Path Lines of Code ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml 56 ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml 39 ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml 39 ctakes-assertion/desc/analysis_engine/AttributeDiscoveryPreprocessor.xml 162 ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml 130 ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml 130 ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml 136 ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml 136 ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml 136 ctakes-assertion/desc/assertionAnalysisEngine.xml 128 ctakes-assertion/desc/conceptConverterAnalysisEngine.xml 113 ctakes-assertion/metadata/install.xml 27 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java 31 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java 25 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/GenericFeaturesExtractor.java 32 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/HistoryFeaturesExtractor.java 32 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/SubjectFeaturesExtractor.java 34 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/Chi2FeatureSelection.java 140 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/FeatureSelection.java 50 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/MutualInformationFeatureSelection.java 192 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java 118 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java 225 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/subject/SubjectAttributeClassifier.java 188 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java 349 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/ArgumentInfo.java 9 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java 190 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java 152 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java 1156 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExAnnotation.java 88 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java 146 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/RelationInfo.java 52 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/Span.java 21 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XMLReader.java 138 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XmiCollectionReaderCtakes.java 68 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java 317 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java 1352 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java 202 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/XMIReader.java 57 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java 281 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java 174 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java 93 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java 69 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java 146 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java 70 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java 152 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java 122 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java 354 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionComponents.java 9 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionFeatureAwareDataWriter.java 81 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionSampleFeatureGenerator.java 27 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java 72 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/CreateAssertionDescriptor.java 157 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java 79 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java 80 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java 110 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityFedaCleartkAnalysisEngine.java 91 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java 77 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java 239 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java 90 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveLeftFragmentExtractor.java 27 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AboveRightFragmentExtractor.java 27 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionAboveLeftTreeExtractor.java 32 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/AssertionDependencyTreeExtractor.java 53 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/BrownClusterFeatureFunction.java 42 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ContextWordWindowExtractor.java 102 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java 101 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java 126 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyPathRegexpFeatureExtractor.java 49 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/DependencyWordsFragmentExtractor.java 41 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/ExtractorListFeatureFunctionConverter.java 20 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/FedaFeatureFunction.java 30 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/NegationDependencyFeatureExtractor.java 44 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SRLFeatureExtractor.java 83 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java 18 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java 48 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/UncertaintyFeatureExtractor.java 19 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/ConditionalCleartkAnalysisEngineWindowed.java 71 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/GenericCleartkAnalysisEngineWindowed.java 78 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/HistoryCleartkAnalysisEngineWindowed.java 79 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/PolarityCleartkAnalysisEngineWindowed.java 116 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/SubjectCleartkAnalysisEngineWindowed.java 77 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/UncertaintyCleartkAnalysisEngineWindowed.java 94 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java 378 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/classifier/WindowedGenericAttributeClassifier.java 116 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/classifier/WindowedHistoryAttributeClassifier.java 218 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractLeftToRightContext.java 49 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractRightToLeftContext.java 49 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractWindowedContext.java 44 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/FollowingContext.java 31 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/LastCoveredContext.java 19 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/PrecedingContext.java 32 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/WindowedBag.java 49 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/WindowedContextFeature.java 22 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/AbstractTreeFragmentFeatureExtractor1.java 48 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/AbstractWindowedFeatureExtractor1.java 20 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/WindowedAssertionDependencyTreeExtractor.java 48 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/WindowedContextWordWindowExtractor.java 94 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/WindowedDependencyWordsFragmentExtractor.java 40 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/WindowedGenericFeaturesExtractor.java 31 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/WindowedHistoryFeatureExtractor.java 32 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/feature/extractor/WindowedNegationDependencyFeatureExtractor.java 37 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/CharacterOffsetToLineTokenConverterCtakesImpl.java 192 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructor.java 50 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedBy.java 36 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/ConstraintConstructorFindContainedWithin.java 36 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api/SingleDocumentProcessorCtakes.java 103 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java 106 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java 116 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java 25 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java 303 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/PreprocessingPipeline.java 13 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java 70 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/SharpCorpusSplit.java 42 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java 9 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java 22 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java 14 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java 12 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionFileProcessor.java 12 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.java 12 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java 3 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java 8 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptAnnotation.java 3 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java 6 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/JarafeMEDecoder.java 10 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java 17 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java 16 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java 5 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java 5 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java 46 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java 11 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java 24 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java 30 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/JustJudgeStep.java 17 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java 89 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java 57 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityDomainAdaptationTests.java 94 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityDomainAdaptationTrain.java 62 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/ReadAndPreprocessForAttributeModels.java 41 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/ReadPreprocessTrainTestJudge.java 20 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TestAttributeModels.java 32 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TrainAttributeModels.java 24 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java 64 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java 119 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionTreeUtils.java 155 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationDepRegex.java 321 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationManualDepContextAnalyzer.java 47 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/SemanticClasses.java 22 ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/WriteMultipleDatasets.java 194 ctakes-assertion/src/main/python/negation_rest.py 113 ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml 53