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.INTJ
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.Lemma
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.LST
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.NewlineToken
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.NP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.NumToken
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.O
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.PP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.PRT
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.SBAR
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.SymbolToken
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.UCP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.VP
type - Static variable in class org.apache.ctakes.typesystem.type.syntax.WordToken
type - Static variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.CourseModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.EventMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.Markable
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.Modifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.Predicate
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention
type - Static variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier
type - Static variable in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textspan.List
type - Static variable in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
type - Static variable in class org.apache.ctakes.typesystem.type.textspan.Paragraph
type - Static variable in class org.apache.ctakes.typesystem.type.textspan.Segment
type - Static variable in class org.apache.ctakes.typesystem.type.textspan.Sentence
type - Static variable in class org.apache.ctakes.typesystem.type.util.Pair
type - Static variable in class org.apache.ctakes.typesystem.type.util.Pairs
type - Static variable in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution
type - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation
type - Variable in class org.apache.ctakes.ytex.kernel.model.ClassifierEvaluationIRStat
type - Variable in class org.apache.ctakes.ytex.kernel.tree.Node
type - Variable in class org.apache.ctakes.ytex.kernel.tree.NodeKey
type - Static variable in class org.apache.ctakes.ytex.uima.types.Date
type - Static variable in class org.apache.ctakes.ytex.uima.types.DocKey
type - Static variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair
TYPE_CONTRACTION - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: Contains contractions and possessives (since they cannot be differentiated without context).
TYPE_EOL - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: A EOL token is defined as a line feed or carriage return character.
TYPE_ID_FIELD - Static variable in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
TYPE_NUMBER - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: A number token is defined as a consecutive series of digits.
TYPE_PUNCT - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: A punctuation token is defined as one character that can be either a period, double quote, single quote, question mark, exclamation point, hyphen (if not surrounded by word characters), etc...
TYPE_SYMBOL - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: Characters @!#$%^&*?
TYPE_SYSTEM_DESCRIPTION - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents
TYPE_UNKNOWN - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: The type is unknown.
TYPE_WORD - Static variable in class org.apache.ctakes.core.nlp.tokenizer.Token: A word token is defined as a consecutive series of word characters.
typeDescription(byte) - Static method in class org.apache.ctakes.core.nlp.tokenizer.Token
typeIndexID - Static variable in class org.apache.ctakes.assertion.medfacts.types.Assertion
typeIndexID - Static variable in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
typeIndexID - Static variable in class org.apache.ctakes.assertion.medfacts.types.Concept
typeIndexID - Static variable in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
typeIndexID - Static variable in class org.apache.ctakes.assertion.zoner.types.Heading
typeIndexID - Static variable in class org.apache.ctakes.assertion.zoner.types.Heading_Type
typeIndexID - Static variable in class org.apache.ctakes.assertion.zoner.types.Subzone
typeIndexID - Static variable in class org.apache.ctakes.assertion.zoner.types.Subzone_Type
typeIndexID - Static variable in class org.apache.ctakes.assertion.zoner.types.Zone
typeIndexID - Static variable in class org.apache.ctakes.assertion.zoner.types.Zone_Type
typeIndexID - Static variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree
typeIndexID - Static variable in class org.apache.ctakes.constituency.parser.uima.type.BooleanLabeledTree_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.BooleanLabeledFS_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.DemMarkable
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.DemMarkable_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.Markable
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.Markable_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.MarkablePair
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.MarkablePair_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.MarkablePairSet
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.MarkablePairSet_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.NEMarkable
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.NEMarkable_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.Pair
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.Pair_Type
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.PronounMarkable
typeIndexID - Static variable in class org.apache.ctakes.coreference.type.PronounMarkable_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.ChunkAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.ChunkAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DecimalStrengthAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DosagesAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DosagesAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DrugChangeStatusAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DrugMentionAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DurationAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.DurationAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FormAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FormAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FractionStrengthAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FrequencyAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FrequencyAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.FrequencyUnitAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.RangeStrengthAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.RouteAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.RouteAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.StrengthAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.StrengthAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.StrengthUnitAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.SubSectionAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation
typeIndexID - Static variable in class org.apache.ctakes.drugner.type.SuffixStrengthAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.PSESentence
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.PSESentence_Type
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.PSESentenceFeature_Type
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.SESentence
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.SESentence_Type
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation
typeIndexID - Static variable in class org.apache.ctakes.sideeffect.type.SideEffectAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.i2b2.type.RecordSentence_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DateAttributeValue_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.DocumentID_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NominalAttributeValue_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.NumericAttributeValue_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.libsvm.StringAttributeValue_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.SmokingDocumentClassification_Type
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation
typeIndexID - Static variable in class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Attribute
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Attribute_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodyLaterality_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodySide
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.BodySide_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Course
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Course_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Date
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Date_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.DiseaseDisorder_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Element
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Element_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Entity
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Entity_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Event
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Event_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.EventProperties_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Lab
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Lab_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabDeltaFlag_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabReferenceRange_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabValue
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.LabValue_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Medication
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Medication_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDosage_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationDuration_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationForm_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationFrequency_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationRoute_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.MedicationStrength_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.OntologyConcept_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Procedure
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Procedure_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureDevice_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.ProcedureMethod_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Severity
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Severity_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.SignSymptom_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Time
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.Time_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Affects
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Affects_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAbout_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CausesBringsAboutTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CollectionTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisrupts_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ComplicatesDisruptsTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Contraindicates
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Contraindicates_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ContraindicatesTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.CoreferenceRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOf
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOf_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Diagnoses
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Diagnoses_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.DiagnosesTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ElementRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Indicates
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Indicates_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.IndicatesTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedFor_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.IsIndicatedForTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOf
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOf_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreats
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreats_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManagesTreatsTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOf
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOf_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ManifestationOfTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Prevents
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Prevents_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.PreventsTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Relation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.Relation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.RelationArgument_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOf
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOf_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.ResultOfTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.TemporalTextRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.UMLSRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.relation.UMLSRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.Demographics
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.Demographics_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentClassification_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentID
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.DocumentID_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.Metadata
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.Metadata_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.SourceData
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.structured.SourceData_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADJP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADJP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADVP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ADVP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.BaseToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.Chunk
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.Chunk_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.CONJP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.CONJP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ContractionToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.ContractionToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.INTJ
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.INTJ_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.Lemma
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.Lemma_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.LST
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.LST_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.NewlineToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.NewlineToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.NP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.NP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.NumToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.NumToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.O
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.O_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.PP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.PP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.PRT
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.PRT_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.PunctuationToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.SBAR
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.SBAR_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.StanfordDependency_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.SymbolToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.SymbolToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.TopTreebankNode_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.TreebankNode_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.UCP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.UCP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.VP
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.VP_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.WordToken
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.syntax.WordToken_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.CourseModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.EntityMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.EventMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.EventMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.Markable
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.Markable_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.Modifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.Modifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.Predicate
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.Predicate_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.TimeMention_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.DrugLookupWindowAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.List
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.List_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.Paragraph
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.Paragraph_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.Segment
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.Segment_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.Sentence
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.textspan.Sentence_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.util.Pair
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.util.Pair_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.util.Pairs
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.util.Pairs_Type
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution
typeIndexID - Static variable in class org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type
typeIndexID - Static variable in class org.apache.ctakes.ytex.uima.types.Date
typeIndexID - Static variable in class org.apache.ctakes.ytex.uima.types.Date_Type
typeIndexID - Static variable in class org.apache.ctakes.ytex.uima.types.DocKey
typeIndexID - Static variable in class org.apache.ctakes.ytex.uima.types.DocKey_Type
typeIndexID - Static variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair
typeIndexID - Static variable in class org.apache.ctakes.ytex.uima.types.KeyValuePair_Type
typesStoreCoveredText - Variable in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
typesToDisplay - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
typeSystem - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
typeSystemDescription - Static variable in class org.apache.ctakes.assertion.cr.NegExCorpusReader

U

UCP - Class in org.apache.ctakes.typesystem.type.syntax: An unlike coordinating phrase, e.g., a NP and a PP conjoined via "and" Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.UCP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
UCP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP: Never called.
UCP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP: Internal - constructor used by generator
UCP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP
UCP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP
UCP_Type - Class in org.apache.ctakes.typesystem.type.syntax: An unlike coordinating phrase, e.g., a NP and a PP conjoined via "and" Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.UCP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
UCP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.UCP_Type: initialize variables to correspond with Cas Type and Features
UIMA_ARRAY_INDEX_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_ARRAY_SIZE_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_CAS - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_EMPTY_FSLIST - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_FSARRAY - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_INTARRAY - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_LIST_HEAD_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_LIST_TAIL_KEYWORD - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_NONEMPTY_FSLIST - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_REF_SOFA - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_SOFA - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_SOFA_STRING - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
UIMA_TCAS_DOCUMENT - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const
uimaContext - Variable in class org.apache.ctakes.preprocessor.ae.CdaCasInitializer
uimaContext - Variable in class org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator
uimaHomeDir - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
uimaType - Variable in class org.apache.ctakes.ytex.uima.model.DocumentAnnotation
UimaType - Class in org.apache.ctakes.ytex.uima.model: Reference data.
UimaType() - Constructor for class org.apache.ctakes.ytex.uima.model.UimaType
UimaType(int, String) - Constructor for class org.apache.ctakes.ytex.uima.model.UimaType
uimaTypeId - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
uimaTypeID - Variable in class org.apache.ctakes.ytex.uima.model.UimaType
uimaTypeIdColumnName - Variable in class org.apache.ctakes.ytex.uima.mapper.AnnoMappingInfo
uimaTypeMap - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
uimaTypeName - Variable in class org.apache.ctakes.ytex.uima.model.UimaType
UMLSAddr - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSADDR_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
UMLSADDR_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSADDR_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
UmlsAuiFirstWord - Class in org.apache.ctakes.ytex.umls.model
UmlsAuiFirstWord() - Constructor for class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
UmlsAuiFirstWord(String, String) - Constructor for class org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord
UMLSBasedTokenFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
UMLSBasedTokenFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.UMLSBasedTokenFeaturesExtractor
UmlsConcept - Class in org.apache.ctakes.typesystem.type.refsem: Concepts in the Unified Medical Language System (UMLS) Metathesaurus have a concept unique identifier (CUI) and a type unique identifier (TUI, i.e., semantic type) which are curated, normalized codes.
UmlsConcept() - Constructor for class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: Never called.
UmlsConcept(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.UmlsConcept: Internal - constructor used by generator
UmlsConcept(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.UmlsConcept
UmlsConcept_Type - Class in org.apache.ctakes.typesystem.type.refsem: Concepts in the Unified Medical Language System (UMLS) Metathesaurus have a concept unique identifier (CUI) and a type unique identifier (TUI, i.e., semantic type) which are curated, normalized codes.
UmlsConcept_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.UmlsConcept_Type: initialize variables to correspond with Cas Type and Features
umlsDao - Variable in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
UMLSDao - Interface in org.apache.ctakes.ytex.umls.dao
UMLSDaoImpl - Class in org.apache.ctakes.ytex.umls.dao
UMLSDaoImpl() - Constructor for class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
UmlsDictionaryLookupAnnotator - Class in org.apache.ctakes.dictionary.lookup.ae: UIMA annotator that identified entities based on lookup.
UmlsDictionaryLookupAnnotator() - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
umlsExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
umlsExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
umlsExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
UmlsFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
UmlsFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.UmlsFeatureExtractor
umlsFirstWordComparator - Static variable in class org.apache.ctakes.ytex.web.search.ConceptLookupBean
umlsFirstWordComparator - Static variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
umlsFirstWordService - Variable in class org.apache.ctakes.ytex.web.search.SemanticSearchBean
UmlsJdbcConceptFactory - Class in org.apache.ctakes.dictionary.lookup2.concept
UmlsJdbcConceptFactory(String, UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory
UmlsJdbcRareWordDictionary - Class in org.apache.ctakes.dictionary.lookup2.dictionary
UmlsJdbcRareWordDictionary(String, UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
UMLSPW - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSPW_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
UMLSPW_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSPW_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
UMLSRelation - Class in org.apache.ctakes.typesystem.type.relation: A biomedical relationship between two spans of text that have been mapped to UMLS concepts.
UMLSRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.UMLSRelation: Never called.
UMLSRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.UMLSRelation: Internal - constructor used by generator
UMLSRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.UMLSRelation
UMLSRelation_Type - Class in org.apache.ctakes.typesystem.type.relation: A biomedical relationship between two spans of text that have been mapped to UMLS concepts.
UMLSRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.UMLSRelation_Type: initialize variables to correspond with Cas Type and Features
umlsSemanticType - Variable in class org.apache.ctakes.temporal.data.analysis.EventPrinterPipeline.EventWriter
UmlsSingleFeatureExtractor - Class in org.apache.ctakes.temporal.ae.feature
UmlsSingleFeatureExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.UmlsSingleFeatureExtractor
UmlsToSnomedConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym.
UmlsToSnomedConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
UmlsToSnomedDbConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym, by looking in a database for SNOMED codes that map to the identified CUI.
UmlsToSnomedDbConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
UmlsToSnomedDbConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
UmlsToSnomedLuceneConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae: Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity objects only the ones that have a SNOMED synonym, by looking in a lucene index for SNOMED codes that map to the identified CUI.
UmlsToSnomedLuceneConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
UmlsToSnomedLuceneConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
UMLSUser - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSUSER_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
UMLSUSER_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSUSER_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
UmlsUserApprover - Enum in org.apache.ctakes.dictionary.lookup2.util: Used to validate UMLS license / user.
UmlsUserApprover() - Constructor for enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
UmlsUserApprover.DotPlotter - Class in org.apache.ctakes.dictionary.lookup2.util
UmlsUserApprover.DotPlotter() - Constructor for class org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.DotPlotter
UMLSVendor - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSVENDOR_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
UMLSVENDOR_PARAM - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator
UMLSVENDOR_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
uncertainty - Variable in class org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader.DelayedRelation
UncertaintyCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
UncertaintyCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
UncertaintyFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
UncertaintyFeatureExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.UncertaintyFeatureExtractor
UncertaintyModifier - Class in org.apache.ctakes.typesystem.type.textsem: An introduction of a measure of doubt into a statement.
UncertaintyModifier() - Constructor for class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier: Never called.
UncertaintyModifier(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier: Internal - constructor used by generator
UncertaintyModifier(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier
UncertaintyModifier(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier
UncertaintyModifier_Type - Class in org.apache.ctakes.typesystem.type.textsem: An introduction of a measure of doubt into a statement.
UncertaintyModifier_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type: initialize variables to correspond with Cas Type and Features
UnexpandedTokenFeaturesExtractor - Class in org.apache.ctakes.temporal.ae.feature
UnexpandedTokenFeaturesExtractor() - Constructor for class org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor
unexpectedParamValueMsg - Static variable in class org.apache.ctakes.utils.test.TestUtil
union(int, int) - Method in class org.apache.ctakes.coreference.util.ParentPtrTree
UNKNOWN_TABLE_TYPE - Static variable in class org.apache.ctakes.preprocessor.ClinicalNotePreProcessor
UnknownSmokerNamedEntityAnnotation - Class in org.apache.ctakes.smokingstatus.type: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-smoking-status/target/jcasgen/typesystem.xml
UnknownSmokerNamedEntityAnnotation() - Constructor for class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation: Never called.
UnknownSmokerNamedEntityAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation: Internal - constructor used by generator
UnknownSmokerNamedEntityAnnotation(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation
UnknownSmokerNamedEntityAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation
UnknownSmokerNamedEntityAnnotation_Type - Class in org.apache.ctakes.smokingstatus.type: Updated by JCasGen Wed Sep 30 11:06:03 EDT 2015
UnknownSmokerNamedEntityAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.UnknownSmokerNamedEntityAnnotation_Type: initialize variables to correspond with Cas Type and Features
UnknownSmokerNamedEntityLookupConsumerImpl - Class in org.apache.ctakes.smokingstatus.lookup.ae: copied from edu.may.bmi.uima.lookup.ae.NamedEntityLookupConsumerImpl in the "Dictionary Lookup" project
UnknownSmokerNamedEntityLookupConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.smokingstatus.lookup.ae.UnknownSmokerNamedEntityLookupConsumerImpl
unknownWords - Variable in class org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator
unmarshaller - Variable in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind
unmarshalSrcXml(String) - Method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind
unmarshalStrXml(String) - Method in class org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind
unsetConfig() - Static method in class org.apache.ctakes.ytex.uima.mapper.MapperConfig
UP_ARC_A - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
UP_ARC_A - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
UP_ARC_A - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
UP_ARC_B - Static variable in class org.apache.ctakes.dependency.parser.util.Delim
UP_ARC_B - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyPath
UP_ARC_B - Static variable in class org.apache.ctakes.dependency.parser.util.DependencyRegex
UP_NODES - Static variable in class org.apache.ctakes.assertion.pipelines.GenerateDependencyRepresentation
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.temporal.ae.feature.selection.BinaryAlphaFeatureSelection.AlphaScorer
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.MutualInformationStats
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.temporal.ae.feature.selection.OddsRatioFeatureSelection.OddsRatioScorer
updateChildren(FeatureRank, Map<String, FeatureRank>, FeatureEvaluation, ConceptGraph, Map<String, Double>, Map<String, Double>, Map<FeatureRank, Set<FeatureRank>>, double, double) - Method in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl: add the children of parentConcept to mapChildConcept.
updateConceptGraph(ValueChangeEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSimBean: handle selecting different concept graph
updateLabelClassMapTransductive() - Method in class org.apache.ctakes.ytex.kernel.BaseSparseDataFormatter: add the 'unlabeled' class id to the classIndexMap if it isn't there already
updateList(ValueChangeEvent) - Method in class org.apache.ctakes.ytex.web.search.ConceptLookupBean: Called when a user has modifed the SelectInputText value.
updateList(ValueChangeEvent) - Method in class org.apache.ctakes.ytex.web.search.SemanticSearchBean: Called when a user has modifed the SelectInputText value.
updateNames(String, List<String>, Map<String, String>) - Method in class org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl
updateParent(Map<ConcRel, Integer>, HashSet<ConcRel>, HashSet<ConcRel>, int, Map<ConcRel, List<ConcRel>>) - Static method in class org.apache.ctakes.ytex.kernel.model.ConcRel: perform 1 iteration of breadth-first search on lcs.
updateSemiSupervisedPredictions(ClassifierEvaluation, List<List<Long>>, boolean, int[]) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser: used by semil & svmlin to store semisupervised predictions.
updateSemiSupervisedPredictions(ClassifierEvaluation, List<BaseClassifierEvaluationParser.InstanceClassInfo>, boolean, String[], Map<String, Integer>) - Method in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
updateSize(AnnoMappingInfo, String, int, int) - Method in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl: update column size for given column, if the column has been mapped
url - Variable in class org.apache.ctakes.jdl.data.base.JdlConnection
URL_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
urlStarters - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
urlToFile(URL) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
urlToSchema(URL) - Static method in class org.apache.ctakes.jdl.data.xml.SchemaUtil
usage(Logger) - Static method in class org.apache.ctakes.core.ae.SentenceDetector
usage() - Static method in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
usage(Logger) - Static method in class org.apache.ctakes.ytex.uima.annotators.SentenceDetector
USE_DEFAULT_EXTRACTORS - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
USE_DEFAULT_EXTRACTORS - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
USE_DEFAULT_EXTRACTORS - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
useCache - Variable in class org.apache.ctakes.utils.wiki.WikiIndex
useClosure - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
useClosure - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
useClosure - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
useClosure - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
useClosure - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
useCmdCache - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
useCmdCache - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
useEvaluationLogFile - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
useFrags - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
useGoldAttributes - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations
useGoldAttributes - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations
useGoldAttributes - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations
useGoldAttributes - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations
useGoldAttributes - Variable in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations
useLemmaCache - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
useLemmaCache - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
useLemmatizer - Variable in class org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE
usePrepStmtVals - Variable in class org.apache.ctakes.core.cr.JdbcCollectionReader
user - Variable in class org.apache.ctakes.jdl.data.base.JdlConnection
USER_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
useSegments - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
useSegments - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
useSegments - Variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
useTmp - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
useTokenEnd - Variable in class org.apache.ctakes.core.sentence.SentenceDetectorCtakes
useXMI - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
useYtexNegation - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
Utility - Class in org.apache.ctakes.preprocessor
Utility() - Constructor for class org.apache.ctakes.preprocessor.Utility
Utils - Class in org.apache.ctakes.relationextractor.ae.baselines
Utils() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Utils
Utils - Class in org.apache.ctakes.relationextractor.data.analysis: Various useful classes and methods.
Utils() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.Utils
Utils - Class in org.apache.ctakes.temporal.duration: Various useful classes and methods for evaluating event duration data.
Utils() - Constructor for class org.apache.ctakes.temporal.duration.Utils
Utils.Callback - Class in org.apache.ctakes.relationextractor.data.analysis: Read word embeddings from file.
Utils.Callback() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
Utils.Callback - Class in org.apache.ctakes.temporal.duration: Read event duration distributions from file.
Utils.Callback() - Constructor for class org.apache.ctakes.temporal.duration.Utils.Callback

V

v1 - Variable in class org.apache.ctakes.utils.wiki.Cache
v1 - Variable in class org.apache.ctakes.ytex.kernel.model.ObjPair
v2 - Variable in class org.apache.ctakes.utils.wiki.Cache
v2 - Variable in class org.apache.ctakes.ytex.kernel.model.ObjPair
val - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
validate(SHARPXMI.EvaluationOptions) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
validateDegreeOfArgumentTypes(RelationExtractorAnnotator.IdentifiedAnnotationPair) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Are entity types of the arguments valid for degree_of relation? The following are the valid combinations: degree-of(disease/disorder/2, modifier) degree-of(sign/symptom/3, modifier)
validateHyphenMap(Map<String, Integer>) - Static method in class org.apache.ctakes.core.nlp.tokenizer.Tokenizer: Validate the structure of the hyphen map.
validateLocationOfArgumentTypes(RelationExtractorAnnotator.IdentifiedAnnotationPair) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Are entity types of the arguments valid for location_of relation? The following combinations are allowed: location-of(anatomical site/6, disorder/2) location-of(anatomical site/6, sign/symptom/3) location-of(anatomical site/6, procedure/5)
validateProps(Properties) - Method in interface org.apache.ctakes.ytex.kernel.CytoscapeHelper
validateProps(Properties) - Method in class org.apache.ctakes.ytex.kernel.CytoscapeHelperImpl
Validation - Class in org.apache.ctakes.jdl.data.xml: Validation between Schema and XML.
Validation(Schema) - Constructor for class org.apache.ctakes.jdl.data.xml.Validation
Validation(String) - Constructor for class org.apache.ctakes.jdl.data.xml.Validation
Validation(Schema, Document) - Constructor for class org.apache.ctakes.jdl.data.xml.Validation
Validation(Schema, String) - Constructor for class org.apache.ctakes.jdl.data.xml.Validation
VALIDATION_FEATURE_ID - Static variable in class org.apache.ctakes.jdl.data.xml.SaxParser: Validation feature id (http://xml.org/sax/features/validation).
validator - Variable in class org.apache.ctakes.jdl.data.xml.Validation
validCG - Variable in class org.apache.ctakes.ytex.kernel.metric.LinMetric
validOtherEmailAddressCharacters - Variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
validTemporalType(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.AddClosure
validTemporalType(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddClosure
validTemporalType(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddClosure
validTemporalType(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfI2B2TemporalRelations.AddClosure
validTemporalType(String) - Static method in class org.apache.ctakes.temporal.eval.EvaluationOfSelfEventTimeRelations.AddClosure
value - Variable in class org.apache.ctakes.assertion.cr.ArgumentInfo
value - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.Option
value - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser.Slot
value - Variable in class org.apache.ctakes.relationextractor.knowtator.ArgumentInfo
value - Variable in class org.apache.ctakes.ytex.kernel.tree.Node
value - Variable in class org.apache.ctakes.ytex.kernel.tree.NodeKey
valueOf(String) - Static method in enum org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.CombineScoreMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.assertion.cc.JudgeAttributeInstances.Selector: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.assertion.eval.AssertionEvaluation.Corpus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.FEATURE_CONFIG: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.ATTRIBUTE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.assertion.pipelines.SharpCorpusSplit.Subcorpus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.coreference.eval.helpers.B3Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.coreference.eval.helpers.CEAFType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.coreference.eval.helpers.KAlphaType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.coreference.eval.helpers.MatType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.coreference.eval.helpers.PairType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.dictionary.lookup2.concept.ConceptCode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.FIELD_INDEX: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluateOn: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.CombineScoreMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.temporal.ae.THYMETreebankReader.TOKEN_TYPE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Subcorpus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.temporal.utils.AnnotationIdCollection.ArgComparator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.temporal.utils.TlinkType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator.MeasureType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.ytex.kernel.SparseDataExporter.ScopeEnum: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixType: Deprecated.

Returns the enum constant of this type with the specified name.
values() - Static method in enum org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.CombineScoreMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.assertion.cc.JudgeAttributeInstances.Selector: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.assertion.eval.AssertionEvaluation.Corpus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.FEATURE_CONFIG: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.ATTRIBUTE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.assertion.pipelines.SharpCorpusSplit.Subcorpus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.coreference.eval.helpers.B3Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.coreference.eval.helpers.CEAFType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.coreference.eval.helpers.KAlphaType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.coreference.eval.helpers.MatType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.coreference.eval.helpers.PairType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.dictionary.lookup.vo.LookupTokenComparator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.dictionary.lookup2.concept.ConceptCode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.FIELD_INDEX: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
values() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
values() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
values() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
values() - Method in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
values() - Static method in enum org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluateOn: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.temporal.ae.feature.selection.MutualInformationFeatureSelection.CombineScoreMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.temporal.ae.THYMETreebankReader.TOKEN_TYPE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.temporal.eval.Evaluation_ImplBase.Subcorpus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.temporal.utils.AnnotationIdCollection.ArgComparator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.temporal.utils.TlinkType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser.ParseOption: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluator.MeasureType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService.SimilarityMetricEnum: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.ytex.kernel.SparseDataExporter.ScopeEnum: Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class org.apache.ctakes.ytex.kernel.tree.NodeMappingInfo
values() - Static method in enum org.apache.ctakes.ytex.weka.GramMatrixExporterImpl.GramMatrixType: Deprecated.

Returns an array containing the constants of this enum type, in the order they are declared.
VariantPhraseBuilderImpl - Class in org.apache.ctakes.dictionary.lookup.phrasebuilder: Builds phrases based on various variants of a LookupToken.
VariantPhraseBuilderImpl(String[], boolean) - Constructor for class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl: Constructor
VariantPhraseBuilderImpl.AttributeTextImpl - Class in org.apache.ctakes.dictionary.lookup.phrasebuilder: Implementation that extracts text from an attribute of a LookupToken.
VariantPhraseBuilderImpl.AttributeTextImpl(String) - Constructor for class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl.AttributeTextImpl: Constructor
VariantPhraseBuilderImpl.OriginalTextImpl - Class in org.apache.ctakes.dictionary.lookup.phrasebuilder: Implementation that extracts text from the original text of a LookupToken.
VariantPhraseBuilderImpl.OriginalTextImpl() - Constructor for class org.apache.ctakes.dictionary.lookup.phrasebuilder.VariantPhraseBuilderImpl.OriginalTextImpl
VariantPhraseBuilderImpl.TextExtractor - Interface in org.apache.ctakes.dictionary.lookup.phrasebuilder: Common interface to extract text from a LookupToken.
vcdim - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
vClinicalNumber - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
vdate - Variable in class org.apache.ctakes.drugner.elements.StartDateElement
vecCreator - Variable in class org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
vecCreator - Variable in class org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
vector - Variable in class org.apache.ctakes.utils.distsem.WordVector
vectors - Variable in class org.apache.ctakes.utils.distsem.WordEmbeddings
VENDOR_PARAM - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
VERBOSE - Variable in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
VERBOSE - Static variable in class org.apache.ctakes.assertion.cr.XMLReader
verbTensePatternExtractor - Variable in class org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
verbTensePatternExtractor - Variable in class org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator
verbTensePatternExtractor - Variable in class org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator
verbTensePatternExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexAdmissionTimeAnnotator
verbTensePatternExtractor - Variable in class org.apache.ctakes.temporal.ae.TimexDischargeTimeAnnotator
verify(int, int, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
viewButton - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
viewDocuments() - Method in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
vNoteDate - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel
VP - Class in org.apache.ctakes.typesystem.type.syntax: A verb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.VP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-ytex-uima/target/jcasgen/typesystem.xml
VP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.VP: Never called.
VP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.VP: Internal - constructor used by generator
VP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.VP
VP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.VP
VP_Type - Class in org.apache.ctakes.typesystem.type.syntax: A verb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.VP Updated by JCasGen Wed Sep 30 11:06:15 EDT 2015
VP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.VP_Type: initialize variables to correspond with Cas Type and Features
vRevDate - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel

W

WEEKLY - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement
weight - Variable in class org.apache.ctakes.ytex.kernel.model.SVMClassifierEvaluation
WeightedPolynomialMixingKernel - Class in org.apache.ctakes.ytex.kernel.evaluator: weighted polynomial mixing kernel: (\sum w_i * k(x_i, y_i) \div \sum w_i ) ^ l Apply the delegate kernel to the respective 'parts' of this node (x_i, y_i) Multiply the result by the weight (w_i * k(x_i,y_i)) Sum everything up, divide by the sum of the weights take the power of everything to l WeightedPolynomialMixingKernel.pow the power to raise things to
WeightedPolynomialMixingKernel.attributeKey the children of this node form a 'vector'.
WeightedPolynomialMixingKernel() - Constructor for class org.apache.ctakes.ytex.kernel.evaluator.WeightedPolynomialMixingKernel
weightFunction(int) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
weights - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
WekaAttributeEvaluator - Interface in org.apache.ctakes.ytex.weka
WekaAttributeEvaluatorImpl - Class in org.apache.ctakes.ytex.weka
WekaAttributeEvaluatorImpl() - Constructor for class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl
WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter - Class in org.apache.ctakes.ytex.weka
WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter(String, String, String) - Constructor for class org.apache.ctakes.ytex.weka.WekaAttributeEvaluatorImpl.WekaAttributeEvaluatorFormatter
wekaAttributes - Variable in class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
WekaBagOfWordsExporter - Interface in org.apache.ctakes.ytex.weka
WekaBagOfWordsExporterImpl - Class in org.apache.ctakes.ytex.weka
WekaBagOfWordsExporterImpl() - Constructor for class org.apache.ctakes.ytex.weka.WekaBagOfWordsExporterImpl
WekaFormatterFactory - Class in org.apache.ctakes.ytex.weka
WekaFormatterFactory() - Constructor for class org.apache.ctakes.ytex.weka.WekaFormatterFactory
WekaFormatterFactory.WekaFormatter - Class in org.apache.ctakes.ytex.weka
WekaFormatterFactory.WekaFormatter(KernelUtil) - Constructor for class org.apache.ctakes.ytex.weka.WekaFormatterFactory.WekaFormatter
WekaResultInstanceImporter - Interface in org.apache.ctakes.ytex.weka: Import the weka results for the specified instance.
WekaResultsImporter - Interface in org.apache.ctakes.ytex.weka: parse weka instance output when classifier run with -p option.
WekaResultsImporterImpl - Class in org.apache.ctakes.ytex.weka: parse weka instance output when classifier run with -p option.
WekaResultsImporterImpl() - Constructor for class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl
WekaResultsImporterImpl.ClassifierEvaluationInstanceImporter - Class in org.apache.ctakes.ytex.weka
WekaResultsImporterImpl.ClassifierEvaluationInstanceImporter(ClassifierEvaluation, boolean) - Constructor for class org.apache.ctakes.ytex.weka.WekaResultsImporterImpl.ClassifierEvaluationInstanceImporter
wiki - Variable in class org.apache.ctakes.coreference.util.SvmVectorCreator
wiki - Variable in class org.apache.ctakes.coreference.util.SyntaxAttributeCalculator
WikiIndex - Class in org.apache.ctakes.utils.wiki: A wrapper for a wikipedia lucene index.
WikiIndex(int, String, String, boolean) - Constructor for class org.apache.ctakes.utils.wiki.WikiIndex
WikiIndex(int, String, String) - Constructor for class org.apache.ctakes.utils.wiki.WikiIndex
WikiIndex() - Constructor for class org.apache.ctakes.utils.wiki.WikiIndex
WINDOW_ANNOT_PRP_KEY - Static variable in class org.apache.ctakes.dictionary.lookup.ae.FirstTokenPermLookupInitializerImpl
WINDOW_ANNOT_PRP_KEY - Static variable in class org.apache.ctakes.ytex.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
WINDOW_ANNOTATION_CLASS_PARAM - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator: "WindowAnnotationClass" is a required, single, string parameter that specifies the annotation type of the windows that specify the hard boundaries of scopes.
WindowProcessor - Interface in org.apache.ctakes.dictionary.lookup2.ae: Processes an Annotation window in the cas, adding discovered terms to a map.
windowSize - Variable in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
windowType - Variable in class org.apache.ctakes.necontexts.ContextAnnotator
word - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator.LemmaLocalClass
word - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator.LemmaLocalClass
word - Variable in class org.apache.ctakes.utils.distsem.WordVector
word2class - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.BrownClusterFeatureFunction
WordEmbeddings - Class in org.apache.ctakes.utils.distsem
WordEmbeddings(int) - Constructor for class org.apache.ctakes.utils.distsem.WordEmbeddings
WordEmbeddings(Map<String, WordVector>) - Constructor for class org.apache.ctakes.utils.distsem.WordEmbeddings
wordFreqFile - Variable in class org.apache.ctakes.core.cc.TokenFreqCasConsumer
wordFreqs - Variable in class org.apache.ctakes.core.cc.TokenFreqCasConsumer
wordMap - Static variable in class org.apache.ctakes.assertion.util.AssertionTreeUtils
WordNetFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that are based on WordNet.
WordNetFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.WordNetFeatureExtractor
wordNetPath - Static variable in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils
WordNetUtils - Class in org.apache.ctakes.relationextractor.ae.features: This is a wrapper for the MIT WordNet inteface that simplifies basic operations such as retrieving synonyms and hypernyms for a word.
WordNetUtils() - Constructor for class org.apache.ctakes.relationextractor.ae.features.WordNetUtils
WordSenseDisambiguator - Interface in org.apache.ctakes.ytex.kernel.wsd
WordSenseDisambiguatorImpl - Class in org.apache.ctakes.ytex.kernel.wsd
WordSenseDisambiguatorImpl() - Constructor for class org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl
WordSetCondition - Class in org.apache.ctakes.core.fsm.condition
WordSetCondition(Set<String>, boolean) - Constructor for class org.apache.ctakes.core.fsm.condition.WordSetCondition
wordsInPattern - Variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
wordsToExclude - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
wordsToIgnore - Variable in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster
WordToken - Interface in org.apache.ctakes.core.fsm.token
WordToken - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a word rather than a punctuation, symbol, newline, contraction, or number.
WordToken() - Constructor for class org.apache.ctakes.typesystem.type.syntax.WordToken: Never called.
WordToken(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.WordToken: Internal - constructor used by generator
WordToken(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.WordToken
WordToken(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.WordToken
WordToken_Type - Class in org.apache.ctakes.typesystem.type.syntax: Differentiates a token as being a word rather than a punctuation, symbol, newline, contraction, or number.
WordToken_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.WordToken_Type: initialize variables to correspond with Cas Type and Features
WordTokenAdapter - Class in org.apache.ctakes.core.fsm.adapters: Adapts JCas token annotation to interface expected by the Context Dependent Tokenizer.
WordTokenAdapter(WordToken) - Constructor for class org.apache.ctakes.core.fsm.adapters.WordTokenAdapter
WordTokenAdapter - Class in org.apache.ctakes.core.fsm.token.adapter: Adapts a Context Free Tokenizer token into a Context Dependent Tokenizer WordToken.
WordTokenAdapter(Token) - Constructor for class org.apache.ctakes.core.fsm.token.adapter.WordTokenAdapter
wordTokenLen - Variable in class org.apache.ctakes.core.nlp.tokenizer.ContractionResult
wordTokenOrNumToken(String, int, int) - Method in class org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB
wordToVector - Variable in class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
wordTypeExtractor - Variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
wordTypes - Variable in class org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator
wordTypes - Variable in class org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor
WordValueCondition - Class in org.apache.ctakes.core.fsm.condition
WordValueCondition(String, boolean) - Constructor for class org.apache.ctakes.core.fsm.condition.WordValueCondition
WordVector - Class in org.apache.ctakes.utils.distsem
WordVector(String, double[]) - Constructor for class org.apache.ctakes.utils.distsem.WordVector
WordVectorReader - Class in org.apache.ctakes.utils.distsem
WordVectorReader(InputStream) - Constructor for class org.apache.ctakes.utils.distsem.WordVectorReader
wrapAsFsmTokens(List) - Method in class org.apache.ctakes.drugner.ae.impl.NegContextInitializerImpl
wrapAsFsmTokens(List<? extends Annotation>) - Method in class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer: This method converts Token annotations to TextTokens required by the fsm library used by both subclasses of this class.
wrapAsFsmTokens(List<? extends Annotation>) - Method in class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer: This method converts Token annotations to TextTokens required by the fsm library used by both subclasses of this class.
writeAggregateDescriptions(AggregateBuilder, AnalysisEngineDescription, AnalysisEngineDescription, File, String) - Static method in class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
WriteClearNLPDescriptors - Class in org.apache.ctakes.dependency.parser.ae.util: Use this to generate UIMA xml description files for the ClearNLP analysis engines.
WriteClearNLPDescriptors() - Constructor for class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors
WriteClearNLPDescriptors.Options - Class in org.apache.ctakes.dependency.parser.ae.util
WriteClearNLPDescriptors.Options() - Constructor for class org.apache.ctakes.dependency.parser.ae.util.WriteClearNLPDescriptors.Options
writeConceptGraph(String, String, ConceptGraph) - Method in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl: write the concept graph, create parent directories as required
writeDesc(File, Class<?>, AnalysisEngineDescription) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
writeDesc(File, String, AnalysisEngineDescription) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
writeDictionary(Map<String, Set<String>>, PrintStream) - Static method in class org.apache.ctakes.postagger.TagDictionaryCreator
writeInstance(String, List<Feature>, String) - Static method in class org.apache.ctakes.temporal.duration.Utils: Output label and list of cleartk features to a file for debugging.
writeJCasInformation(JCas, int, long, String, Timestamp) - Method in class org.apache.ctakes.core.cc.AbstractJdbcWriter: The main "process" method, called from processCas
writeJCasInformation(JCas, int, long, String, Timestamp) - Method in class org.apache.ctakes.core.cc.JdbcWriterTemplate: The main "process" method, called from processCas
writeLibsvmLine(BufferedWriter, SortedMap<Integer, Double>) - Method in class org.apache.ctakes.ytex.libsvm.LibSVMFormatterFactory.LibSVMFormatter
writeObject(ObjectOutputStream) - Method in class org.apache.ctakes.ytex.kernel.model.ConcRel: serialize parent/children concept ids, not the objects
writeProps(String, Properties) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil
writeSemilEvalFile(List<String>, List<String>, File) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil: write file for label
writeSvmEvalFile(Properties, File, File, String) - Method in class org.apache.ctakes.ytex.kernel.ClassifierEvalUtil: generate parameter grid for each training file.
writeTableRow(PreparedStatement, int, Map<? extends AbstractJdbcWriter.FieldInfo, Object>) - Static method in class org.apache.ctakes.core.cc.AbstractJdbcWriter: Adds a new row of values to a batch in the prepared statement.
writeToFile(String, String) - Method in class org.apache.ctakes.core.cc.FilesInDirectoryCasConsumer
writeToFile(String, String) - Method in class org.apache.ctakes.core.cc.NormalizedFilesInDirectoryCasConsumer
writeToFile(String, List<String>) - Method in class org.apache.ctakes.core.cc.TokenOffsetsCasConsumer
writeToFile(String) - Method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
writeToFormatLucene(String, String, String) - Method in class org.apache.ctakes.dictionary.assertion.CreateAssertionLuceneIndexFromDelimitedFile
writeXCas(CAS, String) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
writeXmi(CAS, String) - Method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
writeXmi(CAS, File) - Static method in class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES: Serialize a CAS to a file in XMI format
writeXmi(CAS, File) - Method in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes: Serialize a CAS to a file in XMI format
writeXmi(CAS, File, String) - Method in class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes: Serialize a CAS to a file in XMI format
wsd - Variable in class org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
wsDotPattern - Static variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
wsPattern - Static variable in class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser
WuPalmerMetric - Class in org.apache.ctakes.ytex.kernel.metric
WuPalmerMetric(ConceptSimilarityService) - Constructor for class org.apache.ctakes.ytex.kernel.metric.WuPalmerMetric

X

XCAS - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances: The name of the XCAS XML scheme.
XcasAnnotation - Class in org.apache.ctakes.utils.xcas_comparison: An XcasAnnotation object represents an element under the CAS tag in an XCAS file.
XcasAnnotation() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Default constructor.
XcasAnnotation(String) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation: Constructs an object with the specified type.
XcasAnnotation.MyVector - Class in org.apache.ctakes.utils.xcas_comparison
XcasAnnotation.MyVector() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation.MyVector
XcasDiff - Class in org.apache.ctakes.utils.xcas_comparison: An XcasDiff object represents the comparison results of two XCAS files.
XcasDiff() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Default constructor.
XcasDiff(XcasFile, XcasFile) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasDiff: Construct an XCASDiff object from two XcasFile objects.
xcasf - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasProcessor
XcasFile - Class in org.apache.ctakes.utils.xcas_comparison: An XcasFile wraps all XcasAnnotationss in it and also contains their position information in terms of line and column numbers.
XcasFile() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasFile: Default constructor.
XcasFile(String) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasFile: Constructs an XcasFile with the specified name.
XcasFile(File) - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasFile: Constructs an XcasFile with the specified name.
XcasProcessor - Class in org.apache.ctakes.utils.xcas_comparison: A SAX parser that parses an XCAS file.
XcasProcessor() - Constructor for class org.apache.ctakes.utils.xcas_comparison.XcasProcessor: Default constructor.
xeroxTreebankMap - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
xeroxTreebankMap - Variable in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator
xLeftover - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
xMerge - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters
XMI - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances: The name of the XMI XML scheme.
XmiCollectionReaderCtakes - Class in org.apache.ctakes.assertion.cr: A simple collection reader that reads CASes in XMI format from a directory in the filesystem.
XmiCollectionReaderCtakes() - Constructor for class org.apache.ctakes.assertion.cr.XmiCollectionReaderCtakes
XmiCollectionReaderCtakes - Class in org.apache.ctakes.core.cr: A simple collection reader that reads CASes in XMI format from a directory in the filesystem.
XmiCollectionReaderCtakes() - Constructor for class org.apache.ctakes.core.cr.XmiCollectionReaderCtakes
xmiDirectory - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
xmiDirectory - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader
xmiDirectory - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIWriter
xmiExists - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
xmiOutputDirectory - Variable in class org.apache.ctakes.ytex.uima.annotators.DBConsumer
XMIReader - Class in org.apache.ctakes.assertion.eval: UIMA CollectionReader that reads in CASes from XMI files.
XMIReader() - Constructor for class org.apache.ctakes.assertion.eval.XMIReader
XMIReader - Class in org.apache.ctakes.core.cr: UIMA CollectionReader that reads in CASes from XMI files.
XMIReader() - Constructor for class org.apache.ctakes.core.cr.XMIReader
XMIReader - Class in org.apache.ctakes.dependency.parser.ae.util: UIMA CollectionReader that reads in CASes from XMI files.
XMIReader() - Constructor for class org.apache.ctakes.dependency.parser.ae.util.XMIReader
XMIReader - Class in org.apache.ctakes.relationextractor.eval: UIMA CollectionReader that reads in CASes from XMI files.
XMIReader() - Constructor for class org.apache.ctakes.relationextractor.eval.XMIReader
XmiWriterCasConsumerCtakes - Class in org.apache.ctakes.core.cc: A simple CAS consumer that writes the CAS to XMI format.
XmiWriterCasConsumerCtakes() - Constructor for class org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes
xmlDirectory - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
xmlFormat - Variable in class org.apache.ctakes.temporal.eval.Evaluation_ImplBase
XmlLoader - Class in org.apache.ctakes.jdl.data.loader: Loader of XML file.
XmlLoader(XmlLoadType, Document) - Constructor for class org.apache.ctakes.jdl.data.loader.XmlLoader
xmlOutputter - Variable in class org.apache.ctakes.core.knowtator.KnowtatorXMLParser
xmlRB - Variable in class org.apache.ctakes.ytex.tools.DBAnnotationViewerMain
xmlRB - Variable in class org.apache.ctakes.ytex.tools.docanalyzer.DBAnnotationViewerDialog
XMLReader - Class in org.apache.ctakes.assertion.cr
XMLReader() - Constructor for class org.apache.ctakes.assertion.cr.XMLReader
XMLReader - Class in org.apache.ctakes.relationextractor.knowtator
XMLReader() - Constructor for class org.apache.ctakes.relationextractor.knowtator.XMLReader
xmlSchemeName - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
XSD - Static variable in class org.apache.ctakes.jdl.AppJdl
xtMaps - Variable in class org.apache.ctakes.lvg.ae.LvgAnnotator
xVals - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: the possible values of X (e.g.
xVals - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.Parameters

Y

yates - Variable in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection.Chi2Scorer
yates - Variable in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
yates - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection.Chi2Scorer
yates - Variable in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection
YES - Static variable in interface org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser
YTEX_NEGATION_DESCRIPTOR - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
ytexApplicationContext - Static variable in class org.apache.ctakes.ytex.uima.ApplicationContextHolder
ytexProperties - Static variable in class org.apache.ctakes.ytex.dao.DBUtil
ytexProperties - Variable in class org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
ytexProperties - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl
ytexProperties - Static variable in class org.apache.ctakes.ytex.uima.ApplicationContextHolder
ytexProperties - Variable in class org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl
ytexProperties - Variable in class org.apache.ctakes.ytex.web.search.ConceptSearchServiceImpl
ytexProperties - Variable in class org.apache.ctakes.ytex.web.search.DocumentSearchServiceImpl
ytexProperties - Variable in class org.apache.ctakes.ytex.web.search.DocumentViewBean
yVals - Variable in class org.apache.ctakes.ytex.kernel.ImputedFeatureEvaluatorImpl.JointDistribution: the possible values of Y (e.g.

Z

Zone - Class in org.apache.ctakes.assertion.zoner.types: A document Zone, including its heading Updated by JCasGen Wed Sep 30 11:06:06 EDT 2015 XML source: /Users/pei/workspace/apache-ctakes/3.2.2/ctakes-assertion-zoner/target/jcasgen/typesystem.xml
Zone() - Constructor for class org.apache.ctakes.assertion.zoner.types.Zone: Never called.
Zone(int, TOP_Type) - Constructor for class org.apache.ctakes.assertion.zoner.types.Zone: Internal - constructor used by generator
Zone(JCas) - Constructor for class org.apache.ctakes.assertion.zoner.types.Zone
Zone(JCas, int, int) - Constructor for class org.apache.ctakes.assertion.zoner.types.Zone
Zone_Type - Class in org.apache.ctakes.assertion.zoner.types: A document Zone, including its heading Updated by JCasGen Wed Sep 30 11:06:06 EDT 2015
Zone_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.zoner.types.Zone_Type: initialize variables to correspond with Cas Type and Features

_

__allHits - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupDataStore
__batchCount - Variable in class org.apache.ctakes.core.cc.AbstractJdbcWriter.TableSqlInfo
__class - Variable in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
__cui - Variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
__cui - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
__end - Variable in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey
__end - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupHitKey
__hashCode - Variable in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey
__hashCode - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupHitKey
__hashcode - Variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
__hashcode - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
__index - Variable in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
__index - Variable in enum org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.FIELD_INDEX
__lookupSpec - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupDataStore
__name - Variable in enum org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2FieldInfo
__prefTerm - Variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
__preparedStatement - Variable in class org.apache.ctakes.core.cc.AbstractJdbcWriter.TableSqlInfo
__start - Variable in class org.apache.ctakes.dictionary.lookup.ae.BaseLookupConsumerImpl.LookupHitKey
__start - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator.LookupHitKey
__term - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm
__tui - Variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory.CuiTuiTerm
_antSiteTuiSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
_attributeMap - Variable in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter
_binaryLookupCacheMap - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_boundaryWordSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
_boundaryWordSet - Variable in class org.apache.ctakes.necontexts.NamedEntityContextAnalyzer
_boundaryWordSet - Variable in class org.apache.ctakes.smokingstatus.context.NamedEntityContextAnalyzer
_codes - Variable in class org.apache.ctakes.dictionary.lookup2.concept.Concept
_codingScheme - Variable in class org.apache.ctakes.dictionary.lookup2.consumer.AbstractTermConsumer
_collectionCreator - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
_collectionFilterList - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_conceptFactories - Variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
_conceptMap - Variable in class org.apache.ctakes.dictionary.lookup2.concept.MemConceptFactory
_consecutiveSkipMax - Variable in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
_count - Variable in class org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.DotPlotter
_count - Variable in class org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover.DotPlotter
_ctakesSemantics - Variable in class org.apache.ctakes.dictionary.lookup2.concept.Concept
_cui - Variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
_cui - Variable in class org.apache.ctakes.dictionary.lookup2.concept.Concept
_cuiCode - Variable in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
_delegate - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.ArrayListMap
_delegate - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.DefaultCollectionMap
_delegate - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.EnumSetMap
_delegate - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.HashSetMap
_delegateConceptFactory - Variable in class org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory
_delegateDictionary - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.BsvRareWordDictionary
_delegateDictionary - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
_delegateFactory - Variable in class org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory
_dictionaries - Variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
_dictionary - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_dictionarySpec - Variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
_disorderTuiSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
_duplicateDataMap - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
_end - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
_end - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
_entityIdCollection - Variable in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
_entityIdList - Variable in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
_entityIdMap - Variable in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
_exclusionPartsOfSpeech - Variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
_findingTuiSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
_hashcode - Variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup.BaseMetaDataHitImpl: Deprecated.
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup.vo.LookupHit
_hashcode - Variable in class org.apache.ctakes.dictionary.lookup2.concept.Concept
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
_hashCode - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
_idAnnotationMap - Variable in class org.apache.ctakes.temporal.utils.AnnotationIdCollection
_idHitConsumer - Variable in class org.apache.ctakes.dictionary.lookup2.consumer.PrecisionTermConsumer
_idHitConsumer - Variable in class org.apache.ctakes.dictionary.lookup2.consumer.SemanticCleanupTermConsumer
_index - Variable in enum org.apache.ctakes.temporal.utils.TlinkType
_indexSearcher - Variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
_initTerminalNodes(TreebankNode, List<TerminalTreebankNode>) - Static method in class org.apache.ctakes.temporal.ae.THYMETreebankReader
_jcasAnnotation - Variable in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter
_keepCase - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
_logger - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedUmlsDictionaryLookupAnnotator
_logger - Variable in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
_lookupAlgorithm - Variable in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
_lookupConsumer - Variable in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
_lookupInitializer - Variable in class org.apache.ctakes.dictionary.lookup.ae.LookupSpec
_lookupSpecSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
_lookupWindowType - Variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
_luceneDoc - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
_maxListSize - Variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
_maxListSize - Static variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
_medicationSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
_metaFieldNames - Variable in class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary
_metaLookupCacheMap - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_minimumLookupSpan - Variable in class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
_missingSpans - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
_name - Variable in class org.apache.ctakes.dictionary.lookup2.concept.AbstractConceptFactory
_name - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.AbstractRareWordDictionary
_nameSet - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
_nameValueMap - Variable in class org.apache.ctakes.dictionary.lookup.GenericMetaDataHitImpl
_negIndicatorFSM - Variable in class org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
_negIndicatorFSM - Variable in class org.apache.ctakes.smokingstatus.context.negation.NegationContextAnalyzer
_outputDirPath - Variable in class org.apache.ctakes.core.cc.SentenceTokensPrinter
_pairConceptFactoryNames - Variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
_pairDictionaryNames - Variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
_pairNames - Variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
_postLookupFilterList - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_preferredText - Variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate.I2b2Concept
_preferredText - Variable in class org.apache.ctakes.dictionary.lookup2.concept.Concept
_preLookupFilterList - Variable in class org.apache.ctakes.dictionary.lookup.DictionaryEngine
_preparedStatement - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl
_procedureTuiSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
_properties - Variable in class org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl
_properties - Variable in class org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl
_protectedMap - Variable in class org.apache.ctakes.dictionary.lookup2.util.collection.ImmutableCollectionMap
_rareWord - Variable in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
_rareWordIndex - Variable in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
_rareWordTerm - Variable in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
_rareWordTermMap - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.MemRareWordDictionary
_selectIcd10Call - Variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
_selectIcd9Call - Variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
_selectPrefTermCall - Variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
_selectRxNormCall - Variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
_selectSnomedCall - Variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
_selectTermCall - Variable in class org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
_selectTuiCall - Variable in class org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory
_start - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.DefaultTextSpan
_start - Variable in class org.apache.ctakes.dictionary.lookup2.textspan.MultiTextSpan
_statusIndicatorFSM - Variable in class org.apache.ctakes.necontexts.status.StatusContextAnalyzer
_strSet - Variable in class org.apache.ctakes.dictionary.lookup.filter.StringPreLookupFilterImpl
_strTableRow - Variable in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRowMetaDataHitImpl
_tableName - Variable in class org.apache.ctakes.core.cc.JdbcWriterTemplate
_tableSqlInfoMap - Variable in class org.apache.ctakes.core.cc.AbstractJdbcWriter
_termConsumer - Variable in class org.apache.ctakes.dictionary.lookup2.util.DefaultDictionarySpec
_text - Variable in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
_text - Variable in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
_textSpan - Variable in class org.apache.ctakes.dictionary.lookup2.term.SpannedRareWordTerm
_textSpan - Variable in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken
_tlinkTypes - Variable in class org.apache.ctakes.temporal.utils.TlinkTypeSet
_tlinkTypesArray - Variable in class org.apache.ctakes.temporal.utils.TLinkTypeArray2
_tokenCount - Variable in class org.apache.ctakes.dictionary.lookup2.term.RareWordTerm
_totalSkipMax - Variable in class org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
_validTuiSet - Variable in class org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedConsumerImpl
_validUsers - Static variable in enum org.apache.ctakes.dictionary.lookup2.util.UmlsUserApprover
_valueList - Variable in class org.apache.ctakes.dictionary.lookup.lucene.LuceneDocumentMetaDataHitImpl
_variant - Variable in class org.apache.ctakes.dictionary.lookup2.util.FastLookupToken

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