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

A

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
 
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>, Function<ANNOTATION_TYPE, SPAN_TYPE>, Function<ANNOTATION_TYPE, OUTCOME_TYPE>) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
Update the statistics, comparing the reference annotations to the predicted annotations.
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.
adjustOffsetToBestMatch(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
allAnnotationTypes - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
AlternateCuePhraseAnnotator - Class in org.apache.ctakes.assertion.medfacts.cleartk
 
AlternateCuePhraseAnnotator() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
 
AnnotationStatisticsCompact<OUTCOME_TYPE extends 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.
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.
annotationTypes - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
annotationTypes - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
apply(Feature) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
 
apply(Feature) - Method in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
 
ArgumentInfo - Class in org.apache.ctakes.assertion.cr
Information about a relation argument.
Assertion - Class in org.apache.ctakes.assertion.medfacts.types
Updated by JCasGen Thu Nov 28 10:38:43 CST 2013 XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/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 Thu Nov 28 10:38:43 CST 2013
Assertion_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
initialize variables to correspond with Cas Type and Features
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
 
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
 
AssertionEvaluation - Class in org.apache.ctakes.assertion.eval
 
AssertionEvaluation(File, File, ArrayList<String>, Class<? extends AssertionCleartkAnalysisEngine>, Class<? extends DataWriter<String>>, String...) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
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
 
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
 

B

BASE_DIRECTORY - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
CHANGE THESE
begin - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
 
beginTreeMap - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
buildSentenceBoundaryMap() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
buildTokenBoundaryMap() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 

C

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
 
CasIndexer<T extends org.apache.uima.jcas.tcas.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
 
category - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
 
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
 
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
classConditionalCounts - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
 
classCounts - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
 
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
 
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
 
coin - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
compare(Sentence, Sentence) - Method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier.SentComparator
 
compareTo(AssertionEvaluation.HashableAnnotation) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
 
Concept - Class in org.apache.ctakes.assertion.medfacts.types
Updated by JCasGen Thu Nov 28 10:38:43 CST 2013 XML source: C:/build-Apache-cTAKES/ctakes-3.1.1/rc2/checkout/ctakes/target/checkout/ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/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_Type - Class in org.apache.ctakes.assertion.medfacts.types
Updated by JCasGen Thu Nov 28 10:38:43 CST 2013
Concept_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Concept_Type
initialize variables to correspond with Cas Type and Features
ConceptConverterAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts
 
ConceptConverterAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
 
ConceptLookup - Class in org.apache.ctakes.assertion.medfacts
 
ConceptLookup() - Constructor for class org.apache.ctakes.assertion.medfacts.ConceptLookup
 
ConditionalCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk
 
ConditionalCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
 
confusions() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
Returns the ConfusionMatrix tabulating reference outcomes matched to predicted outcomes.
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
 
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
 
contextFeatureExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
ContextWordWindowExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
 
ContextWordWindowExtractor(String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
 
convert(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
convert2DTokenArrayToText(ArrayList<ArrayList<String>>) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
 
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
 
Converti2b2AnnotationsToCTAKES - Class in org.apache.ctakes.assertion.medfacts
 
Converti2b2AnnotationsToCTAKES() - Constructor for class org.apache.ctakes.assertion.medfacts.Converti2b2AnnotationsToCTAKES
 
convertToDebugOutput(String, T) - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
 
ConvertXMIAssertionsToi2b2Format - Class in org.apache.ctakes.assertion.medfacts
 
ConvertXMIAssertionsToi2b2Format() - Constructor for class org.apache.ctakes.assertion.medfacts.ConvertXMIAssertionsToi2b2Format
 
CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
countCorrectOutcomes() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
countCorrectOutcomes(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
countFalseNegatives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
countFalsePositives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
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
 
countTrueNegatives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
countTruePositives(OUTCOME_TYPE...) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
CreateAssertionDescriptor - Class in org.apache.ctakes.assertion.medfacts.cleartk
 
CreateAssertionDescriptor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
 
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.SubjectCleartkAnalysisEngine
 
createFeatureSelection(double) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
 
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.SubjectCleartkAnalysisEngine
 
createFeatureSelectionURI(File) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
 
createFilteredIterator(int, int, Type) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.ConstraintConstructor
 
createTestDescriptor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
 
createTrainDescriptor() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
 
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
 
crossValidationFolds - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents
 
CtakesFileNamer - Class in org.apache.ctakes.assertion.pipelines
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.assertion.pipelines.CtakesFileNamer
 
cuePhraseInWindowExtractor - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
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
 

D

DATA_DIR - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
dataWriterFactoryClass - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.CreateAssertionDescriptor
 
debugAnnotationsInCas(JCas, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
 
devDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
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
 

E

elevateListConcepts(JCas, TreebankNode) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
 
end - Variable in class org.apache.ctakes.assertion.cr.Span
 
end - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
 
entityFeatureExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
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.AssertionEvaluation.HashableAnnotation
 
evalOnly - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
evalOutputDir - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
evaluationLogFilePath - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
evaluationOutputDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
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
 
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.attributes.features.GenericFeaturesExtractor
 
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.attributes.features.HistoryFeaturesExtractor
 
extract(JCas, Annotation) - 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, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveLeftFragmentExtractor
 
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveRightFragmentExtractor
 
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor
 
extract(JCas, Annotation) - 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, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 
extract(JCas, Annotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.UncertaintyFeatureExtractor
 
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
 
extractZoneFeatures(Map<IdentifiedAnnotation, Collection<Zone>>, IdentifiedAnnotation) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 

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
 
f1() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
f1(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
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_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
 
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
 
FEATURE_SELECTION_NAME - Static 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
 
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
 
featureSelectionThreshold - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
featureSelectionThreshold - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
featureSelectionURI - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
fileNamerClassName - Variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
 
findNegationContext(List<ConllDependencyNode>, ConllDependencyNode) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
Executes the regular expressions on paths.
findPreviousOrCurrentSentence(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
frags - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 

G

generateAnnotationMap(JCas) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
 
generateAnnotationMap(JCas, Integer) - Method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
 
GenerateTreeRepresentation - Class in org.apache.ctakes.assertion.pipelines
 
GenerateTreeRepresentation() - Constructor for class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
 
GenerateTreeRepresentation.Options - Class in org.apache.ctakes.assertion.pipelines
 
GenerateTreeRepresentation.Options() - Constructor for class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
 
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
 
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
 
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
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
 
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.
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
 
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
 
getDataWriterClass() - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
getDescription(Object...) - Static method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
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
getEntityTypes(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader
Type of each named entity indexed on mention ids
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
 
getFeatureName(Feature) - Method in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
 
getFSGenerator() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion_Type
 
getFSGenerator() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept_Type
 
getGeneric(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.attributes.generic.GenericAttributeClassifier
 
getHIstory(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
 
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
 
getKnowtatorURI(JCas) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
Get the URI for the Knowtator XML file that should be loaded
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
 
getNumFeatures() - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
 
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
 
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
 
getRegexName(int) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
 
getRelations(Document) - Static method in class org.apache.ctakes.assertion.cr.XMLReader
 
getScoreFunction(MutualInformationFeatureSelection.CombineScoreMethod) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
 
getSubject(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
 
getTextURI(JCas) - Method in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
Get the URI that the text in this class was loaded from
getTypeIndexID() - Method in class org.apache.ctakes.assertion.medfacts.types.Assertion
 
getTypeIndexID() - Method in class org.apache.ctakes.assertion.medfacts.types.Concept
 
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
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
 
goldViewName - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 

H

hashCode() - Method in class org.apache.ctakes.assertion.cr.RelationInfo
 
hashCode() - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
 
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
 
HistoryAttributeClassifier - Class in org.apache.ctakes.assertion.attributes.history
 
HistoryAttributeClassifier() - Constructor for class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier
 
HistoryAttributeClassifier.SentComparator - Class in org.apache.ctakes.assertion.attributes.history
 
HistoryAttributeClassifier.SentComparator() - Constructor for class org.apache.ctakes.assertion.attributes.history.HistoryAttributeClassifier.SentComparator
 
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
 

I

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_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_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
I2B2Challenge2010CollectionReader - Class in org.apache.ctakes.assertion.cr
 
I2B2Challenge2010CollectionReader() - Constructor for class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
 
id1 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
 
id2 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
 
identifiedAnnotationId - Variable in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
 
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
 
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
 
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.SubjectCleartkAnalysisEngine
 
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
 
initialize(UimaContext) - Method in class org.apache.ctakes.assertion.pipelines.CtakesFileNamer
 
initialize() - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
 
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.SubjectCleartkAnalysisEngine
 
initializeFeatureSelection() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
 
inputDir - Variable in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances.Options
 
inputDirectory - Static variable in class org.apache.ctakes.assertion.cr.GoldEntityAndAttributeReader
 
instanceGatheringOutputDir - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
isBoundary(Annotation, int) - Method in class org.apache.ctakes.assertion.util.NegationDepRegex
 
isBoundary(Annotation, int) - Method in class org.apache.ctakes.assertion.util.NegationManualDepContextAnalyzer
 
isDonorTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
 
isFamilyTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
 
isOtherTerm(Annotation) - Static method in class org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier
 
isTrained - Variable in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
 
iv_copulaSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_modalVerbsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negAdjectivesSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negCollocSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negColPartSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negDeterminersSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negDetPlusPrepSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negParticlesSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negPrepositionsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_negVerbsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_regNounsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_regPrepositionsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
iv_regVerbsSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 

J

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
 
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
 
JustJudgeStep - Class in org.apache.ctakes.assertion.train
 
JustJudgeStep() - Constructor for class org.apache.ctakes.assertion.train.JustJudgeStep
 

L

lastLabel - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
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
 
logger - Variable in class org.apache.ctakes.assertion.attributes.GenericAttributeAnalysisEngine
 
logger - Variable in class org.apache.ctakes.assertion.attributes.SubjectAttributeAnalysisEngine
 
logger - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SurroundingExtractor
 
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 - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
lookupByAddress(int) - Method in class org.apache.ctakes.assertion.medfacts.CasIndexer
 
lookupConceptType(FSArray) - Static method in class org.apache.ctakes.assertion.medfacts.ConceptLookup
 

M

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[]) - Static method in class org.apache.ctakes.assertion.eval.TestFeatureSelection
 
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.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.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
 
mapByAddress - Variable in class org.apache.ctakes.assertion.medfacts.CasIndexer
 
mapI2B2AssertionValueToCtakes(String, IdentifiedAnnotation) - Static method in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine
 
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
 
MiPACQ_CORPUS - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
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_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
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
 
modelDirectory - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
modelOutputDirectory - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
 
modelsDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
mutualInformation(String, OUTCOME_T) - Method in class org.apache.ctakes.assertion.attributes.features.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.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.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
 

N

nameFile(JCas) - Method in class org.apache.ctakes.assertion.pipelines.CtakesFileNamer
 
NEGATED - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
 
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
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
 
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_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
NEGEX_TEST - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTests
 
NEGEX_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
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
 
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
 
noCleartk - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
NOT_NEGATED - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
 

O

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.GenerateTreeRepresentation
 
options - Static variable in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances
 
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
 
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
 
outFile - Variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
 
outputDir - Variable in class org.apache.ctakes.assertion.pipelines.RunJudgeAttributeInstances.Options
 

P

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_FEATURE_SELECTION_THRESHOLD - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
PARAM_FEATURE_SELECTION_URI - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
PARAM_FILE_NAMER_CLASS_NAME - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
The parameter name for the configuration parameter that specifies the name of the class that implements the file namer
PARAM_FILES - Static variable in class org.apache.ctakes.assertion.eval.XMIReader
 
PARAM_FNMATCH - Static variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader
 
PARAM_GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
PARAM_INPUT_DIR - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AlternateCuePhraseAnnotator
 
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_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_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_OUTPUTDIR - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 
PARAM_PREFIX - Static variable in class org.apache.ctakes.assertion.pipelines.CtakesFileNamer
The parameter name for the configuration parameter that specifies a fixed prefix for all returned file names.
PARAM_PRINT_ERRORS - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
PARAM_PROBABILITY_OF_KEEPING_DEFAULT_EXAMPLE - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
PARAM_SEMDIR - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 
PARAM_SET_DEFAULTS - Static variable in class org.apache.ctakes.assertion.cr.MiPACQKnowtatorXMLReader
 
PARAM_SUFFIX - Static variable in class org.apache.ctakes.assertion.pipelines.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_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.
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
 
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
 
postprocess() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
 
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
 
preExecutionTest() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
 
prefix - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 
preprocess(File) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
preprocess() - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
 
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
 
preprocessRootDirectory - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
DON'T CHANGE THESE
printErrors - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
printScore(Map<String, AnnotationStatisticsCompact>, String) - Static method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
probabilityOfKeepingADefaultExample - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
problemSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
 
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
 
processDocument(JCas) - Static method in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation
 
processForEntityType(JCas, int, Class<? extends IdentifiedAnnotation>) - Method in class org.apache.ctakes.assertion.medfacts.ConceptConverterAnalysisEngine
 
prompt(String) - Static method in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
 

R

randomizeWords(SimpleTree, boolean) - Method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
 
ReadAndPreprocessForAttributeModels - Class in org.apache.ctakes.assertion.train
 
ReadAndPreprocessForAttributeModels() - Constructor for class org.apache.ctakes.assertion.train.ReadAndPreprocessForAttributeModels
 
readI2B2Challenge2010(File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
 
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
 
ReadPreprocessTrainTestJudge - Class in org.apache.ctakes.assertion.train
 
ReadPreprocessTrainTestJudge() - Constructor for class org.apache.ctakes.assertion.train.ReadPreprocessTrainTestJudge
 
readSharpUmlsCem(File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
 
readSharpUmlsCem(File, File, File, File) - Static method in class org.apache.ctakes.assertion.pipelines.GoldEntityAndAttributeReaderPipelineForSeedCorpus
 
recall() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
recall(OUTCOME_TYPE) - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
regexSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
rel_conjunctSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 
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.
replaceWordsWithSemanticClasses(SimpleTree, SemanticClasses) - Static method in class org.apache.ctakes.assertion.util.AssertionTreeUtils
 
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
 
role - Variable in class org.apache.ctakes.assertion.cr.ArgumentInfo
 
role1 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
 
role2 - Variable in class org.apache.ctakes.assertion.cr.RelationInfo
 
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
 

S

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
 
selectedFeatureNames - Variable in class org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection
 
SemanticClasses - Class in org.apache.ctakes.assertion.util
 
SemanticClasses(String) - Constructor for class org.apache.ctakes.assertion.util.SemanticClasses
 
sems - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 
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
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.ConditionalCleartkAnalysisEngine
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.GenericCleartkAnalysisEngine
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine
 
setClassLabel(IdentifiedAnnotation, Instance<String>) - Method in class org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine
 
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
 
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
 
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
 
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
 
SHARP_I2B2_MIPACQ_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
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_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
SHARP_MIPACQ_MODEL - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
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_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_TRAIN - Static variable in class org.apache.ctakes.assertion.train.PolarityCotrainingTrain
 
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
 
SingleDocumentProcessorCtakes - Class in org.apache.ctakes.assertion.medfacts.i2b2.api
 
SingleDocumentProcessorCtakes() - Constructor for class org.apache.ctakes.assertion.medfacts.i2b2.api.SingleDocumentProcessorCtakes
 
smoothingCount - Variable in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
 
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
 
split(File) - Static method in class org.apache.ctakes.assertion.pipelines.SharpCorpusSplit
 
SRLFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
 
SRLFeatureExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SRLFeatureExtractor
 
start - Variable in class org.apache.ctakes.assertion.cr.Span
 
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
 
SurroundingExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
 
SurroundingExtractor() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.SurroundingExtractor
 

T

targetType - Variable in class org.apache.ctakes.assertion.medfacts.CasIndexer
 
test(CollectionReader, File) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
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
 
testDirectories - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
testDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
TestFeatureSelection - Class in org.apache.ctakes.assertion.eval
 
TestFeatureSelection() - Constructor for class org.apache.ctakes.assertion.eval.TestFeatureSelection
 
testMaxent() - Method in class org.apache.ctakes.assertion.medfacts.cleartk.TrainAssertionModel
 
testOnly - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
testSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
 
tokenBeginEndTreeSet - Variable in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl
 
tokenCleartkExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
tokenContextFeatureExtractors - Variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine
 
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
 
toString() - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation
 
toTsv() - Method in class org.apache.ctakes.assertion.eval.AnnotationStatisticsCompact
 
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection
 
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection
 
train(CollectionReader, File) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
trainAndPackage(String, File, String[]) - Method in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
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
 
trainDirectory - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
trainDirectory - Variable in class org.apache.ctakes.assertion.pipelines.GenerateTreeRepresentation.Options
 
trainingDirectories - Static variable in class org.apache.ctakes.assertion.util.AssertionConst
 
trainOnly - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 
transform(Instance<OUTCOME_T>) - 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
 
treatmentSet - Static variable in class org.apache.ctakes.assertion.medfacts.ConceptLookup
 
TreeFragmentFeatureExtractor - Class in org.apache.ctakes.assertion.medfacts.cleartk.extractors
 
TreeFragmentFeatureExtractor(String, String) - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.extractors.TreeFragmentFeatureExtractor
 
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_SYSTEM_DESCRIPTION - Static variable in class org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents
 
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
 

U

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
 
update(String, OUTCOME_T, int) - Method in class org.apache.ctakes.assertion.attributes.features.selection.MutualInformationFeatureSelection.MutualInformationStats
 
useEvaluationLogFile - Static variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation
 
useYtexNegation - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options
 

V

value - Variable in class org.apache.ctakes.assertion.cr.ArgumentInfo
 
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.pipelines.SharpCorpusSplit.Subcorpus
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.pipelines.SharpCorpusSplit.Subcorpus
Returns an array containing the constants of this enum type, in the order they are declared.

X

XCAS - Static variable in class org.apache.ctakes.assertion.cc.JudgeAttributeInstances
The name of the XCAS XML scheme.
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
 
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
 
XMLReader - Class in org.apache.ctakes.assertion.cr
 
XMLReader() - Constructor for class org.apache.ctakes.assertion.cr.XMLReader
 

_

_boundaryWordSet - Variable in class org.apache.ctakes.assertion.util.NegationDepRegex
 

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

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