path	# lines of code
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java	33
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventAndTimeExtractionPipeline.java	46
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventExtractionPipeline.java	39
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java	101
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java	41
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/EventPrintingPipeline.java	57
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintFailedTimeNormalizations.java	80
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/TimexTreeAlignmentStatistics.java	85
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintInconsistentAnnotations.java	145
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java	156
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java	104
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNonrelatedEvents.java	78
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/PrintNormalizedTemporalExpressions.java	36
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/CompareFeatureStructures.java	269
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java	147
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextViewerPipeline.java	147
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDoctimerelPairProbabilities.java	72
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TlinkTypeSet.java	62
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java	74
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/PatientViewsUtil.java	53
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java	94
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TLinkTypeArray2.java	275
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TimeRelationConstants.java	11
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CalendarUtil.java	187
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TlinkType.java	170
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java	86
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SoftMaxUtil.java	35
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TokenPreprocForWord2Vec.java	32
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/AnnotationIdCollection.java	76
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/ScriptStringOutcomeClassifier.java	86
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/ScriptStringOutcomeClassifierBuilder.java	80
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/KerasStringFeatureDataWriter.java	15
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/KerasStringOutcomeClassifier.java	15
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/ScriptStringOutcomeDataWriter.java	47
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/KerasStringOutcomeDataWriter.java	20
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/KerasStringOutcomeClassifierBuilder.java	57
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/ScriptStringFeatureDataWriter.java	54
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/SimpleMedDatesFinder.java	323
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java	209
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java	204
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java	329
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalSequenceAnnotator_ImplBase.java	19
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEKnowtatorXMLReader.java	93
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DeepPheAnaforaXMLReader.java	207
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationGoldContainerAnnotator.java	211
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventEventRelationAnnotator.java	204
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotator.java	103
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeApproximator.java	77
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexDischargeTimeAnnotator.java	192
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java	173
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEQAAnaforaXMLReader.java	300
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/I2B2TemporalXMLReader.java	141
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelWithTreeAnnotator.java	1
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java	172
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationSeedBasedAnnotator.java	206
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotator.java	174
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java	233
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NeuralEventTimeSelfRelationAnnotator.java	173
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java	227
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java	386
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java	343
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/RelationSyntacticEmbeddingFeatureExtractor.java	179
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyParseUtils.java	103
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeForMixEventTimeExtractor.java	45
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DateAndMeasurementExtractor.java	81
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventTimeBetweenCandidatesExtractor.java	51
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/IdentifiedAnnotationFeatureExtractor.java	92
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionFeatureExtractor.java	93
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SpecialAnnotationRelationExtractor.java	110
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPositionRelationFeaturesExtractor.java	94
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyPathFeaturesExtractor.java	27
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeWordTypeExtractor.java	50
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventArgumentPropertyExtractor.java	70
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderRelationExtractor.java	73
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/EventTimeFlatTreeFeatureExtractor.java	78
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPathExtractor.java	64
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalPETExtractor.java	111
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/TemporalFTExtractor.java	65
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/DependencySingleTreeExtractor.java	46
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/treekernel/SyntaticSingleTreeExtractor.java	40
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoveredTextToValuesExtractor.java	88
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NumberOfEventsInTheSameSentenceExtractor.java	76
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseFeatureExtractor.java	35
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalAttributeFeatureExtractor.java	35
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/RelationSyntacticETEmbeddingFeatureExtractor.java	135
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java	55
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ChunkingExtractor.java	31
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationExpectationFeatureExtractor.java	56
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventTimeFeatureExtractor.java	45
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationTimeUnitFeatureExtractor.java	38
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationEventEventFeatureExtractor.java	46
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/duration/DurationDistributionFeatureExtractor.java	38
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EmptyFeaturesExtractor.java	13
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java	73
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/RelationEmbeddingFeatureExtractor.java	119
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CheckSpecialWordRelationExtractor.java	91
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXPropertyRelationFeaturesExtractor.java	46
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java	134
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TemporalPETFlatExtractor.java	141
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UMLSBasedTokenFeaturesExtractor.java	76
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java	119
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TokenPropertyFeaturesExtractor.java	97
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DocTimeRelFeatureExtractor.java	27
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NoOtherETPuntInBetweenFeaturesExtractor.java	36
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/OverlappedHeadFeaturesExtractor.java	67
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXRelationFeaturesExtractor.java	66
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DeterminerRelationFeaturesExtractor.java	31
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependingVerbsFeatureExtractor.java	83
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/FramesetCategoryExtractor.java	45
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsSingleFeatureExtractor.java	40
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ParseSpanFeatureExtractor.java	53
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventPropertyExtractor.java	221
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SyntacticParentFeatureExtractor.java	21
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ListFeaturesExtractor.java	90
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationFeatureExtractor.java	87
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/MutualInformationFeatureSelection.java	192
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java	160
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/ZscoreNormalizationExtractor.java	141
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/FeatureSelection.java	50
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/OddsRatioFeatureSelection.java	121
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/BinaryAlphaFeatureSelection.java	150
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/CoordinateFeaturesExtractor.java	53
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearestFlagFeatureExtractor.java	73
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UmlsFeatureExtractor.java	57
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UnexpandedTokenFeaturesExtractor.java	49
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ContinuousTextExtractor.java	51
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/PredicateArgumentExtractor.java	47
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/DependencyFeatureExtractor.java	55
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java	62
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/EventTimeRelationsFeaturesExtractor.java	37
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ConjunctionRelationFeaturesExtractor.java	49
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SRLRelationFeaturesExtractor.java	62
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseRelationExtractor.java	59
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java	35
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java	25
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ThymePatientViewAnnotator.java	63
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java	66
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java	181
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java	239
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationRuleAnnotator.java	156
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventCRFRelationAnnotator.java	226
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalEntityAnnotator_ImplBase.java	28
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/WithinSentenceBeforeRelationAnnotator.java	131
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java	177
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java	222
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexAdmissionTimeAnnotator.java	193
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java	67
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CrossSentenceTemporalRelationAnnotator.java	95
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventEventRelationAnnotator.java	58
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TimidBaselineEventTimeRelationAnnotator.java	70
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java	84
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/PrecisionBaselineEventTimeRelationAnnotator.java	82
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/TreeHeightBaseline.java	80
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/RecallBaselineEventTimeRelationAnnotator.java	73
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventCNNAnnotator.java	265
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java	250
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocumentCreationTimeAnnotator.java	26
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/MetaTimeAnnotator.java	186
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeCNNAnnotator.java	267
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java	211
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java	51
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CRFTimeAnnotator.java	148
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/Utils.java	319
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventEventRelationsInGold.java	70
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/ExtractDurationsUsingContainsRelation.java	137
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventEventRelationsInGold.java	59
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveUMLSEventTimeRelationsInGold.java	76
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventsInGold.java	39
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/PreserveCertainEventTimeRelationsInGold.java	73
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventEventDurationStatistics.java	108
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventTimeDurationStatistics.java	117
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java	204
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/concurrent/ThreadSafeEventEventRelAnnotator.java	87
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/concurrent/ThreadSafeBackTimeAnnotator.java	93
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/concurrent/ThreadSafeEventTimeRelAnnotator.java	87
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/concurrent/ThreadSafeDocTimeRelAnnotator.java	82
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/concurrent/ThreadSafeEventAnnotator.java	90
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java	1083
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java	239
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/CommandLine.java	27
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKTimeSpans.java	79
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java	300
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java	792
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventSpans.java	80
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java	929
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventHybridModelsRelations.java	629
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventDeepPheRelations.java	726
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java	566
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsEvaluation.java	871
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java	198
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventPropertiesTk.java	1
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/RemoveTreeAlignedMentions.java	48
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java	70
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfBothEEAndETRelations.java	700
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/THYMEData.java	53
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTemporalRelations_ImplBase.java	222
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java	187
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java	166
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java	130
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventDocTimeRelDeepPhe.java	411
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/I2B2Data.java	61
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java	146
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventCRFRelations.java	659
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventEventRelationsCNNEvaluation.java	621
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java	652
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java	203
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeDeepPheRelations.java	730
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/NeuralEventTimeRelationsCNNEvaluation.java	842
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java	68
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventAllPairRelPrinter.java	190
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPrinter.java	157
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/GoldEventPrinterWithLabels.java	142
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/ArgContextProvider.java	352
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/GoldEventPrinter.java	140
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPrinter.java	143
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java	142
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java	152
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/DtrRelPrinter.java	146
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventEventTokenAndPosBasedAnnotator.java	186
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePosBasedAnnotator.java	160
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventEventTokenBasedAnnotator.java	346
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventEventTokenAndBIOBasedAnnotator.java	186
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/WindowBasedAnnotator.java	250
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenBasedAnnotator.java	330
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventEventPositionBasedAnnotator.java	183
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimePositionBasedAnnotator.java	160
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndPosBasedAnnotator.java	254
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/JointRelationTokenBasedAnnotator.java	388
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventEventPosBasedAnnotator.java	183
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/ae/EventTimeTokenAndBIOBasedAnnotator.java	254
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralJointRelations.java	679
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventTimeNeuralEvaluation.java	845
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EvaluationOfNeuralEEAndETRelations.java	678
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eval/EventEventNeuralEvaluation.java	625
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/cc/EventTimeAnaforaWriter.java	256
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/cc/SimpleMedDatesPrinter.java	63
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/resnet-predict.py	49
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/et_resnet_func2_train-and-package.py	97
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/et_neural_train-and-package.py	63
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/et_RCNN_train-and-package.py	112
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/keras-predict.py	42
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/rCNN-predict.py	84
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/dima-predict.py	51
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/et_cleartk_io.py	117
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/et_neural_testCNN.py	59
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/nn_models.py	83
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/dataset.py	105
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/cleartk_io.py	109
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/keras/et_dimaCNN_train-and-package.py	77
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_train_hybrid.py	90
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_classify_hybrid.py	67
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/dataset_position.py	87
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/lstm_train_hybrid.py	76
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_classify.py	52
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/et_cleartk_io.py	117
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/lstm_classify.py	47
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/lstm_train.py	56
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_train.py	72
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/nn_models.py	83
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/dataset_hybrid.py	71
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/dataset.py	53
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_train_position.py	88
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cleartk_io.py	109
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/lstm_classify_hybrid.py	61
ctakes-temporal/src/user/resources/org/apache/ctakes/temporal/scripts/nn/cnn_classify_position.py	81
ctakes-type-system/src/main/java/org/apache/ctakes/typesystem/type/constants/CONST.java	164
ctakes-type-system/src/main/java/org/apache/ctakes/log/ObservableLogger.java	368
ctakes-type-system/src/main/java/org/apache/ctakes/log/ObservableLoggerFactory.java	15
ctakes-type-system/src/main/java/org/slf4j/LoggerFactory.java	39
ctakes-type-system/src/main/java/org/slf4j/Slf4jLoggerFactory_Actual.java	322
ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml	2823
ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystemDescription.xsl	39
ctakes-type-system/src/user/config/log4j2.xml	25
ctakes-type-system/metadata/install.xml	13
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebService.java	14
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/SimServiceInfo.java	27
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityWebServiceImpl.java	82
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/ws/ConceptSimilarityRestService.java	25
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchService.java	7
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptLookupBean.java	143
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/SemanticSearchBean.java	193
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/SearchConfigBean.java	11
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/SemanticSimServiceBean.java	27
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/FullTextSearchBean.java	31
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptSearchServiceImpl.java	115
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchServiceImpl.java	116
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/FullTextDocumentViewBean.java	33
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/SemanticSimBean.java	263
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/SemanticSimRegistryBean.java	38
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/ConceptFirstWord.java	30
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchService.java	11
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentViewBean.java	72
ctakes-ytex-web/src/main/java/org/apache/ctakes/ytex/web/search/DocumentSearchResult.java	66
ctakes-ytex-web/src/main/webapp/viewDocument.xhtml	23
ctakes-ytex-web/src/main/webapp/metricCheckboxes.xhtml	41
ctakes-ytex-web/src/main/webapp/semanticSimMulti.xhtml	92
ctakes-ytex-web/src/main/webapp/semanticSim.xhtml	128
ctakes-ytex-web/src/main/webapp/timeout.jsp	15
ctakes-ytex-web/src/main/webapp/css/menuStyle.css	31
ctakes-ytex-web/src/main/webapp/css/mainscript.css	34
ctakes-ytex-web/src/main/webapp/semanticSearch.xhtml	134
ctakes-ytex-web/src/main/webapp/about.xhtml	23
ctakes-ytex-web/src/main/webapp/WEB-INF/applicationContext.xml	10
ctakes-ytex-web/src/main/webapp/WEB-INF/inc-content/header.xhtml	26
ctakes-ytex-web/src/main/webapp/WEB-INF/inc-templates/commonLayout.xhtml	27
ctakes-ytex-web/src/main/webapp/WEB-INF/faces-config.xml	88
ctakes-ytex-web/src/main/webapp/WEB-INF/web.xml	76
ctakes-ytex-web/src/main/webapp/index.jsp	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/TextMentionElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/AssociatedCodeElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/StartDateElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/FrequencyUnitElement.java	29
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/DosageElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/StrengthElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/DurationElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/DrugChangeStatusElement.java	29
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/ConfidenceScoreElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/FormElement.java	47
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/AssociatedSecondaryCodeElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/RouteElement.java	35
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/FrequencyElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/StrengthUnitElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/elements/AssociatedPrimaryCodeElement.java	22
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java	2893
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/CopyDrugAnnotator.java	121
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/impl/NegContextInitializerImpl.java	95
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/DrugModel.java	31
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/DrugMention.java	1156
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/cc/ConsumeNamedEntityRecordModel.java	392
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/states/util/IndentStartState.java	16
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/StrengthCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/FrequencyUnitCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/StrengthUnitCombinedCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/RangeStrengthCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/ContainsSetTextValueCondition.java	55
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/DrugChangeStatusCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/DecimalStrengthStatusCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/TimeCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/FractionCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/DosageCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/RouteCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/FractionStrengthCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/StrengthUnitCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/FormCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/elements/conditions/RangeDosageCondition.java	14
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FrequencyUnitFSM.java	1100
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/RangeStrengthFSM.java	330
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/StrengthFSM.java	348
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FractionStrengthFSM.java	186
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DurationFSM.java	330
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DrugChangeStatusFSM.java	538
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DecimalStrengthFSM.java	90
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/RouteFSM.java	527
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/StrengthUnitFSM.java	327
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FormFSM.java	181
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FrequencyFSM.java	467
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DosagesFSM.java	329
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/NegIndicatorFSM.java	390
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/HyphenatedDrugFSM.java	145
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/SuffixStrengthFSM.java	129
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/StatusIndicatorFSM.java	254
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/SubSectionIndicatorFSM.java	223
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/NonIndicatorFSM.java	120
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/util/SuffixFrequencyFSM.java	658
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/StrengthToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/FrequencyToken.java	8
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/AssociatedCodeToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/DurationToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/FrequencyUnitToken.java	32
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/BaseTokenImpl.java	20
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/StrengthUnitToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/RouteToken.java	26
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/DosageToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/DrugChangeStatusToken.java	26
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/StrengthUnitCombinedToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/ConfidenceScoreToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/elements/FormToken.java	6
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/FractionStrengthToken.java	9
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/RangeToken.java	9
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/SuffixStrengthToken.java	7
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/HyphenatedDrugToken.java	9
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/NonIndicator.java	9
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/FractionToken.java	9
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/SubSectionIndicator.java	19
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/DecimalStrengthToken.java	9
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/SuffixFrequencyToken.java	7
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/output/util/RangeStrengthToken.java	9
ctakes-drug-ner/src/main/resources/org/apache/ctakes/drug/ner/lookup/LookupDesc_DrugNER.xml	124
ctakes-drug-ner/src/main/resources/org/apache/ctakes/drug/ner/types/TypeSystem.xml	313
ctakes-drug-ner/metadata/install.xml	35
ctakes-drug-ner/desc/cas_consumer/DrugNERCasConsumer.xml	90
ctakes-drug-ner/desc/collection_processing_engine/DrugNER_PlainText_CPE.xml	58
ctakes-drug-ner/desc/collection_processing_engine/DrugNER_CPE.xml	58
ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml	129
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/filter/CORSFilter.java	21
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/ResponseFormatter.java	9
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/XmiFormatter.java	24
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/PropertyListFormatter.java	25
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/CuiListFormatter.java	16
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/UmlsJsonFormatter.java	96
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/FhirJsonFormatter.java	10
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/response/PrettyPrintFormatter.java	25
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/RestPipelineRunner.java	62
ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/TinyController.java	46
ctakes-tiny-rest/src/main/webapp/js/app.js	128
ctakes-tiny-rest/src/main/webapp/css/index.css	33
ctakes-tiny-rest/src/main/webapp/WEB-INF/ctakes-rest-service-servlet.xml	15
ctakes-tiny-rest/src/main/webapp/WEB-INF/web.xml	23
ctakes-tiny-rest/src/main/webapp/index.jsp	28
ctakes-distribution/src/main/assembly/bin.xml	374
ctakes-distribution/RELEASE_NOTES.html	11
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/IntegerRange.java	6
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java	137
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/Utility.java	49
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/Annotation.java	7
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/DocumentMetaData.java	49
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ClinicalNotePreProcessor.java	855
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/PreProcessor.java	5
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/SegmentMetaData.java	8
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/DTDloader.java	19
ctakes-preprocessor/desc/CdaCasInitializer.xml	75
ctakes-preprocessor/desc/CPE_CdaCasInitializer.xml	42
ctakes-preprocessor/desc/AggregateAE.xml	41
ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/OpenNLPPOSCollectionReader.java	94
ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/TagDictionaryCreator.java	115
ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/ClearNLPPOSTaggerAE.java	80
ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/concurrent/ThreadSafePosTagger.java	76
ctakes-pos-tagger/src/main/java/org/apache/ctakes/postagger/POSTagger.java	99
ctakes-pos-tagger/src/user/resources/org/apache/ctakes/pos/tagger/scripts/java/data/pos/training/GeniaPosTrainingDataExtractor.java	149
ctakes-pos-tagger/src/user/resources/org/apache/ctakes/pos/tagger/scripts/java/data/pos/training/GeniaPosTrainingDataExtractorTests.java	71
ctakes-pos-tagger/src/user/resources/org/apache/ctakes/pos/tagger/scripts/java/data/pos/dictionary/ListTags.java	94
ctakes-pos-tagger/src/user/resources/org/apache/ctakes/pos/tagger/scripts/perl/trees2opennlppostags.pl	24
ctakes-pos-tagger/desc/POSTaggerAggregate.xml	86
ctakes-pos-tagger/desc/OpenNLPPOSCollectionReader.xml	47
ctakes-pos-tagger/desc/ClearNLPPOSTagger.xml	45
ctakes-pos-tagger/desc/AggregateAE.xml	56
ctakes-pos-tagger/desc/POSTaggerCPE.xml	64
ctakes-pos-tagger/desc/POSTagger.xml	60
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java	140
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/ChunkCreator.java	10
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/DefaultChunkCreator.java	16
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/Chunker.java	116
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/PhraseTypeChunkCreator.java	43
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/concurrent/ThreadSafeChunker.java	65
ctakes-chunker/src/user/resources/org/apache/ctakes/chunker/scripts/java/data/chunk/genia/Genia2PTB.java	40
ctakes-chunker/src/user/resources/org/apache/ctakes/chunker/scripts/java/data/chunk/Chunklink2OpenNLP.java	28
ctakes-chunker/src/user/resources/org/apache/ctakes/chunker/scripts/groovy/data/chunk/TagReport.groovy	27
ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml	61
ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml	60
ctakes-chunker/desc/ChunkerCPE.xml	58
ctakes-chunker/desc/AdjustOPhraseToIncludeFollowingO.xml	60
ctakes-chunker/desc/SimpleSegmentAnnotator.xml	43
ctakes-chunker/desc/ChunkerAggregate.xml	86
ctakes-chunker/desc/ChunkAdjuster.xml	61
ctakes-chunker/desc/Chunker.xml	70
ctakes-chunker/desc/AggregateAE.xml	86
ctakes-chunker/desc/POSTagger.xml	78
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/DBAnnotationViewerDialog.java	434
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBPing.java	55
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java	207
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java	592
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/ExportCAS.java	67
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/RunCPE.java	108
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperServiceImpl.java	1106
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/ColumnMappingInfo.java	103
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/AnnoMappingInfo.java	108
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/DocumentMapperService.java	8
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/MapperConfig.java	36
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/mapper/ISO8601Converter.java	37
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/SegmentRegex.java	61
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/DocumentClass.java	43
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/DocumentAnnotation.java	54
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.java	73
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/BooleanUtil.java	25
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/AnnotationContainmentLink.java	33
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/UimaType.java	58
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/model/Document.java	73
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/StemmedLookupAnnotationToJCasAdapter.java	39
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java	218
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/ApplicationContextHolder.java	61
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/dao/NamedEntityRegexDaoImpl.java	17
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/dao/DocumentDaoImpl.java	19
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/dao/DocumentDao.java	5
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/dao/SegmentRegexDao.java	6
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/dao/NamedEntityRegexDao.java	6
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/dao/SegmentRegexDaoImpl.java	17
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/NegexAnnotator.java	526
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetector.java	250
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexAnnotator.java	92
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DBConsumer.java	96
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotator.java	69
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/MetaMapToCTakesAnnotator.java	205
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexAnnotator.java	125
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/SentenceSpan.java	170
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotator.java	149
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/resource/InitableJdbcConnectionResourceImpl.java	72
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java	220
ctakes-ytex-uima/src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml	59
ctakes-ytex-uima/desc/cpe/fracture_demo.xml	50
ctakes-ytex-uima/desc/analysis_engine/MetaMapToCTakesAnnotator.xml	59
ctakes-ytex-uima/desc/analysis_engine/YTEXPipeline.xml	162
ctakes-ytex-uima/desc/analysis_engine/DictionaryLookupAnnotator.xml	136
ctakes-ytex-uima/desc/analysis_engine/NegexAnnotator.xml	56
ctakes-ytex-uima/desc/analysis_engine/DateAnnotator.xml	34
ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml	254
ctakes-ytex-uima/desc/analysis_engine/NamedEntityRegexAnnotator.xml	34
ctakes-ytex-uima/desc/analysis_engine/SentenceDetectorAnnotator.xml	60
ctakes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml	35
ctakes-ytex-uima/desc/analysis_engine/DBConsumer.xml	148
ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml	51
ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessorMinimal.xml	230
ctakes-ytex-uima/desc/collection_reader/DBCollectionReader.xml	92
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextHitConsumer.java	18
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/negation/NegationContextAnalyzer.java	28
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHit.java	16
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHitConsumer.java	9
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextHitConsumerAdapter.java	9
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/concurrent/ThreadSafeContextAnnotator.java	66
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnalyzerAdapter.java	16
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnalyzer.java	16
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextHitConsumer.java	23
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextAnalyzer.java	48
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java	24
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/NamedEntityContextAnalyzer.java	68
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/ContextAnnotator.java	252
ctakes-ne-contexts/src/main/resources/org/apache/ctakes/ne/contexts/desc/NegationAnnotator.xml	140
ctakes-ne-contexts/desc/NegationAnnotator.xml	140
ctakes-ne-contexts/desc/AggregateAE.xml	42
ctakes-ne-contexts/desc/StatusAnnotator.xml	141
ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java	241
ctakes-template-filler/desc/analysis_engine/RelationExtractorAggregateWithoutOrangeBook.xml	462
ctakes-template-filler/desc/analysis_engine/AggregateTemplateFiller.xml	58
ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator.xml	24
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/FollowingWithPadding.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/MinContext.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/MaxContext.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/ContinuousTextExtractor.java	67
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/SumContext.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/PrecedingWithPadding.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/ci/TextModifier.java	5
ctakes-core/src/main/java/org/apache/ctakes/core/ci/HyphenTextModifierImpl.java	182
ctakes-core/src/main/java/org/apache/ctakes/core/ci/TextModification.java	38
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionals.java	234
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java	245
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java	124
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java	85
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitLocator.java	209
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java	108
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileRunner.java	89
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/ProgressManager.java	74
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/GenerateSentenceBIODescriptors.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java	432
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java	75
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/StandardCliOptions.java	73
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java	159
ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticGroup.java	68
ctakes-core/src/main/java/org/apache/ctakes/core/semantic/SemanticTui.java	192
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java	100
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java	71
ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java	26
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java	106
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java	222
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PausableFileLoggerAE.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java	88
ctakes-core/src/main/java/org/apache/ctakes/core/ae/inert/PausableAE.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonPipper.java	65
ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java	52
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java	49
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java	1329
ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java	17
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java	84
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SubjectSectionFixer.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java	258
ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java	109
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorBIO.java	330
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenConverter.java	167
ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java	84
ctakes-core/src/main/java/org/apache/ctakes/core/ae/UmlsEnvironmentConfiguration.java	27
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java	235
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java	70
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java	150
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PiperFileRunEngine.java	129
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ExitForcer.java	54
ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java	79
ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java	312
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java	156
ctakes-core/src/main/java/org/apache/ctakes/core/ae/NamedEngine.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/ae/AbstractCommandRunner.java	95
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java	79
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java	136
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java	94
ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java	328
ctakes-core/src/main/java/org/apache/ctakes/core/ae/EolSentenceFixer.java	113
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java	98
ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java	311
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/TokenizerHelper.java	46
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/ContractionsPTB.java	241
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/HyphenatedPTB.java	208
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/TokenizerPTB.java	781
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/Token.java	110
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/ContractionResult.java	17
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/Tokenizer.java	443
ctakes-core/src/main/java/org/apache/ctakes/core/nlp/tokenizer/OffsetComparator.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java	20
ctakes-core/src/main/java/org/apache/ctakes/core/util/textspan/TextSpan.java	8
ctakes-core/src/main/java/org/apache/ctakes/core/util/textspan/DefaultTextSpan.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/util/textspan/DefaultAspanComparator.java	14
ctakes-core/src/main/java/org/apache/ctakes/core/util/textspan/DefaultSpanComparator.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/TimeoutMatcher.java	73
ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/ThreadString.java	29
ctakes-core/src/main/java/org/apache/ctakes/core/util/regex/RegexSpanFinder.java	92
ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java	181
ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java	60
ctakes-core/src/main/java/org/apache/ctakes/core/util/ParamUtil.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/util/FSUtil.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/util/NumberedSuffixComparator.java	70
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/DocIdUtil.java	112
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/SourceMetadataUtil.java	106
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java	76
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/JCasBuilder.java	220
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/NoteSpecs.java	107
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySectionBuilder.java	41
ctakes-core/src/main/java/org/apache/ctakes/core/util/DateParser.java	85
ctakes-core/src/main/java/org/apache/ctakes/core/util/ListFactory.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticGroup.java	125
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java	359
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/SemanticTui.java	241
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationUtil.java	100
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/EssentialAnnotationUtil.java	494
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java	23
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/ConceptBuilder.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java	226
ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/util/Pair.java	35
ctakes-core/src/main/java/org/apache/ctakes/core/util/MutableUimaContext.java	168
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/CollectionCreatorFactory.java	33
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/ImmutableCollectionMap.java	102
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/CollectionMap.java	15
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/CollectionCreator.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/HashSetMap.java	107
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/ArrayListMap.java	107
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/DefaultCollectionMap.java	162
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/EnumSetMap.java	102
ctakes-core/src/main/java/org/apache/ctakes/core/util/ListIterable.java	30
ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java	197
ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java	30
ctakes-core/src/main/java/org/apache/ctakes/core/util/BannerWriter.java	53
ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java	39
ctakes-core/src/main/java/org/apache/ctakes/core/util/RelationArgumentUtil.java	207
ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentSection.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/util/log/DotLogger.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/util/log/FinishedLogger.java	117
ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java	21
ctakes-core/src/main/java/org/apache/ctakes/core/util/CalendarUtil.java	214
ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java	26
ctakes-core/src/main/java/org/apache/ctakes/core/util/EssentialAnnotationUtil.java	57
ctakes-core/src/main/java/org/apache/ctakes/core/util/StringUtil.java	29
ctakes-core/src/main/java/org/apache/ctakes/core/util/WordTokenUtil.java	13
ctakes-core/src/main/java/org/apache/ctakes/core/util/JCasUtil.java	23
ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java	75
ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java	160
ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java	102
ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiTreeReader.java	26
ctakes-core/src/main/java/org/apache/ctakes/core/cr/JCasBuilder.java	219
ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java	81
ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java	105
ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java	57
ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/PassThroughDecryptor.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/Decryptor.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/JdbcNotesReader.java	601
ctakes-core/src/main/java/org/apache/ctakes/core/cr/jdbc/DecryptorWrapper.java	23
ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java	260
ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java	562
ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java	134
ctakes-core/src/main/java/org/apache/ctakes/core/sentence/SentenceDetectorCtakes.java	196
ctakes-core/src/main/java/org/apache/ctakes/core/sentence/EndOfSentenceScannerImpl.java	39
ctakes-core/src/main/java/org/apache/ctakes/core/sentence/SentenceSpan.java	68
ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetectorBio.java	72
ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetector.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeWrapper.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java	307
ctakes-core/src/main/java/org/apache/ctakes/core/resource/LinesFromFileStringsResourceImpl.java	43
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResource.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResource.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/resource/LuceneIndexReaderResource.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/resource/LuceneIndexReaderResourceImpl.java	45
ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResource.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResourceImpl.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileReadWriteUtil.java	42
ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileResource.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResourceImpl.java	71
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringsResource.java	5
ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileResourceImpl.java	39
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResourceImpl.java	65
ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorXMLParser.java	193
ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorAnnotation.java	97
ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java	149
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java	89
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CASConsumerTestDriver.java	43
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/SemanticGroup.java	143
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/row/ItemRow.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/row/DefaultItemRow.java	65
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java	301
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterFit.java	40
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriterUima.java	46
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java	1105
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/CssWriter.java	194
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/html/JsWriter.java	50
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/UmlsItemCell.java	5
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/BaseItemCell.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/AbstractItemCell.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/DefaultUmlsItemCell.java	87
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/EventCell.java	52
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/TimexCell.java	40
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/DefaultBaseItemCell.java	37
ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/cell/ItemCell.java	9
ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java	46
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java	177
ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java	119
ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java	204
ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java	293
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJCasFileWriter.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java	112
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java	42
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractTableFileWriter.java	183
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractOutputFileWriter.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenTableFileWriter.java	35
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java	1223
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.java	52
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/CssWriter.java	201
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/JsWriter.java	57
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java	102
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java	61
ctakes-core/src/main/java/org/apache/ctakes/core/cc/XMISerializer.java	144
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJCasJdbcWriter.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java	58
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java	32
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactTable.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java	133
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractUmlsTable.java	76
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/AbstractJdbcTable.java	52
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/table/JdbcTable.java	44
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/JdbcRow.java	17
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/AbstractJdbcField.java	17
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/TextField.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/IntField.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/LongField.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/DoubleField.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/TimeField.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/FloatField.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/BooleanField.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/field/JdbcField.java	8
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/JdbcDb.java	30
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/AbstractJdbcDb.java	46
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/DefaultJdbcDb.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java	68
ctakes-core/src/main/java/org/apache/ctakes/core/cc/SemanticTableFileWriter.java	159
ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java	55
ctakes-core/src/main/java/org/apache/ctakes/core/cc/NonTerminalConsumer.java	7
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java	125
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java	120
ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/cc/MedicationTableFileWriter.java	127
ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterFit.java	66
ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriterUima.java	45
ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java	210
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/state/NamedState.java	13
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/state/NonTerminalEndState.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/TimeFSM.java	95
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/FSM.java	7
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/DateFSM.java	185
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/RomanNumeralFSM.java	90
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/StatusIndicatorFSM.java	172
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/MeasurementFSM.java	208
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/RangeFSM.java	129
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/NegationFSM.java	265
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/PersonTitleFSM.java	78
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/FractionFSM.java	121
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/DayNightWordCondition.java	20
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/RomanNumeralCondition.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/NegateCondition.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/IntegerRangeCondition.java	21
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/RangeCondition.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/DecimalRangeCondition.java	21
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/WordSetCondition.java	25
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/DisjoinCondition.java	15
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/PunctuationValueCondition.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/TextValueCondition.java	27
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/TextSetCondition.java	25
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/SymbolValueCondition.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/IntegerCondition.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/IntegerValueCondition.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/CombineCondition.java	15
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/DecimalValueCondition.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/HourMinuteCondition.java	43
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/NumberCondition.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/WordValueCondition.java	27
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/DecimalCondition.java	12
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/EolToken.java	3
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/ContractionToken.java	3
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/WordToken.java	14
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/SymbolToken.java	3
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/IntegerToken.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/TextToken.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/PunctuationToken.java	3
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/CharacterToken.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/NumberToken.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/BaseToken.java	5
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/DecimalToken.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/CharacterTokenAdapter.java	14
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/NumberTokenAdapter.java	26
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/PunctuationTokenAdapter.java	9
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/TokenConverter.java	37
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/IntegerTokenAdapter.java	37
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/WordTokenAdapter.java	41
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/DecimalTokenAdapter.java	14
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/token/adapter/BaseTokenAdapter.java	15
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/CharacterTokenAdapter.java	17
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/TextTokenAdapter.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/NumberTokenAdapter.java	34
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/PunctuationTokenAdapter.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/IntegerTokenAdapter.java	45
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/NewlineTokenAdapter.java	11
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/WordTokenAdapter.java	44
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/DecimalTokenAdapter.java	30
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/BaseTokenAdapter.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/SymbolTokenAdapter.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/ContractionTokenAdapter.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/package.html	5
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/MeasurementToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/RangeToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/RomanNumeralToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/StatusIndicator.java	14
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/FractionToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/PersonTitleToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/TimeToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/DateToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/BaseTokenImpl.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/NegationIndicator.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java	70
ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java	297
ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientFileWriter.java	51
ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientViewUtil.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteCollector.java	21
ctakes-core/src/main/resources/org/apache/ctakes/core/train/sentdetect/sample_sd_included.mod	85
ctakes-core/src/main/resources/org/apache/ctakes/core/cc/jdbc/TestBinding.xml	38
ctakes-core/src/main/resources/org/apache/ctakes/core/template.xml	65
ctakes-core/src/user/resources/org/apache/ctakes/core/scripts/groovy/cTAKES_clinical_pipeline.groovy	247
ctakes-core/src/user/resources/org/apache/ctakes/core/scripts/groovy/run_cTAKES.groovy	47
ctakes-core/src/user/resources/org/apache/ctakes/core/list/DefaultListRegex.bsv	11
ctakes-core/src/user/resources/org/apache/ctakes/core/sections/SameLineSectionRegex.bsv	87
ctakes-core/src/user/resources/org/apache/ctakes/core/sections/DefaultSectionRegex.bsv	84
ctakes-core/src/user/resources/org/apache/ctakes/core/sections/NaaccrXmlSections.bsv	7
ctakes-core/desc/cas_consumer/PropertyTextWriter.xml	44
ctakes-core/desc/cas_consumer/NormalizedFilesInDirectoryCasConsumer.example.xml	40
ctakes-core/desc/cas_consumer/PrettyTextWriter.xml	46
ctakes-core/desc/cas_consumer/HtmlTableCasConsumer.xml	65
ctakes-core/desc/cas_consumer/JdbcCasConsumer.xml	148
ctakes-core/desc/cas_consumer/XCasWriterCasConsumer.xml	46
ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml	52
ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml	44
ctakes-core/desc/cas_consumer/FilesInDirectoryCasConsumer.example.xml	36
ctakes-core/desc/cas_consumer/TokenFreqCasConsumer.xml	38
ctakes-core/desc/cas_consumer/EmbeddedXmlCasConsumer.xml	61
ctakes-core/desc/cas_consumer/SentenceTokensPrinter.xml	42
ctakes-core/desc/cas_consumer/JdbcWriterTemplate.xml	142
ctakes-core/desc/cas_consumer/TokenOffsetsCasConsumer.example.xml	50
ctakes-core/desc/collection_processing_engine/SentencesAndTokensCPE.xml	58
ctakes-core/desc/collection_processing_engine/SentenceDetectorCPE.xml	58
ctakes-core/desc/collection_processing_engine/PiperFileCPE.xml	23
ctakes-core/desc/analysis_engine/SentencesAndTokensAggregate.xml	59
ctakes-core/desc/analysis_engine/FilterAnnotator.xml	29
ctakes-core/desc/analysis_engine/TokensAndSentencesTAE.xml	45
ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml	60
ctakes-core/desc/analysis_engine/PiperFileAggregate.xml	38
ctakes-core/desc/analysis_engine/OverlapAnnotator.xml	130
ctakes-core/desc/analysis_engine/BsvRegexSectionizer.xml	54
ctakes-core/desc/analysis_engine/CDASegmentAnnotator.xml	51
ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml	44
ctakes-core/desc/analysis_engine/PiperFileRunEngine.xml	49
ctakes-core/desc/analysis_engine/AggregateTemplateFiller.xml	58
ctakes-core/desc/analysis_engine/TokenizerAnnotatorVersion1.xml	91
ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml	60
ctakes-core/desc/analysis_engine/SectionFilter.xml	51
ctakes-core/desc/analysis_engine/AggregateAE.xml	59
ctakes-core/desc/analysis_engine/SentenceDetectorAggregate.xml	42
ctakes-core/desc/analysis_engine/SectionSegmentAnnotator.xml	82
ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml	56
ctakes-core/desc/analysis_engine/TemplateFillerAnnotator.xml	24
ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml	52
ctakes-core/desc/analysis_engine/CopyAnnotator.xml	91
ctakes-core/desc/analysis_engine/NullAnnotator.xml	26
ctakes-core/desc/analysis_engine/SentenceDetectorAnnotatorBIO.xml	2572
ctakes-core/desc/collection_reader/JdbcCollectionReader.example.xml	191
ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml	46
ctakes-core/desc/collection_reader/LinesFromFileCollectionReader.xml	85
ctakes-core/desc/collection_reader/FilesInDirectoryCollectionCyclicalReads.xml	84
ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml	72
ctakes-core/desc/cas_initializer/XCasReaderCasInitializer.xml	33
ctakes-core/desc/cas_initializer/NseCasInitializer.xml	47
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/PSESentenceAnnotator.java	80
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SideEffectAnnotator.java	504
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceClassifierAnnotator.java	83
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java	193
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java	226
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/PatternMatch.java	57
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectSentenceCasConsumer.java	68
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/cc/SideEffectCasConsumer.java	86
ctakes-side-effect/src/main/resources/org/apache/ctakes/side/effect/types/TypeSystem.xml	60
ctakes-side-effect/desc/cas_consumer/SideEffectSentenceCasConsumer.xml	51
ctakes-side-effect/desc/cas_consumer/SideEffectCasConsumer.xml	49
ctakes-side-effect/desc/collection_processing_engine/SideEffectSentence_CDA_CPE.xml	58
ctakes-side-effect/desc/collection_processing_engine/SideEffectSentenceCPE.xml	58
ctakes-side-effect/desc/collection_processing_engine/SideEffectCPE.xml	78
ctakes-side-effect/desc/collection_processing_engine/SideEffect_CDA_CPE.xml	78
ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffect.xml	245
ctakes-side-effect/desc/analysis_engine/SESentenceClassifierAnnotator.xml	41
ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE_UMLS.xml	119
ctakes-side-effect/desc/analysis_engine/VG2LookupWindow.xml	92
ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE_UMLS.xml	193
ctakes-side-effect/desc/analysis_engine/LookupWindowAnnotator_sideEffect.xml	68
ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml	105
ctakes-side-effect/desc/analysis_engine/SESentenceFeatureAnnotator.xml	43
ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregate_CDA_TAE.xml	193
ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml	105
ctakes-side-effect/desc/analysis_engine/SideEffectSentenceAggregateTAE.xml	119
ctakes-side-effect/desc/analysis_engine/PSESentenceAnnotator.xml	42
ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml	322
ctakes-side-effect/desc/analysis_engine/SideEffectAnnotator.xml	236
ctakes-side-effect/desc/analysis_engine/AdjP2LookupWindow.xml	93
ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE_UMLS.xml	167
ctakes-side-effect/desc/analysis_engine/SideEffectAggregate_CDA_TAE.xml	167
ctakes-ytex/scripts/data/mssql/kernel/drop_tables.sql	63
ctakes-ytex/scripts/data/mssql/kernel/create_tables.sql	217
ctakes-ytex/scripts/data/mssql/esld/create_view.sql	60
ctakes-ytex/scripts/data/mssql/esld/create_document.sql	1
ctakes-ytex/scripts/data/mssql/esld/abs/create_sp.sql	20
ctakes-ytex/scripts/data/mssql/esld/abs/create_abstraction.sql	109
ctakes-ytex/scripts/data/mssql/esld/abs/drop_abstraction.sql	5
ctakes-ytex/scripts/data/mssql/esld/insert_reference.sql	40
ctakes-ytex/scripts/data/mssql/esld/postprocessing/create_view.sql	50
ctakes-ytex/scripts/data/mssql/esld/postprocessing/insert_radiology_review.sql	11
ctakes-ytex/scripts/data/mssql/esld/postprocessing/delete_analysis_batch.sql	3
ctakes-ytex/scripts/data/mssql/esld/postprocessing/score_report_all.sql	94
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_varices.sql	87
ctakes-ytex/scripts/data/mssql/esld/postprocessing/link_documents.sql	34
ctakes-ytex/scripts/data/mssql/esld/postprocessing/mark_duplicates.sql	40
ctakes-ytex/scripts/data/mssql/esld/postprocessing/score_report.sql	100
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_ascites.sql	53
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql	87
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql	243
ctakes-ytex/scripts/data/mssql/umls/index_umls.sql	9
ctakes-ytex/scripts/data/mssql/umls/import_umls.sql	30
ctakes-ytex/scripts/data/mssql/umls/drop_tables.sql	3
ctakes-ytex/scripts/data/mssql/umls/create_indices.sql	2
ctakes-ytex/scripts/data/mssql/umls/create_view.sql	9
ctakes-ytex/scripts/data/mssql/umls/insert_view.sql	28
ctakes-ytex/scripts/data/mssql/umls/mssql_drop.sql	159
ctakes-ytex/scripts/data/mssql/umls/create_tables.sql	7
ctakes-ytex/scripts/data/mssql/umls/mssql_net_tables.sql	42
ctakes-ytex/scripts/data/mssql/umls/index_view.sql	2
ctakes-ytex/scripts/data/mssql/umls/mssql_indexes.sql	70
ctakes-ytex/scripts/data/mssql/umls/mssql_tables.sql	422
ctakes-ytex/scripts/data/mssql/umls/drop_view.sql	6
ctakes-ytex/scripts/data/mssql/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/mssql/uima/drop_document.sql	75
ctakes-ytex/scripts/data/mssql/uima/create_view.sql	50
ctakes-ytex/scripts/data/mssql/uima/create_document.sql	215
ctakes-ytex/scripts/data/mssql/uima/drop_reference.sql	18
ctakes-ytex/scripts/data/mssql/uima/create_reference.sql	40
ctakes-ytex/scripts/data/mssql/uima/drop_view.sql	12
ctakes-ytex/scripts/data/snomedct/sct2f_concept.xml	11
ctakes-ytex/scripts/data/snomedct/sct2_relationship.xml	16
ctakes-ytex/scripts/data/snomedct/sct2f_relationship.xml	16
ctakes-ytex/scripts/data/snomedct/sct2_concept.xml	11
ctakes-ytex/scripts/data/snomedct/sct2f_description.xml	17
ctakes-ytex/scripts/data/snomedct/sct2_description.xml	17
ctakes-ytex/scripts/data/umls/AMBIGLUI.xml	8
ctakes-ytex/scripts/data/umls/MRSAB.xml	31
ctakes-ytex/scripts/data/umls/MRSMAP.xml	17
ctakes-ytex/scripts/data/umls/MRHIST.xml	15
ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.xml	12
ctakes-ytex/scripts/data/umls/MRCONSO.xml	24
ctakes-ytex/scripts/data/umls/MRXNS_ENG.xml	11
ctakes-ytex/scripts/data/umls/MRCOLS.xml	14
ctakes-ytex/scripts/data/umls/MRSAT.xml	19
ctakes-ytex/scripts/data/umls/MRHIER.xml	15
ctakes-ytex/scripts/data/umls/SRSTRE1.xml	9
ctakes-ytex/scripts/data/umls/MRDEF.xml	14
ctakes-ytex/scripts/data/umls/MRREL.xml	22
ctakes-ytex/scripts/data/umls/MRXNW_ENG.xml	11
ctakes-ytex/scripts/data/umls/MRCOC.xml	15
ctakes-ytex/scripts/data/umls/MRAUI.xml	15
ctakes-ytex/scripts/data/umls/umls_aui_fword.xml	11
ctakes-ytex/scripts/data/umls/MRDOC.xml	10
ctakes-ytex/scripts/data/umls/MRSTY.xml	12
ctakes-ytex/scripts/data/umls/SRSTRE2.xml	9
ctakes-ytex/scripts/data/umls/MRRANK.xml	10
ctakes-ytex/scripts/data/umls/MRMAP.xml	32
ctakes-ytex/scripts/data/umls/MRCUI.xml	13
ctakes-ytex/scripts/data/umls/MRFILES.xml	12
ctakes-ytex/scripts/data/umls/SRFIL.xml	12
ctakes-ytex/scripts/data/umls/SRFLD.xml	10
ctakes-ytex/scripts/data/umls/AMBIGSUI.xml	8
ctakes-ytex/scripts/data/umls/MRXW_ENG.xml	11
ctakes-ytex/scripts/data/umls/SRSTR.xml	10
ctakes-ytex/scripts/data/umls/SRDEF.xml	16
ctakes-ytex/scripts/data/hsql/kernel/drop_tables.sql	21
ctakes-ytex/scripts/data/hsql/kernel/ic_create.sql	7
ctakes-ytex/scripts/data/hsql/kernel/create_tables.sql	228
ctakes-ytex/scripts/data/hsql/kernel/ic_copy.template.sql	14
ctakes-ytex/scripts/data/hsql/umls/index_umls.sql	10
ctakes-ytex/scripts/data/hsql/umls/import_umls.sql	31
ctakes-ytex/scripts/data/hsql/umls/drop_tables.sql	1
ctakes-ytex/scripts/data/hsql/umls/create_indices.sql	2
ctakes-ytex/scripts/data/hsql/umls/create_view.sql	8
ctakes-ytex/scripts/data/hsql/umls/insert_view.sql	26
ctakes-ytex/scripts/data/hsql/umls/create_tables.sql	7
ctakes-ytex/scripts/data/hsql/umls/index_view.sql	3
ctakes-ytex/scripts/data/hsql/umls/drop_view.sql	2
ctakes-ytex/scripts/data/hsql/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/hsql/uima/drop_document.sql	28
ctakes-ytex/scripts/data/hsql/uima/create_view.sql	43
ctakes-ytex/scripts/data/hsql/uima/create_document.sql	180
ctakes-ytex/scripts/data/hsql/uima/drop_reference.sql	6
ctakes-ytex/scripts/data/hsql/uima/create_reference.sql	38
ctakes-ytex/scripts/data/hsql/uima/drop_view.sql	8
ctakes-ytex/scripts/data/mysql/kernel/drop_tables.sql	21
ctakes-ytex/scripts/data/mysql/kernel/ic_create.sql	7
ctakes-ytex/scripts/data/mysql/kernel/create_tables.sql	211
ctakes-ytex/scripts/data/mysql/kernel/ic_copy.template.sql	14
ctakes-ytex/scripts/data/mysql/snomedct/index_tables_full.sql	8
ctakes-ytex/scripts/data/mysql/snomedct/create_tables.sql	36
ctakes-ytex/scripts/data/mysql/snomedct/index_tables.sql	8
ctakes-ytex/scripts/data/mysql/snomedct/create_tables_full.sql	37
ctakes-ytex/scripts/data/mysql/umls/index_umls.sql	10
ctakes-ytex/scripts/data/mysql/umls/import_umls.sql	30
ctakes-ytex/scripts/data/mysql/umls/drop_tables.sql	1
ctakes-ytex/scripts/data/mysql/umls/create_indices.sql	2
ctakes-ytex/scripts/data/mysql/umls/create_view.sql	8
ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql	26
ctakes-ytex/scripts/data/mysql/umls/create_tables.sql	7
ctakes-ytex/scripts/data/mysql/umls/index_view.sql	3
ctakes-ytex/scripts/data/mysql/umls/drop_view.sql	2
ctakes-ytex/scripts/data/mysql/util/update_anno_contain.sql	21
ctakes-ytex/scripts/data/mysql/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/mysql/uima/drop_document.sql	28
ctakes-ytex/scripts/data/mysql/uima/create_view.sql	43
ctakes-ytex/scripts/data/mysql/uima/create_document.sql	198
ctakes-ytex/scripts/data/mysql/uima/delete_orphan.sql	72
ctakes-ytex/scripts/data/mysql/uima/drop_reference.sql	6
ctakes-ytex/scripts/data/mysql/uima/create_reference.sql	44
ctakes-ytex/scripts/data/mysql/uima/drop_view.sql	8
ctakes-ytex/scripts/data/ref_uima_type.xml	9
ctakes-ytex/scripts/data/orcl/kernel/create_tables_trg.sql	21
ctakes-ytex/scripts/data/orcl/kernel/drop_tables.sql	15
ctakes-ytex/scripts/data/orcl/kernel/create_tables.sql	32
ctakes-ytex/scripts/data/orcl/umls/index_umls.sql	16
ctakes-ytex/scripts/data/orcl/umls/import_umls.sql	28
ctakes-ytex/scripts/data/orcl/umls/drop_tables.sql	3
ctakes-ytex/scripts/data/orcl/umls/create_indices.sql	2
ctakes-ytex/scripts/data/orcl/umls/create_view.sql	9
ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql	26
ctakes-ytex/scripts/data/orcl/umls/create_tables.sql	7
ctakes-ytex/scripts/data/orcl/umls/index_view.sql	3
ctakes-ytex/scripts/data/orcl/umls/drop_view.sql	5
ctakes-ytex/scripts/data/orcl/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/orcl/uima/drop_document.sql	47
ctakes-ytex/scripts/data/orcl/uima/create_view.sql	47
ctakes-ytex/scripts/data/orcl/uima/create_document_trg.sql	28
ctakes-ytex/scripts/data/orcl/uima/create_document.sql	226
ctakes-ytex/scripts/data/orcl/uima/drop_reference.sql	12
ctakes-ytex/scripts/data/orcl/uima/create_reference.sql	53
ctakes-ytex/scripts/data/orcl/uima/create_reference_trg.sql	14
ctakes-ytex/scripts/data/orcl/uima/drop_view.sql	4
ctakes-ytex/scripts/data/stopword.xml	7
ctakes-ytex/scripts/build-classpath.xml	2
ctakes-ytex/scripts/build-setup.xml	2
ctakes-ytex/scripts/build-nonasf.xml	2
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/AppJdl.java	76
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/CsvLoader.java	189
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/XmlLoader.java	89
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/Loader.java	15
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/base/JdlConnection.java	66
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/base/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/SaxParser.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/DomUtil.java	81
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/Validation.java	80
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/DomParser.java	39
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/SchemaUtil.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/jaxb/ObjectFactoryUtil.java	63
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/jaxb/ObjectFactoryBind.java	41
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/jaxb/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/PropFile.java	29
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/PropertiesFile.java	27
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/Singleton.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/FileUtil.java	24
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/App.java	8
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/AppMain.java	44
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHelper.java	33
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/FoldGenerator.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/ProductKernel.java	32
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/MethodCachingInterceptor.java	64
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/AttributeProductKernel.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CacheKernel.java	52
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/NamedEntityNegationKernel.java	24
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/LinKernel.java	8
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/TreePrinter.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SemanticTypeKernel.java	257
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CacheKeyGenerator.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/Kernel.java	4
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CorpusKernelEvaluatorImpl.java	404
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CorpusKernelEvaluator.java	11
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SumKernel.java	19
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SymmetricPairCacheKeyGenerator.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/NodeAttributeKernel.java	31
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SemanticSimKernel.java	111
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/ConvolutionKernel.java	43
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/EqualityKernel.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/WeightedPolynomialMixingKernel.java	71
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/NormKernel.java	79
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/FoldGeneratorImpl.java	233
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataFormatter.java	25
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationResult.java	31
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseData.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluationIRStat.java	127
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ClassifierInstanceEvaluation.java	50
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ConceptGraph.java	51
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/FeatureEvaluation.java	73
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/FeatureParentChild.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ObjPair.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/CrossValidationFold.java	69
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/KernelEvaluation.java	55
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/SVMClassifierEvaluation.java	53
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ConcRel.java	334
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/SemiLClassifierEvaluation.java	60
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/CrossValidationFoldInstance.java	50
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/FeatureRank.java	98
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/KernelEvaluationInstance.java	70
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.java	92
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/pagerank/PageRankService.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/pagerank/PageRankServiceImpl.java	315
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluator.java	11
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/OrderedPair.java	45
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataFormatterFactory.java	4
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ClassifierEvaluationDao.java	58
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/SortedSetUserType.java	76
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/StringArrayUserType.java	81
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java	386
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/KernelEvaluationDaoImpl.java	135
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/KernelEvaluationDao.java	20
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ClassifierEvaluationDaoImpl.java	300
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDao.java	10
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/KernelUtilImpl.java	320
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/InfoContentEvaluator.java	8
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/Pair.java	40
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SvmlinEvaluationParser.java	129
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/InfoContentEvaluatorImpl.java	143
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/RRFtoWideTab.java	45
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvalUtil.java	328
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java	283
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BagOfWordsData.java	70
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/KernelUtil.java	29
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SVMLinFormatterFactory.java	140
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationParser.java	28
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationResults.java	45
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/InstanceData.java	50
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SimSvcContextHolder.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BagOfWordsExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/FileUtil.java	185
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java	158
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java	315
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/KernelContextHolder.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/CytoscapeHelperImpl.java	205
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/wsd/WordSenseDisambiguatorImpl.java	124
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/wsd/WordSenseDisambiguator.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporter.java	22
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IRMetrics.java	70
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationImporter.java	79
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BaseSparseDataFormatter.java	135
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ImputedFeatureEvaluator.java	20
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/CytoscapeHelper.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BaseClassifierEvaluationParser.java	278
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/InstanceTreeBuilder.java	10
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/Node.java	69
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/NodeMappingInfo.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/QueryMappingInfo.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/TreeMappingInfo.java	43
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/NodeKey.java	40
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/InstanceTreeBuilderImpl.java	150
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/RadaMetric.java	22
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/SokalSneathMetric.java	18
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptPairSimilarity.java	37
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LinMetric.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicPathMetric.java	21
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/WuPalmerMetric.java	23
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicRadaMetric.java	21
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityService.java	48
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/PathMetric.java	17
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/BaseSimilarityMetric.java	51
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptPair.java	71
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LCSPath.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/JaccardMetric.java	18
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/PageRankMetric.java	17
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/SimilarityMetric.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptInfo.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicLCHMetric.java	23
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LCHMetric.java	22
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/SimilarityInfo.java	67
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityServiceImpl.java	648
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ImputedFeatureEvaluatorImpl.java	757
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BagOfWordsDecorator.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaResultInstanceImporter.java	7
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaResultsImporter.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/DocumentResultInstanceImporter.java	32
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaAttributeEvaluator.java	10
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaResultsImporterImpl.java	122
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/GramMatrixExporterImpl.java	191
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaBagOfWordsExporterImpl.java	203
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ImportWekaResults.java	128
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaAttributeEvaluatorImpl.java	198
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ExportGramMatrix.java	15
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/GramMatrixExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ExportBagOfWords.java	11
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaBagOfWordsExporter.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaFormatterFactory.java	172
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/sparsematrix/SparseMatrixFormatterFactory.java	101
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/sparsematrix/InstanceDataExporterImpl.java	101
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/sparsematrix/InstanceDataExporter.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/semil/SemiLFormatterFactory.java	147
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/semil/SemiLEvaluationParser.java	148
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/dao/DBUtil.java	78
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/MRREL.java	74
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/MRSTY.java	83
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/UmlsAuiFirstWord.java	52
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/MRCONSO.java	157
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java	16
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java	97
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/svmlight/SGTFormatterFactory.java	47
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/svmlight/SVMLightParser.java	113
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/svmlight/SVMLightFormatterFactory.java	123
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMParser.java	202
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMUtil.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMFormatterFactory.java	115
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMUtilImpl.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMGramMatrixExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMGramMatrixExporterImpl.java	215
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/R/RGramMatrixExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/R/RGramMatrixExporterImpl.java	146
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/KernelLauncher.java	145
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernel/model/KernelEvaluation.hbm.xml	63
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.hbm.xml	298
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml	16
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml	18
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml	37
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml	43
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml	55
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml	17
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml	57
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml	14
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml	16
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml	115
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml	21
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml	20
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-kernel.xml	292
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml	4
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.template.xml	4
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.template.xml	4
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml	15
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml	14
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml	38
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml	37
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml	73
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml	29
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml	25
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml	24
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml	34
ctakes-ytex/src/main/resources/ehcache.xml	6
ctakes-ytex/src/assemble/dist.xml	25
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java	153
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/TreeFeatureConsumer.java	181
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java	50
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java	143
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java	20
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationViewer.java	74
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorConsumer.java	58
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java	66
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/EventAndEntityViewer.java	52
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java	118
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/Stats.java	83
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationStatsCalculator.java	191
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/GoldAnnotationAnalysisPipeline.java	41
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/Constants.java	28
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/Splitter.java	68
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/CategoricalDistribution.java	37
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/LocationOfRelationExtractorAnnotator.java	115
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java	83
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/CausesBringsAboutRelationExtractorAnnotator.java	76
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManagesTreatsRelationExtractorAnnotator.java	78
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetUtils.java	108
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyParseUtils.java	91
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java	52
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java	82
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyPathFeaturesExtractor.java	28
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PrepositionFeatureExtractor.java	37
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TreeFragmentFeatureExtractor.java	59
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EntitySpanFeatureExtractor.java	30
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PunctuationFeatureExtractor.java	28
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PhraseChunkingExtractor.java	93
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PETFeatureExtractor.java	31
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/EmbeddingFeatureExtractor.java	85
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/RelationFeaturesExtractor.java	9
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java	36
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/ArgumentOrderFeatureExtractor.java	20
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/DependencyTreeFeaturesExtractor.java	34
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/WordNetFeatureExtractor.java	33
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/FlatTreeFeatureExtractor.java	44
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java	210
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ManifestationOfRelationExtractorAnnotator.java	72
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java	53
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java	71
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java	40
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4EntityMentionPairRelationExtractorAnnotator.java	65
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java	88
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java	96
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java	77
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java	89
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline4DegreeOfRelationExtractorAnnotator.java	42
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java	100
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/IdentifiedAnnotationExpander.java	79
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeModifierExtractor.java	78
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeDegreeExtractor.java	79
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/concurrent/ThreadSafeLocationExtractor.java	79
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/AnatomicalSiteListExtractorPipeline.java	117
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/MetastasisXmiGenerationPipeline.java	131
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/metastasis/MetastasisAnaforaXMLReader.java	162
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/PrintRelationStatistics.java	68
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationEvaluation_ImplBase.java	71
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/SHARPXMI.java	156
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ParameterSettings.java	52
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/CorpusXMI.java	97
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/XMIReader.java	60
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java	825
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java	144
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/CopyFromGold.java	67
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/ArgumentInfo.java	9
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/XMLReader.java	102
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/RelationInfo.java	52
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/knowtator/Span.java	28
ctakes-relation-extractor/metadata/install.xml	13
ctakes-relation-extractor/desc/analysis_engine/RelationExtractorPreprocessor.xml	170
ctakes-relation-extractor/desc/analysis_engine/DegreeOfRelationExtractorAnnotator.xml	87
ctakes-relation-extractor/desc/analysis_engine/RemoteDictionary.xml	10
ctakes-relation-extractor/desc/analysis_engine/LocationOfRelationExtractorAnnotator.xml	87
ctakes-relation-extractor/desc/analysis_engine/ModifierExtractorAnnotator.xml	74
ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate.xml	448
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SystemOutPanel.java	91
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/LoggerPanel.java	131
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothToolTip.java	78
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/LoggerTextFilter.java	65
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileTableCellEditor.java	60
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/DisablerPane.java	137
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererPanel.java	69
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothTipTable.java	14
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/SmoothTipList.java	13
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/CellRendererLabel.java	68
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/PositionedSplitPane.java	56
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/FileChooserPanel.java	111
ctakes-gui/src/main/java/org/apache/ctakes/gui/component/TextLineNumber.java	233
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperFileView.java	35
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperFinder.java	65
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperInfo.java	26
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/piper/PiperTextFilter.java	252
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoComparator.java	74
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoRenderer.java	91
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductRenderer.java	39
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/RoleRenderer.java	74
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/ProductIconFactory.java	56
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/TypeProductListModel.java	34
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/info/PipeBitInfoPanel.java	76
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitFinder.java	89
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitCellRenderer.java	20
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesListModel.java	44
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/available/AvailablesRenderer.java	62
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/PipeBitPainter.java	113
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitInfoPanel.java	98
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBit.java	10
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserParameterInfoPanel.java	21
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/DefaultUserBit.java	77
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitListModel.java	101
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/user/UserBitRenderer.java	90
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/BitInfoPanel.java	130
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterCellRenderer.java	23
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterTableModel.java	116
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterInfoPanel.java	122
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterHolder.java	11
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/ParameterMapper.java	47
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/bit/parameter/DefaultParameterHolder.java	57
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java	503
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperCreator.java	63
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java	240
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java	571
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperDisplayModel.java	6
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java	63
ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/GenericRunnerGui.java	46
ctakes-gui/src/main/java/org/apache/ctakes/gui/generic/MainPanel.java	173
ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java	800
ctakes-gui/src/main/java/org/apache/ctakes/gui/util/FileChooserUtil.java	33
ctakes-gui/src/main/java/org/apache/ctakes/gui/util/ColorFactory.java	18
ctakes-gui/src/main/java/org/apache/ctakes/gui/util/IconLoader.java	38
ctakes-gui/src/main/java/org/apache/ctakes/gui/action/GlobalHotKeyManager.java	44
ctakes-gui/src/main/java/org/apache/ctakes/gui/action/HotKeyManager.java	5
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoIndex.java	8
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/DoseUtil.java	50
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java	215
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/VocabularyStore.java	86
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiTableModel.java	96
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/Concept.java	111
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/CuiCodeUtil.java	86
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrstyIndex.java	8
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java	29
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrstyParser.java	70
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/LanguageTableModel.java	87
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java	137
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/TuiCellRenderer.java	23
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/UmlsTermUtil.java	252
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrsabIndex.java	8
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/AutoTermExtractor.java	8
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/RareWordUtil.java	104
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/RareWordDbWriter.java	171
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/HsqlUtil.java	53
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/JdbcUtil.java	72
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/TokenUtil.java	55
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/FileUtil.java	177
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/TextTokenizer.java	165
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/MainPanel.java	275
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryXmlWriter.java	121
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryCreator.java	59
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryDownloader.java	130
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/Synonym.java	21
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/Ranks.java	33
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedPiperWriter.java	140
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedDictionaryCreator.java	53
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedMainPanel.java	383
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/table/SemanticTuiModel.java	91
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/table/TextTypeModel.java	78
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/CasedReadmeWriter.java	71
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/file/MrRel.java	19
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/file/MrSty.java	9
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/file/MrConso.java	21
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/file/MrSat.java	16
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/file/Tty.java	284
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/UmlsParser.java	171
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/IsPref.java	5
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Rel.java	38
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Stype.java	8
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Rela.java	954
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Ts.java	5
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Srl.java	16
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Stt.java	8
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Lat.java	35
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/umls/abbreviation/Atn.java	663
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/term/CuiTerm.java	257
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/term/TermLine.java	33
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/term/CustomTermLine.java	38
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/term/ConsoLine.java	102
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/cased/HsqlWriter.java	271
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java	202
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjReceiverAE.java	92
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjJmsSender.java	101
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStopper.java	72
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/ArtemisStarter.java	52
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjPipper.java	62
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java	185
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjStompSender.java	124
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/util/PbjConstants.java	13
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/util/ArtemisController.java	64
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/cr/PbjReceiver.java	205
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/component/pbj_receiver.py	48
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/component/pbj_sender.py	63
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/component/__init__.py	1
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/component/collection_reader.py	18
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/component/cas_annotator.py	15
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pipeline/__init__.py	1
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pipeline/pbj_pipeline.py	91
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/scripts/__init__.py	1
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/scripts/get_typesystems.py	18
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/__init__.py	1
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/type_system/__init__.py	1
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/type_system/ctakes_const.py	161
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/type_system/ctakes_types.py	167
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/type_system/type_system_loader.py	15
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/__init__.py	1
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/token_tools.py	12
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/create_type.py	14
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/stomp_receiver.py	71
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/helper_functions.py	39
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/event_creator.py	20
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/arg_parser.py	17
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/get_common_types.py	52
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/pbj_defaults.py	12
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/create_relation.py	11
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/pyproject.toml	40
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/setup.py	3
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/setup.cfg	25
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/types/TypeSystem.xml	2823
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/LineAndTokenPosition.java	27
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/MayoZoneTranslator.java	88
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/CharacterOffsetToLineTokenConverterDefaultImpl.java	65
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/LineTokenToCharacterOffsetConverter.java	242
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java	1298
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/CharacterOffsetToLineTokenConverter.java	5
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerRunner.java	81
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ParsedTextFile.java	22
ctakes-mastif-zoner/src/user/resources/org/mitre/medfacts/zoner/section_regex.xml	851
ctakes-mastif-zoner/src/user/resources/org/mitre/medfacts/zoner/section_regex_with_attributes.xml	1228
ctakes-mastif-zoner/src/user/resources/org/mitre/medfacts/zoner/mayo_sections.xml	317
ctakes-mastif-zoner/src/user/resources/org/mitre/medfacts/zoner/section_regex_with_attributes_and_generics.xml	1237
ctakes-web-rest/src/main/java/org/apache/ctakes/rest/filter/CORSFilter.java	24
ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasFormatter.java	109
ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/XMLParser.java	222
ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java	95
ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java	40
ctakes-web-rest/src/main/webapp/js/app.js	22
ctakes-web-rest/src/main/webapp/WEB-INF/ctakes-rest-service-servlet.xml	15
ctakes-web-rest/src/main/webapp/WEB-INF/web.xml	23
ctakes-web-rest/src/main/webapp/index.jsp	18
ctakes-web-rest/docker/customDictionary.xml	54
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/backbone/CompositionSectionCreator.java	32
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/util/FhirNoteSpecs.java	128
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirXmlFileReader.java	22
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleReader.java	56
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleParser.java	141
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/FhirJsonFileReader.java	22
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java	147
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java	157
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ParagraphCreator.java	17
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationCreator.java	49
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionParser.java	39
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SentenceCreator.java	18
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SentenceParser.java	14
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirResourceParser.java	7
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/AnnotationParser.java	44
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java	83
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirPractitioner.java	64
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionParser.java	16
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ParagraphParser.java	14
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CtakesTypeCreator.java	142
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BaseTokenParser.java	49
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/SectionCreator.java	35
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BaseTokenCreator.java	20
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/BundleCreator.java	25
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirBasicParser.java	18
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/AnnotationCreator.java	17
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java	32
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirBasicCreator.java	21
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirResourceCreator.java	8
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/PractitionerCtakes.java	53
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonFileWriter.java	48
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirJsonWriter.java	52
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cc/FhirDocComposer.java	146
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java	188
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java	37
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java	60
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java	29
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java	101
ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml	58
ctakes-clinical-pipeline/desc/collection_processing_engine/test1.xml	58
ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml	167
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml	206
ctakes-clinical-pipeline/desc/analysis_engine/NP2LookupWindow.xml	90
ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml	44
ctakes-clinical-pipeline/desc/analysis_engine/MaxLookupWindows.xml	125
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml	204
ctakes-clinical-pipeline/desc/analysis_engine/AggregateCdaUMLSProcessor.xml	231
ctakes-clinical-pipeline/desc/analysis_engine/CuisOnlyPlaintextUMLSProcessor.xml	124
ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml	44
ctakes-clinical-pipeline/desc/analysis_engine/NegationAnnotator.xml	140
ctakes-clinical-pipeline/desc/analysis_engine/AggregateCdaProcessor.xml	228
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml	255
ctakes-clinical-pipeline/desc/analysis_engine/ExtractionPrepAnnotator.xml	52
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/InstallHelper.java	22
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/BaseInstaller.java	53
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/CopyFileSpec.java	20
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java	106
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/MavenHelper.java	90
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/RestDockerBuilder.java	51
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/DisablerPane.java	136
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Option.java	139
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/GoalPom.java	48
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/Feature.java	58
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/feature/FeatureComponent.java	67
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/MainPanel.java	19
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/wizard/InstallTypeStep.java	91
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/wizard/FeaturesStep.java	104
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/wizard/DescriptionStep.java	55
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/wizard/DhWizardController.java	45
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/wizard/DhWizardStep.java	9
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/wizard/OutputStep.java	69
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/SinglePackageFabricator.java	34
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/Output.java	49
ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/gui/output/OutputComponent.java	28
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/NoteMarkupProgressUI.java	78
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/InfoPanel.java	51
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/ProgressNote.java	29
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/NoteProgressDialog.java	83
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/SummaryStep.java	59
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/WizardController.java	119
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java	164
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/RunnerUtil.java	31
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/DialogUtil.java	105
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/NavigationPanel.java	70
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/TocPanel.java	34
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/WizardPanel.java	19
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/WizardStep.java	13
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/AbstractWizardStep.java	40
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/ContentsPanel.java	33
ctakes-dockhand/src/main/resources/log4j2.xml	25
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_coref_pom.xml	168
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/temporal_pom.xml	168
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/entity_pom.xml	128
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_coref_pom.xml	173
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/coreference_pom.xml	172
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/attribute_pom.xml	146
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_pom.xml	164
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_pom.xml	159
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/token_pom.xml	93
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/local/pom/relation_temporal_coreference_pom.xml	164
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_coref_pom.xml	152
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/temporal_pom.xml	152
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/entity_pom.xml	112
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_coref_pom.xml	157
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/coreference_pom.xml	156
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/attribute_pom.xml	144
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_pom.xml	148
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_pom.xml	143
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/token_pom.xml	77
ctakes-dockhand/src/main/resources/org/apache/ctakes/dockhand/goal/rest/pom/relation_temporal_coreference_pom.xml	148
ctakes-dockhand/src/main/resources/log4j_not.xml	38
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/NonSmokerNamedEntityLookupConsumerImpl.java	58
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/SmokerNamedEntityLookupConsumerImpl.java	58
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/lookup/ae/UnknownSmokerNamedEntityLookupConsumerImpl.java	58
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/KuRuleBasedClassifierAnnotator.java	103
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ClassifiableEntries.java	384
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifierAnnotator_libsvm.java	164
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/PcsClassifier.java	207
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/ResolutionAnnotator.java	168
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/ae/SentenceAdjuster.java	134
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java	13
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/ClassifiableEntry.java	9
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/util/TruthValue.java	7
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java	159
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java	213
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/cc/RecordResolutionCasConsumer.java	96
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/types/TypeSystem.xml	170
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/PcsClassifierAnnotator_libsvm.xml	116
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml	52
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/SentenceAdjuster.xml	91
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml	98
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/ArtificialSentenceAnnotator.xml	74
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/ProductionPostSentenceAggregate_step1.xml	46
ctakes-smoking-status/src/main/resources/org/apache/ctakes/smoking/status/analysis_engine/KuRuleBasedClassifierAnnotator.xml	86
ctakes-smoking-status/desc/cas_consumer/RecordResolutionCasConsumer.xml	83
ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_flatfile.xml	63
ctakes-smoking-status/desc/collection_processing_engine/Sample_SmokingStatus_output_cda.xml	69
ctakes-smoking-status/desc/analysis_engine/ResolutionAnnotator.xml	59
ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE.xml	50
ctakes-smoking-status/desc/analysis_engine/PcsClassifierAnnotator_libsvm.xml	116
ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml	53
ctakes-smoking-status/desc/analysis_engine/SentenceAdjuster.xml	91
ctakes-smoking-status/desc/analysis_engine/ExternalBaseAggregateTAE_CDA.xml	72
ctakes-smoking-status/desc/analysis_engine/NonsmokerDictionaryLookupAnnotator.xml	82
ctakes-smoking-status/desc/analysis_engine/SmokingStatusDictionaryLookupAnnotator.xml	98
ctakes-smoking-status/desc/analysis_engine/ArtificialSentenceAnnotator.xml	74
ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml	46
ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml	68
ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml	50
ctakes-smoking-status/desc/analysis_engine/Sentence.xml	26
ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml	86
ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml	145
ctakes-context-tokenizer/src/main/java/org/apache/ctakes/context/tokenizer/ae/ContextDependentTokenizerAnnotator.java	152
ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml	35
ctakes-context-tokenizer/desc/analysis_engine/AggregateAE.xml	45
ctakes-context-tokenizer/desc/analysis_engine/TestTAE.xml	44
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan/MultiTextSpan.java	56
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan/TextSpan.java	6
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/textspan/DefaultTextSpan.java	39
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/AbstractJCasTermAnnotator.java	186
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DictionaryLookupFactory.java	45
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/DefaultJCasTermAnnotator.java	77
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/OverlapJCasTermAnnotator.java	169
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/JCasTermAnnotator.java	26
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/ae/WindowProcessor.java	12
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/WsdTermConsumer.java	1
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/SemanticCleanupTermConsumer.java	99
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/UmlsConceptCreator.java	9
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/TermConsumer.java	19
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/PrecisionTermConsumer.java	93
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/AbstractTermConsumer.java	63
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultTermConsumer.java	180
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/consumer/DefaultUmlsConceptCreator.java	51
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/TuiCodeUtil.java	43
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/DefaultDictionarySpec.java	114
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/CuiCodeUtil.java	86
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/tool/SemanticTableComparator.java	226
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/tool/DictionaryCuiCounter.java	60
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/tool/DictionaryComparator.java	69
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/FastLookupToken.java	47
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/LookupUtil.java	25
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java	206
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java	103
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/SemanticUtil.java	10
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/DictionarySpec.java	15
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concurrent/ThreadSafeFastLookup.java	66
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/relation/CuiRelationsJdbc.java	1
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/term/SpannedRareWordTerm.java	36
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/term/RareWordTerm.java	64
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionary.java	9
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/UmlsJdbcRareWordDictionary.java	34
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordTermMapCreator.java	286
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java	82
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/RareWordDictionaryWrapper.java	1
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/DictionaryDescriptorParser.java	212
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/JdbcRareWordDictionary.java	88
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/AbstractRareWordDictionary.java	25
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/MemRareWordDictionary.java	16
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/UmlsJdbcConceptFactory.java	33
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/MemConceptFactory.java	20
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/JdbcConceptFactory.java	250
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/Concept.java	13
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/AbstractConceptFactory.java	25
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/DefaultConcept.java	75
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java	119
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/ConceptFactory.java	8
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupEngine.java	129
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/ContiguousLookupEngine.java	158
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/LookupToken.java	68
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/DiscoveredTerm.java	42
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/lookup/CandidateTerm.java	165
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/ae/CasedAnnotationFinder.java	334
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/table/column/Synonym.java	21
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/table/column/CodeType.java	17
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/table/column/SchemaCode.java	12
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AlikeSubsumingAnnotationCreator.java	66
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/SemanticSubsumingAnnotationCreator.java	106
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AnnotationCreatorUtil.java	187
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/AnnotationCreator.java	15
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/SubsumptionUtil.java	82
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/annotation/NonSubsumingAnnotationCreator.java	25
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/textspan/MagicTextSpan.java	28
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/textspan/DiscontiguousTextSpan.java	87
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/textspan/ContiguousTextSpan.java	30
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/bsv/StringArrayCreator.java	16
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/bsv/BsvFileParser.java	33
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/bsv/BsvObjectCreator.java	22
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/jdbc/JdbcUtil.java	64
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTermMapper.java	104
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/util/tokenize/TokenizedTerm.java	199
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/wsd/WsdUtil.java	43
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/CasedDictionary.java	8
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/InMemoryDictionary.java	39
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/JdbcDictionary.java	143
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvListDictionary.java	52
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/DictionaryStore.java	26
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/dictionary/BsvDictionary.java	56
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/JdbcEncoder.java	132
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/TermEncoding.java	26
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvListEncoder.java	47
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/CodeSchema.java	38
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/EncoderStore.java	26
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/TermEncoder.java	10
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/InMemoryEncoder.java	20
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/cased/encoder/BsvEncoder.java	48
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/tinyDict.bsv	42
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/custom_cui_bsv.bsv	20
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/custom_cui_tui_bsv.bsv	22
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/CustomCuiBsv.xml	25
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/custom_tui_bsv.bsv	10
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/CustomCuiTuiBsv.xml	35
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/custom_mixed_bsv.bsv	23
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/tinyDictSpec.xml	36
ctakes-dictionary-lookup-fast/src/user/resources/org/apache/ctakes/dictionary/lookup/fast/bsv/CustomCuiTui2Bsv.xml	35
ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsOverlapLookupAnnotator.xml	119
ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml	93
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/assertion/CreateAssertionLuceneIndexFromDelimitedFile.java	278
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/assertion/package-info.java	1
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/TruncateCollectionFilterImpl.java	24
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/SetValuePostLookupFilterImpl.java	107
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PreLookupFilter.java	5
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/StringPreLookupFilterImpl.java	14
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/FilterException.java	7
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/CollectionFilter.java	7
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilterGroupImpl.java	47
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/PostLookupFilter.java	6
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/filter/MetaDataPostLookupFilterImpl.java	49
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/MetaDataHitConst.java	12
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/GenericMetaDataHitImpl.java	25
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/MetaDataHit.java	10
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/AbstractBaseMetaDataHit.java	26
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java	92
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/AssertionCuePhraseConsumerImpl.java	126
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java	170
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedDbConsumerImpl.java	50
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupInitializer.java	22
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DirectLookupInitializerImpl.java	98
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/FirstTokenPermLookupInitializerImpl.java	184
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DebugConsumerImpl.java	37
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupSpec.java	25
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java	92
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/DictionaryLookupAnnotator.java	155
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedUmlsDictionaryLookupAnnotator.java	68
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupConsumer.java	9
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/BaseLookupConsumerImpl.java	41
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/ThreadedDictionaryLookupAnnotator.java	187
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilities.java	236
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java	120
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupParseUtilitiesRefactor.java	216
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/LookupAnnotationToJCasAdapter.java	37
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedLuceneConsumerImpl.java	69
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupTokenComparator.java	23
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupToken.java	4
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotationToTokAdapter.java	38
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupHit.java	64
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/vo/LookupAnnotation.java	10
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/BaseDictionaryImpl.java	21
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/AbstractBaseDictionary.java	14
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDocumentMetaDataHitImpl.java	36
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/lucene/LuceneDictionaryImpl.java	86
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/PermutationUtil.java	94
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java	343
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/LookupAlgorithm.java	12
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/DirectPassThroughImpl.java	58
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/Dictionary.java	8
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/MetaDataHitComparator.java	41
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/jdbc/JdbcDictionaryImpl.java	93
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/BaseMetaDataHitImpl.java	27
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/DictionaryException.java	7
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/DictionaryEngine.java	89
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/VariantPhraseBuilderImpl.java	56
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/phrasebuilder/PhraseBuilder.java	7
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraint.java	5
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRowMetaDataHitImpl.java	24
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableRow.java	20
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/FieldConstraintImpl.java	65
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableFactory.java	81
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTable.java	45
ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/strtable/StringTableDictionaryImpl.java	33
ctakes-dictionary-lookup/src/main/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java	122
ctakes-dictionary-lookup/src/main/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexFromDelimitedFile.java	305
ctakes-dictionary-lookup/src/main/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java	48
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_csv_sample.xml	56
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_example_using_CSV.xml	27
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionCuePhraseDictionaryLookupAnnotator.xml	117
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/data/output/text1.txt.included.used.tag-dictionary.xml	47
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/data/output/text1.txt.included.xml	46
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc.xml	72
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml	74
ctakes-dictionary-lookup/src/main/resources/org/apache/ctakes/dictionary/lookup/AssertionLookupDesc.xml	32
ctakes-dictionary-lookup/desc/lookup/LookupDesc_csv_sample.xml	56
ctakes-dictionary-lookup/desc/lookup/LookupDesc_example_using_CSV.xml	27
ctakes-dictionary-lookup/desc/lookup/LookupDesc.xml	72
ctakes-dictionary-lookup/desc/lookup/LookupDesc_Db.xml	74
ctakes-dictionary-lookup/desc/lookup/AssertionLookupDesc.xml	32
ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorDB.xml	249
ctakes-dictionary-lookup/desc/analysis_engine/AssertionCuePhraseDictionaryLookupAnnotator.xml	117
ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotator.xml	243
ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorCSV.xml	194
ctakes-dictionary-lookup/desc/analysis_engine/TestAggregateTAE.xml	44
ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml	354
ctakes-dictionary-lookup/desc/analysis_engine/AggregateAE.xml	45
ctakes-regression-test/desc/collection_processing_engine/RegressionPipelineCPETest.xml	58
ctakes-regression-test/desc/analysis_engine/RegressionPipelineAggregateTest.xml	192
ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/ThreadSafeLvg.java	35
ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgBaseTokenAnnotator.java	323
ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgAnnotator.java	477
ctakes-lvg/src/main/java/org/apache/ctakes/lvg/ae/LvgSingleton.java	61
ctakes-lvg/src/main/java/org/apache/ctakes/lvg/resource/LvgCmdApiResourceImpl.java	83
ctakes-lvg/src/main/java/org/apache/ctakes/lvg/resource/LvgCmdApiResource.java	7
ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml	240
ctakes-lvg/desc/analysis_engine/AggregateAE.xml	44
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/data/PrintMimicMarkables.java	93
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/KernelMatrixCompositor.java	63
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/RowFillerThread.java	43
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/LinearKernelMatrixWriter.java	122
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/treekernel/training/TreeKernelTrainer.java	118
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientScoringWriter.java	257
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MarkableSalienceAnnotator.java	89
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableExpander.java	137
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkablePairGenerator.java	190
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqMarkableCreator.java	96
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java	214
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PersonChainAnnotator.java	165
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java	139
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java	25
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java	24
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStackFeaturesExtractor.java	43
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterDistSemExtractor.java	103
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterDistanceFeaturesExtractor.java	36
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterMentionFeaturesExtractor.java	57
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterUMLSFeatureExtractor.java	160
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterDepHeadExtractor.java	63
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSemTypeDepPrefsFeatureExtractor.java	57
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSalienceFeaturesExtractor.java	38
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAttributeVectorExtractor.java	16
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAgreementFeaturesExtractor.java	83
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterSectionFeaturesExtractor.java	78
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStringFeaturesExtractor.java	89
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAttributeFeaturesExtractor.java	80
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java	48
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java	108
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java	44
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java	55
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/SalienceFeatureExtractor.java	18
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/AttributeFeatureExtractor.java	50
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java	49
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/DistSemFeatureExtractor.java	76
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java	114
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java	43
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java	115
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainScoringOutput.java	279
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/DeterministicMarkableAnnotator.java	188
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterCoreferenceAnnotator.java	446
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/ClusterMentionPairer_ImplBase.java	67
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/SectionHeaderPairer.java	53
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/CrossDocumentPairer_ImplBase.java	12
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/ClusterPairer.java	42
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/PreviousDocumentPairer.java	29
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/SentenceDistancePairer.java	51
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/HeadwordPairer.java	37
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/cluster/ExactStringPairer.java	39
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/pairing/AnnotationPairer.java	7
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CoreferenceChainCoNLLWriter.java	191
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/ThymeAnaforaCrossDocCorefXmlReader.java	406
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MentionClusterRankingCoreferenceAnnotator.java	471
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java	134
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/EventCoreferenceAnnotator.java	654
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientMentionClusterCoreferencer.java	45
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ParentPtrTree.java	58
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ClusterUtils.java	29
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SyntaxAttributeCalculator.java	350
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThymeCasOrderer.java	38
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableDepUtils.java	22
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationCounter.java	20
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/HobbsTreeNavigator.java	137
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThreadDelegator.java	5
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/CorefConsts.java	11
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnaphoricityAttributeCalculator.java	157
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ClusterMentionFetcher.java	107
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/GoldStandardLabeler.java	119
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmUtils.java	15
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotOffsetComparator.java	9
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AbstractClassifier.java	29
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java	162
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AttributeCalculator.java	114
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/EditDistance.java	41
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java	405
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableTreeUtils.java	67
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableUtilities.java	33
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/TextMatch.java	17
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/FeatureVector.java	90
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java	173
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableCacheRelationExtractor.java	7
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/FSIteratorToList.java	15
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMentionClusterCoreferencer.java	96
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/concurrent/ThreadSafeMarkableSalienceAnnotator.java	84
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfMarkableSalience.java	188
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java	828
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanOffsetComparator.java	22
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/CEAFType.java	2
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/KAlphaType.java	2
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/Span.java	83
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/SpanAlignment.java	67
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/PairType.java	2
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/MatType.java	7
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/eval/helpers/B3Type.java	2
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/extractors/ContinuousBag.java	83
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/extractors/ContinuousTextExtractor.java	47
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/factory/CoreferenceAnnotatorFactory.java	31
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/ODIEVectorFileWriter.java	283
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/cc/PreprocessAndWriteXmi.java	89
ctakes-coreference/src/main/scripts/perl/reorganize_thyme.pl	29
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/CollectionRelation.xml	26
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/BooleanLabeledFS.xml	26
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/CoreferenceRelation.xml	36
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/DiscoveryTechnique.xml	26
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Relation.xml	40
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Pair.xml	26
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/VecInst.xml	68
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/TypeSystem.xml	90
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/BinaryRelation.xml	30
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/PredicateArgRelation.xml	17
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/Properties.xml	26
ctakes-coreference/src/main/resources/org/apache/ctakes/coreference/types/RelationArgument.xml	36
ctakes-coreference/desc/MipacqSvmVectorCreatorAggregate.xml	46
ctakes-coreference/desc/MipacqSvmChainCreator.xml	149
ctakes-coreference/desc/cas_consumer/ODIEVectorFileWriterCasConsumer.xml	146
ctakes-coreference/desc/cas_consumer/EvaluationConsumer.xml	152
ctakes-coreference/desc/MipacqMarkablePairGenerator.xml	55
ctakes-coreference/desc/MipacqSvmCoreferenceResolverAggregate.xml	50
ctakes-coreference/desc/MipacqMarkableExpander.xml	35
ctakes-coreference/desc/collection_processing_engine/SystemScoringCPE.xml	70
ctakes-coreference/desc/collection_processing_engine/SectionModelCPE.xml	52
ctakes-coreference/desc/collection_processing_engine/ODIESvmModelCPE.xml	52
ctakes-coreference/desc/collection_processing_engine/Coref-resolver_CPE.xml	58
ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator.xml	134
ctakes-coreference/desc/analysis_engine/CorefProcessor.xml	130
ctakes-coreference/desc/analysis_engine/MarkablePairPlaintextDBProcessor.xml	149
ctakes-coreference/desc/analysis_engine/CorefUMLSProcessor.xml	138
ctakes-coreference/desc/analysis_engine/ODIESvmVectorCreator_wSection.xml	204
ctakes-coreference/desc/MipacqMarkableCreator.xml	111
ctakes-coreference/desc/MipacqSvmVectorCreator.xml	75
ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java	136
ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/RunZoner.java	126
ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateAssertionZonerDescriptors.java	83
ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/CreateZonerDescriptor.java	40
ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.06162011.xml	523
ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.xml	831
ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/mayo_sections.xml	317
ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex_ctakes5.xml	848
ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.04162012.xml	558
ctakes-assertion-zoner/src/main/resources/org/mitre/medfacts/uima/section_regex.out.xml	1
ctakes-assertion-zoner/src/main/resources/org/apache/ctakes/assertion/zoner/types/TypeSystem.xml	45
ctakes-assertion-zoner/metadata/install.xml	27
ctakes-assertion-zoner/desc/cpe/zonermeds4.xml	58
ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__both_regular_and_mayo.xml	4861
ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__normal.xml	2417
ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__mayo.xml	2417
ctakes-assertion-zoner/desc/ZonerDescriptorStyleMap.xml	3
ctakes-assertion-zoner/desc/ZonerDescriptor.xml	92
ctakes-utils/src/main/java/org/apache/ctakes/utils/kernel/LinearKernel.java	9
ctakes-utils/src/main/java/org/apache/ctakes/utils/kernel/RBFKernel.java	30
ctakes-utils/src/main/java/org/apache/ctakes/utils/kernel/Kernel.java	24
ctakes-utils/src/main/java/org/apache/ctakes/utils/kernel/PolyKernel.java	44
ctakes-utils/src/main/java/org/apache/ctakes/utils/env/EnvironmentVariable.java	29
ctakes-utils/src/main/java/org/apache/ctakes/utils/distsem/WordEmbeddings.java	97
ctakes-utils/src/main/java/org/apache/ctakes/utils/distsem/WordVector.java	28
ctakes-utils/src/main/java/org/apache/ctakes/utils/distsem/DistanceMetrics.java	45
ctakes-utils/src/main/java/org/apache/ctakes/utils/distsem/WordVectorReader.java	32
ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterMap.java	31
ctakes-utils/src/main/java/org/apache/ctakes/utils/struct/CounterTreeMap.java	28
ctakes-utils/src/main/java/org/apache/ctakes/utils/tree/SimpleTree.java	121
ctakes-utils/src/main/java/org/apache/ctakes/utils/tree/FragmentUtils.java	32
ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/TestCosineSimilarity.java	39
ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateMath.java	33
ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java	212
ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/ApproximateSimilarity.java	12
ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/SearchResult.java	12
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/Const.java	39
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/XcasAnnotation.java	129
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/XcasFile.java	72
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/XcasProcessor.java	137
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/XcasDiff.java	131
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/ConvertAndCompare.java	64
ctakes-utils/src/main/java/org/apache/ctakes/utils/xcas_comparison/Compare.java	23
ctakes-utils/src/user/resources/org/apache/ctakes/utils/scripts/knowtatorTools/cTakesNeToKnowtatorAnnotation (for Apache UIMA and cTAKES).launch	14
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel/TreeExtractor.java	150
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/treekernel/TreeKernel.java	91
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java	74
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ParserEvaluationAnnotator.java	91
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/GenerateDescriptors.java	34
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/AnnotationTreeUtils.java	240
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/CommandLineParserUtil.java	41
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/util/TreeUtils.java	300
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/uima/co/ParserTreeWriterConsumer.java	57
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ParserWrapper.java	8
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/concurrent/ThreadSafeConstituencyParser.java	67
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java	81
ctakes-constituency-parser/src/main/resources/org/apache/ctakes/constituency/parser/types/LabeledTree.xml	26
ctakes-constituency-parser/src/user/resources/org/apache/ctakes/constituency/parser/scripts/groovy/parser.groovy	73
ctakes-constituency-parser/desc/cas_consumer/ParseTreeWriterConsumer.xml	36
ctakes-constituency-parser/desc/ConstituencyParserAnnotator.xml	48
ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml	66
ctakes-constituency-parser/desc/analysis_engine/AggregateParsingProcessor.xml	74
ctakes-constituency-parser/desc/analysis_engine/ParserEvaluatorAnnotator.xml	50
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPSemanticRoleLabelerAE.java	230
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/XMIReader.java	62
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/util/WriteClearNLPDescriptors.java	105
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java	169
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/SRLSharedPredictionModel.java	16
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/SRLSharedRoleModel.java	16
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/SRLSharedModel.java	30
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/DependencySharedModel.java	44
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/LemmatizerSharedModel.java	43
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/shared/SRLSharedParserModel.java	16
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/Delim.java	14
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyRegex.java	212
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/AnnotationDepUtils.java	261
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyPath.java	122
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/SRLUtility.java	18
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/ClearDependencyUtility.java	47
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java	282
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/cr/DependencyFileCollectionReader.java	284
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpDepParser.java	77
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/concurrent/ThreadSafeClearNlpSemRoleLabeler.java	78
ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/DependencyNodeWriter.java	110
ctakes-dependency-parser/desc/cas_consumer/DependencyNodeWriter.xml	72
ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerPosLemTestCPE.xml	76
ctakes-dependency-parser/desc/collection_processing_engine/ClearNLPTestCPE.xml	104
ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerPosTestCPE.xml	90
ctakes-dependency-parser/desc/collection_processing_engine/ClearTrainerLemTestCPE.xml	78
ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserTokenizedInfPosAggregate.xml	454
ctakes-dependency-parser/desc/analysis_engine/ClearNLPSRLPlaintextAggregate.xml	633
ctakes-dependency-parser/desc/analysis_engine/LvgBaseTokenAnnotator.xml	239
ctakes-dependency-parser/desc/analysis_engine/ClearNLPSRLTokenizedInfPosAggregate.xml	516
ctakes-dependency-parser/desc/analysis_engine/PosAssigner.xml	33
ctakes-dependency-parser/desc/analysis_engine/LemAssigner.xml	33
ctakes-dependency-parser/desc/analysis_engine/ClearNLPSRLTokenizedAggregate.xml	439
ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml	73
ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserTokenizedAggregate.xml	377
ctakes-dependency-parser/desc/analysis_engine/ClearNLPSemanticRoleLabelerAE.xml	60
ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserPlaintextAggregate.xml	641
ctakes-dependency-parser/desc/collection_reader/DependencyFileCollectionReader.xml	79
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionAnnotation.java	14
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java	5
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java	12
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java	17
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ConceptType.java	6
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/BatchRunner.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/JarafeMEDecoder.java	10
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java	9
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java	11
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/LineTokenToCharacterOffsetConverter.java	16
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java	22
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java	46
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverter.java	3
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java	5
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/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/UncertaintyCleartkAnalysisEngineWindowed.java	94
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/LastCoveredContext.java	19
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/feature/WindowedContextFeature.java	22
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/WindowedGenericFeaturesExtractor.java	31
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/AbstractTreeFragmentFeatureExtractor1.java	48
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/cleartk/windowed/context/feature/extractor/WindowedDependencyWordsFragmentExtractor.java	40
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/WindowedContextWordWindowExtractor.java	94
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/WindowedBag.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/classifier/WindowedHistoryAttributeClassifier.java	218
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/ConditionalCleartkAnalysisEngineWindowed.java	71
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/GenericCleartkAnalysisEngineWindowed.java	78
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/AlternateCuePhraseAnnotator.java	122
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/AssertionCleartkAnalysisEngine.java	354
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/AssertionSampleFeatureGenerator.java	27
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/ConditionalCleartkAnalysisEngine.java	72
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/SRLFeatureExtractor.java	83
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/AssertionAboveLeftTreeExtractor.java	32
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/UncertaintyFeatureExtractor.java	19
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/AboveLeftFragmentExtractor.java	27
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/CueWordTest2.java	126
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/CueWordTest.java	101
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/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/DependencyPathRegexpFeatureExtractor.java	49
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/UncertaintyCleartkAnalysisEngine.java	90
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/PolarityFedaCleartkAnalysisEngine.java	91
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/SubjectCleartkAnalysisEngine.java	77
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConvertXMIAssertionsToi2b2Format.java	70
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/CharacterOffsetToLineTokenConverterCtakesImpl.java	192
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/medfacts/i2b2/api/ConstraintConstructor.java	50
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/Converti2b2AnnotationsToCTAKES.java	152
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptLookup.java	146
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngineFit.java	174
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/ConceptConverterAnalysisEngine.java	69
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/CasIndexer.java	93
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/AssertionAnalysisEngine.java	281
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateDependencyRepresentation.java	106
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/GoldEntityAndAttributeReaderPipelineForSeedCorpus.java	303
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GoldEntityAndAttributeReaderPipeline.java	25
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/SharpCorpusSplit.java	42
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/GenerateTreeRepresentation.java	116
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java	64
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/WriteMultipleDatasets.java	194
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationManualDepContextAnalyzer.java	47
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/SemanticClasses.java	22
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionDepUtils.java	119
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java	146
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/XmiCollectionReaderCtakes.java	68
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/XMLReader.java	138
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/I2B2Challenge2010CollectionReader.java	152
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/RelationInfo.java	52
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExAnnotation.java	88
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/Span.java	21
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java	1156
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/GenericAttributeAnalysisEngine.java	31
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/generic/GenericAttributeClassifier.java	118
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/SubjectAttributeAnalysisEngine.java	25
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java	225
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/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/selection/MutualInformationFeatureSelection.java	192
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/subject/SubjectAttributeClassifier.java	188
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/train/PolarityDomainAdaptationTests.java	94
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/JustJudgeStep.java	17
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityDomainAdaptationTrain.java	62
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TestAttributeModels.java	32
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateChi2GridSearch.java	30
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/CrossValidateAttributeModels.java	24
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java	57
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java	89
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/TrainAttributeModels.java	24
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/cc/JudgeAttributeInstances.java	349
ctakes-assertion/src/main/python/negation_rest.py	113
ctakes-assertion/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml	53
ctakes-assertion/metadata/install.xml	27
ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml	56
ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml	136
ctakes-assertion/desc/analysis_engine/AttributeDiscoveryPreprocessor.xml	162
ctakes-assertion/desc/analysis_engine/UncertaintyCleartkAnalysisEngine.xml	136
ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml	136
ctakes-assertion/desc/analysis_engine/GenericCleartkAnalysisEngine.xml	130
ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml	130
ctakes-assertion/desc/SubjectAttributeAnalysisEngine.xml	39
ctakes-assertion/desc/GenericAttributeAnalysisEngine.xml	39
ctakes-assertion/desc/assertionAnalysisEngine.xml	128
ctakes-assertion/desc/conceptConverterAnalysisEngine.xml	113