org.apache.ctakes.dictionary.lookup2.ae

Class DefaultJCasTermAnnotator

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.DefaultJCasTermAnnotator

All Implemented Interfaces:

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

@PipeBitInfo(name="Dictionary Lookup (Default)",
             description="Annotates clinically-relevant terms.  Terms must match dictionary entries exactly.",
             dependencies={SENTENCE,BASE_TOKEN},
             products=IDENTIFIED_ANNOTATION)
public final class DefaultJCasTermAnnotator
extends AbstractJCasTermAnnotator

A direct string match using phrase permutations Author: SPF Affiliation: CHIP-NLP Date: 11/19/13

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
DefaultJCasTermAnnotator()

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)
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
static boolean	isTermMatch(RareWordTerm rareWordHit, List<FastLookupToken> allTokens, int termStartIndex, int termEndIndex) Hopefully the jit will inline this method

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

getAnnotationsInWindow, getDictionaries, initialize, 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

DefaultJCasTermAnnotator

public DefaultJCasTermAnnotator()

Method Detail

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 - -

isTermMatch

public static boolean isTermMatch(RareWordTerm rareWordHit,
                                  List<FastLookupToken> allTokens,
                                  int termStartIndex,
                                  int termEndIndex)

Hopefully the jit will inline this method

Parameters:

rareWordHit - rare word term to check for match

allTokens - all tokens in a window

termStartIndex - index of first token in allTokens to check

termEndIndex - index of last token in allTokens to check

Returns:

true if the rare word term exists in allTokens within the given indices

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