Path	Lines of Code
ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__both_regular_and_mayo.xml	4861
ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__mayo.xml	2417
ctakes-assertion-zoner/desc/analysis_engine/assertion_zoner__normal.xml	2417
ctakes-assertion-zoner/src/main/java/org/mitre/medfacts/uima/ZoneAnnotator.java	136
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/history/HistoryAttributeClassifier.java	225
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cc/JudgeAttributeInstances.java	349
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/GoldEntityAndAttributeReader.java	190
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/NegExCorpusReader.java	146
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AnnotationStatisticsCompact.java	317
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas.java	202
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AlternateCuePhraseAnnotator.java	122
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java	354
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/TrainAssertionModel.java	239
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java	90
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/TreeFragmentFeatureExtractor.java	48
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/UncertaintyCleartkAnalysisEngineWindowed.java	94
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java	378
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/pipelines/RunJudgeAttributeInstances.java	70
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/Annotation.java	9
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ApiConcept.java	22
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/AssertionDecoderConfiguration.java	12
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/CharacterOffsetToLineTokenConverterDefaultImpl.java	8
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineAndTokenPosition.java	17
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/LineTokenToCharacterOffsetConverter.java	16
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/PartOfSpeechTagger.java	5
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/ScopeParser.java	5
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/SingleDocumentProcessor.java	46
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/stub/StringHandling.java	11
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/JustJudgeStep.java	17
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java	64
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/NegationDepRegex.java	321
ctakes-chunker/src/main/java/org/apache/ctakes/chunker/ae/adjuster/ChunkAdjuster.java	140
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java	81
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/util/AnnotationTreeUtils.java	240
ctakes-constituency-parser/src/user/resources/org/apache/ctakes/constituency/parser/scripts/groovy/parser.groovy	73
ctakes-core/desc/analysis_engine/FilterAnnotator.xml	29
ctakes-core/desc/analysis_engine/SentenceDetectorAnnotatorBIO.xml	2572
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java	150
ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java	52
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java	222
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java	235
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java	120
ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java	46
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/HtmlTextWriter.java	1223
ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java	111
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/property/plaintext/PropertyTextWriter.java	210
ctakes-core/src/main/java/org/apache/ctakes/core/ci/HyphenTextModifierImpl.java	182
ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionCyclicalReads.java	81
ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java	160
ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java	260
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/nlp/tokenizer/TokenizerPTB.java	781
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java	245
ctakes-core/src/main/java/org/apache/ctakes/core/sentence/EndOfSentenceScannerImpl.java	39
ctakes-core/src/main/java/org/apache/ctakes/core/sentence/SentenceDetectorCtakes.java	196
ctakes-core/src/main/java/org/apache/ctakes/core/util/FSUtil.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/IdentifiedAnnotationBuilder.java	226
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-coreference/src/main/java/org/apache/ctakes/coreference/ae/CopyCoreferenceRelations.java	134
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/MentionClusterRankingCoreferenceAnnotator.java	471
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/MipacqSvmChainCreator.java	214
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PatientScoringWriter.java	257
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/ae/PersonChainAnnotator.java	165
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/MentionClusterSectionFeaturesExtractor.java	78
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/java/org/apache/ctakes/coreference/eval/EvaluationOfEventCoreference.java	828
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/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/util/AnaphoricityAttributeCalculator.java	157
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationCounter.java	20
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/HobbsTreeNavigator.java	137
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/MarkableTreeUtils.java	67
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java	405
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/SvmVectorCreator.java	173
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/TextMatch.java	17
ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/ThymeCasOrderer.java	38
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/lookup/ContiguousLookupEngine.java	158
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/util/tokenize/TokenizedTerm.java	199
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/OverlapJCasTermAnnotator.java	169
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/consumer/WsdTermConsumer.java	1
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/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/util/DefaultDictionarySpec.java	114
ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/UmlsUserApprover.java	206
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/BaseMetaDataHitImpl.java	27
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/BaseLookupConsumerImpl.java	41
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/LookupParseUtilities.java	236
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/NamedEntityLookupConsumerImpl.java	92
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/ThreadedDictionaryLookupAnnotator.java	187
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/UmlsToSnomedConsumerImpl.java	170
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/lucene/LuceneDictionaryImpl.java	86
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/SinglePackageFabricator.java	34
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/Option.java	139
ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/WizardController.java	119
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/DrugMention.java	1156
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/impl/NegContextInitializerImpl.java	95
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/machines/util/StatusIndicatorFSM.java	254
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/SubSectionIndicator.java	19
ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/states/util/IndentStartState.java	16
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/cr/BundleParser.java	141
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java	157
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/CompositionCreator.java	32
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/IdentifiedAnnotationParser.java	83
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java	202
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/umls/UmlsParser.java	171
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/util/JdbcUtil.java	72
ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/util/TextTokenizer.java	165
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel.java	240
ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/MainPanel2.java	503
ctakes-gui/src/main/java/org/apache/ctakes/gui/util/WikiPipeLister.java	800
ctakes-mastif-zoner/src/main/java/org/mitre/medfacts/zoner/ZonerCli.java	1298
ctakes-ne-contexts/src/main/java/org/apache/ctakes/necontexts/status/StatusContextHitConsumer.java	24
ctakes-pbj/src/main/java/org/apache/ctakes/pbj/ae/PbjSender.java	185
ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/types/TypeSystem.xml	2823
ctakes-preprocessor/src/main/java/org/apache/ctakes/preprocessor/ae/CdaCasInitializer.java	137
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/features/NamedEntityFeaturesExtractor.java	52
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/pipelines/RelationExtractorConsumer.java	58
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/TreeFeatureConsumer.java	181
ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/ae/SESentenceFeatureAnnotator.java	193
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/Const.java	13
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/PcsClassifier.java	207
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/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/cc/RecordResolutionCasConsumer.java	96
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/patientLevel/PatientLevelSmokingStatus.java	213
ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java	241
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java	51
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocumentCreationTimeAnnotator.java	26
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeCNNAnnotator.java	267
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeSelfRelationAnnotator.java	172
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java	35
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/NEPredicateEventAnnotator.java	67
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEQAAnaforaXMLReader.java	300
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMETreebankReader.java	250
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/DependencyParseUtils.java	103
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/UmlsFeatureExtractor.java	57
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/selection/ZscoreNormalizationExtractor.java	141
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/duration/EventDurationDistribution.java	204
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfAnnotationSpans_ImplBase.java	198
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java	166
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java	566
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfNEPredicateEventSpans.java	70
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfSelfEventTimeRelations.java	652
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java	1083
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/keras/KerasStringOutcomeDataWriter.java	20
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/EventTimePosBasedAnnotator.java	160
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/EventTimeTokenAndBIOBasedAnnotator.java	254
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/EventTimeTokenBasedAnnotator.java	330
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/WindowBasedAnnotator.java	250
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/AnnotationIdCollection.java	76
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TLinkTypeArray2.java	275
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/TlinkType.java	170
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/lstm_classify.py	47
ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml	2823
ctakes-utils/src/main/java/org/apache/ctakes/utils/env/EnvironmentVariable.java	29
ctakes-utils/src/main/java/org/apache/ctakes/utils/kernel/RBFKernel.java	30
ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java	212
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-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java	40
ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml	254
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/DBCollectionReader.java	220
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/lookup/ae/FirstTokenPermLookupInitializerImpl.java	218
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/AppMain.java	44
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/PropFile.java	29
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/Loader.java	15
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/loader/XmlLoader.java	89
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/DomUtil.java	81
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/SchemaUtil.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHelper.java	33
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java	158
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BaseSparseDataFormatter.java	135
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java	386
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityServiceImpl.java	648
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/pagerank/PageRankServiceImpl.java	315
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ImportWekaResults.java	128