org.apache.ctakes.dictionary.lookup2.ae

Class OverlapJCasTermAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator

org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator

All Implemented Interfaces:

JCasTermAnnotator, WindowProcessor, org.apache.uima.analysis_component.AnalysisComponent

@PipeBitInfo(name="Dictionary Lookup (Overlap)",
             description="Annotates clinically-relevant terms.  Terms can overlap dictionary entries.",
             dependencies={SENTENCE,BASE_TOKEN},
             products=IDENTIFIED_ANNOTATION)
public final class OverlapJCasTermAnnotator
extends AbstractJCasTermAnnotator

Checks for terms that overlap a window. All tokens of the term must exist in the window in order, but not necessarily contiguously Author: SPF Affiliation: CHIP-NLP Date: 12/6/13

Field Summary

Fields inherited from class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator

_minimumLookupSpan

Fields inherited from interface org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator

DEFAULT_DICT_DESC_PATH, DEFAULT_EXCLUSION_TAGS, DEFAULT_LOOKUP_WINDOW, DEFAULT_MINIMUM_SPAN, DICTIONARY_DESCRIPTOR_KEY, PARAM_EXC_TAGS_KEY, PARAM_MIN_SPAN_KEY, PARAM_WINDOW_ANNOT_KEY

Constructor Summary

Constructors

Constructor and Description
OverlapJCasTermAnnotator()

Method Summary

Modifier and Type	Method and Description
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription()
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription(String descriptorPath)
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription(String descriptorPath, int consecutiveSkipMax, int totalSkipMax)
void	findTerms(RareWordDictionary dictionary, List<FastLookupToken> allTokens, List<Integer> lookupTokenIndices, CollectionMap<TextSpan,Long,? extends Collection<Long>> termsFromDictionary) Given a dictionary, tokens, and lookup token indices, populate a terms collection with discovered terms
void	initialize(org.apache.uima.UimaContext uimaContext) Set the number of consecutive and total tokens that can be skipped (optional).

Methods inherited from class org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator

getAnnotationsInWindow, getDictionaries, isWindowOk, parseInt, process, processWindow

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.apache.uima.analysis_component.AnalysisComponent

batchProcessComplete, collectionProcessComplete, destroy, getCasInstancesRequired, getRequiredCasInterface, hasNext, next, process, reconfigure, setResultSpecification

Constructor Detail

OverlapJCasTermAnnotator

public OverlapJCasTermAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext uimaContext)
                throws org.apache.uima.resource.ResourceInitializationException

Set the number of consecutive and total tokens that can be skipped (optional). Defaults are 2 and 4.

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class AbstractJCasTermAnnotator

Throws:

org.apache.uima.resource.ResourceInitializationException

findTerms

public void findTerms(RareWordDictionary dictionary,
                      List<FastLookupToken> allTokens,
                      List<Integer> lookupTokenIndices,
                      CollectionMap<TextSpan,Long,? extends Collection<Long>> termsFromDictionary)

Given a dictionary, tokens, and lookup token indices, populate a terms collection with discovered terms

Parameters:

dictionary - -

allTokens - -

lookupTokenIndices - -

termsFromDictionary - -

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription()
                                                                                            throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription(String descriptorPath)
                                                                                            throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription(String descriptorPath,
                                                                                                   int consecutiveSkipMax,
                                                                                                   int totalSkipMax)
                                                                                            throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException