This is an automated email from the ASF dual-hosted git repository.
seanfinan pushed a change to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
from afe638a Remove nashorn @Immutable. Required for jenkins build.
add def3dea More changes for jenkins jdk11, mostly jaxb. Optimize imports
accounts for most of the checkin.
No new revisions were added by this update.
Summary of changes:
.../uima/CreateAssertionZonerDescriptors.java | 10 +--
.../mitre/medfacts/uima/CreateZonerDescriptor.java | 10 +--
.../java/org/mitre/medfacts/uima/RunZoner.java | 14 ++--
.../org/mitre/medfacts/uima/ZoneAnnotator.java | 23 +++---
.../attributes/GenericAttributeAnalysisEngine.java | 9 +--
.../attributes/SubjectAttributeAnalysisEngine.java | 9 +--
.../features/GenericFeaturesExtractor.java | 8 +-
.../features/HistoryFeaturesExtractor.java | 8 +-
.../features/SubjectFeaturesExtractor.java | 8 +-
.../features/selection/Chi2FeatureSelection.java | 19 +----
.../features/selection/FeatureSelection.java | 13 ++--
.../MutualInformationFeatureSelection.java | 28 ++-----
.../generic/GenericAttributeClassifier.java | 26 ++-----
.../subject/SubjectAttributeClassifier.java | 13 ++--
.../assertion/cr/MiPACQKnowtatorXMLReader.java | 75 +++---------------
.../ctakes/assertion/cr/NegExAnnotation.java | 4 +-
.../apache/ctakes/assertion/cr/RelationInfo.java | 4 +-
.../org/apache/ctakes/assertion/cr/XMLReader.java | 8 +-
.../eval/AnnotationStatisticsCompact.java | 22 ++----
.../ctakes/assertion/medfacts/CasIndexer.java | 15 ++--
.../ctakes/assertion/medfacts/ConceptLookup.java | 11 ++-
.../medfacts/ConvertXMIAssertionsToi2b2Format.java | 39 ++++------
.../medfacts/Converti2b2AnnotationsToCTAKES.java | 41 ++++------
.../medfacts/cleartk/AssertionComponents.java | 2 +-
.../cleartk/AssertionFeatureAwareDataWriter.java | 19 +----
.../cleartk/CreateAssertionDescriptor.java | 10 +--
.../cleartk/GenericCleartkAnalysisEngine.java | 8 +-
.../cleartk/HistoryCleartkAnalysisEngine.java | 8 +-
.../cleartk/PolarityCleartkAnalysisEngine.java | 16 ++--
.../cleartk/PolarityFedaCleartkAnalysisEngine.java | 8 +-
.../cleartk/SubjectCleartkAnalysisEngine.java | 6 +-
.../medfacts/cleartk/TrainAssertionModel.java | 13 +---
.../cleartk/UncertaintyCleartkAnalysisEngine.java | 23 ++----
.../extractors/AboveLeftFragmentExtractor.java | 6 +-
.../extractors/AboveRightFragmentExtractor.java | 11 ++-
.../AssertionAboveLeftTreeExtractor.java | 10 +--
.../AssertionDependencyTreeExtractor.java | 5 +-
.../extractors/BrownClusterFeatureFunction.java | 16 ++--
.../extractors/ContextWordWindowExtractor.java | 12 +--
.../medfacts/cleartk/extractors/CueWordTest.java | 12 +--
.../medfacts/cleartk/extractors/CueWordTest2.java | 12 +--
.../DependencyPathRegexpFeatureExtractor.java | 15 ++--
.../DependencyWordsFragmentExtractor.java | 6 +-
.../ExtractorListFeatureFunctionConverter.java | 6 +-
.../cleartk/extractors/FedaFeatureFunction.java | 6 +-
.../NegationDependencyFeatureExtractor.java | 11 +--
.../cleartk/extractors/SRLFeatureExtractor.java | 6 +-
.../cleartk/extractors/SurroundingExtractor.java | 10 +--
.../extractors/TreeFragmentFeatureExtractor.java | 12 +--
.../extractors/UncertaintyFeatureExtractor.java | 7 +-
...racterOffsetToLineTokenConverterCtakesImpl.java | 21 ++---
.../medfacts/i2b2/api/ConstraintConstructor.java | 11 +--
.../i2b2/api/SingleDocumentProcessorCtakes.java | 38 ++-------
.../GoldEntityAndAttributeReaderPipeline.java | 6 +-
...ityAndAttributeReaderPipelineForSeedCorpus.java | 11 ++-
.../pipelines/RunJudgeAttributeInstances.java | 10 +--
.../assertion/stub/AssertionFileProcessor.java | 4 +-
.../apache/ctakes/assertion/stub/BatchRunner.java | 4 +-
...acterOffsetToLineTokenConverterDefaultImpl.java | 2 -
.../ctakes/assertion/stub/JarafeMEDecoder.java | 4 +-
.../assertion/stub/SingleDocumentProcessor.java | 6 +-
.../ctakes/assertion/stub/StringHandling.java | 4 +-
.../train/CrossValidateAttributeModels.java | 4 +-
.../train/CrossValidateChi2GridSearch.java | 4 +-
.../ctakes/assertion/train/JustJudgeStep.java | 4 +-
.../assertion/train/PolarityCotrainingTests.java | 6 +-
.../assertion/train/PolarityCotrainingTrain.java | 6 +-
.../train/PolarityDomainAdaptationTests.java | 8 +-
.../train/PolarityDomainAdaptationTrain.java | 10 +--
.../train/ReadAndPreprocessForAttributeModels.java | 6 +-
.../train/ReadPreprocessTrainTestJudge.java | 4 +-
.../assertion/train/TestAttributeModels.java | 6 +-
.../assertion/train/TrainAttributeModels.java | 5 +-
.../ctakes/assertion/util/AssertionConst.java | 3 -
.../ctakes/assertion/util/AssertionDepUtils.java | 12 +--
.../ctakes/assertion/util/AssertionTreeUtils.java | 10 +--
.../ctakes/assertion/util/NegationDepRegex.java | 20 ++---
.../util/NegationManualDepContextAnalyzer.java | 11 +--
.../assertion/util/WriteMultipleDatasets.java | 30 ++------
ctakes-assertion/src/main/python/negation_rest.py | 15 ++--
.../ctakes/chunker/ae/DefaultChunkCreator.java | 3 +-
.../ctakes/chunker/ae/PhraseTypeChunkCreator.java | 15 +---
.../apache/ctakes/chunker/ChunkAdjusterTests.java | 10 ---
.../org/apache/ctakes/chunker/ChunkerTests.java | 22 ------
.../clinicalpipeline/ClinicalPipelineWithUmls.java | 2 +-
.../ae/ExtractionPrepAnnotator.java | 5 +-
.../runtime/BagOfCUIsGenerator.java | 6 +-
.../parser/ae/ParserEvaluationAnnotator.java | 13 ++--
.../parser/treekernel/TreeExtractor.java | 9 +--
.../constituency/parser/treekernel/TreeKernel.java | 2 -
.../parser/uima/co/ParserTreeWriterConsumer.java | 12 ++-
.../parser/util/AnnotationTreeUtils.java | 11 ++-
.../parser/util/CommandLineParserUtil.java | 11 ++-
.../parser/util/GenerateDescriptors.java | 1 -
.../parser/scripts/groovy/parser.groovy | 90 +++++++++-------------
.../ae/TestContextDependentTokenizerAnnotator.java | 21 ++---
.../apache/ctakes/core/ae/PiperFileRunEngine.java | 5 +-
.../ctakes/core/ae/SHARPKnowtatorXMLReader.java | 3 +-
.../org/apache/ctakes/core/ae/TokenConverter.java | 11 +--
.../ctakes/core/cc/CASConsumerTestDriver.java | 8 +-
.../ctakes/core/cc/TokenTableFileWriter.java | 3 +-
.../ctakes/core/ci/HyphenTextModifierImpl.java | 16 +---
.../core/cleartk/ContinuousTextExtractor.java | 10 +--
.../ctakes/core/cleartk/FollowingWithPadding.java | 8 +-
.../org/apache/ctakes/core/cleartk/MaxContext.java | 8 +-
.../org/apache/ctakes/core/cleartk/MinContext.java | 8 +-
.../ctakes/core/cleartk/PrecedingWithPadding.java | 12 +--
.../org/apache/ctakes/core/cleartk/SumContext.java | 9 +--
.../core/fsm/adapters/NumberTokenAdapter.java | 3 +-
.../core/fsm/condition/DayNightWordCondition.java | 3 +-
.../core/fsm/condition/DecimalCondition.java | 3 +-
.../core/fsm/condition/DecimalRangeCondition.java | 3 +-
.../core/fsm/condition/DecimalValueCondition.java | 3 +-
.../core/fsm/condition/HourMinuteCondition.java | 3 +-
.../core/fsm/condition/IntegerCondition.java | 3 +-
.../core/fsm/condition/IntegerRangeCondition.java | 3 +-
.../core/fsm/condition/IntegerValueCondition.java | 3 +-
.../ctakes/core/fsm/condition/NumberCondition.java | 3 +-
.../fsm/condition/PunctuationValueCondition.java | 3 +-
.../ctakes/core/fsm/condition/RangeCondition.java | 3 +-
.../core/fsm/condition/RomanNumeralCondition.java | 3 +-
.../core/fsm/condition/SymbolValueCondition.java | 3 +-
.../core/fsm/condition/TextSetCondition.java | 5 +-
.../core/fsm/condition/TextValueCondition.java | 3 +-
.../core/fsm/condition/WordSetCondition.java | 5 +-
.../core/fsm/condition/WordValueCondition.java | 3 +-
.../apache/ctakes/core/fsm/machine/DateFSM.java | 22 ++----
.../ctakes/core/fsm/machine/FractionFSM.java | 16 ++--
.../ctakes/core/fsm/machine/MeasurementFSM.java | 22 ++----
.../ctakes/core/fsm/machine/NegationFSM.java | 16 ++--
.../ctakes/core/fsm/machine/PersonTitleFSM.java | 16 ++--
.../apache/ctakes/core/fsm/machine/RangeFSM.java | 16 ++--
.../ctakes/core/fsm/machine/RomanNumeralFSM.java | 16 ++--
.../core/fsm/machine/StatusIndicatorFSM.java | 16 ++--
.../apache/ctakes/core/fsm/machine/TimeFSM.java | 22 ++----
.../core/fsm/token/adapter/TokenConverter.java | 10 +--
.../ctakes/core/knowtator/KnowtatorAnnotation.java | 6 +-
.../ctakes/core/knowtator/KnowtatorXMLParser.java | 15 +---
.../ctakes/core/nlp/tokenizer/ContractionsPTB.java | 7 +-
.../ctakes/core/nlp/tokenizer/HyphenatedPTB.java | 6 +-
.../ctakes/core/nlp/tokenizer/Tokenizer.java | 6 +-
.../ctakes/core/nlp/tokenizer/TokenizerPTB.java | 27 ++-----
.../pipeline/GenerateSentenceBIODescriptors.java | 6 +-
.../ctakes/core/resource/FileResourceImpl.java | 9 +--
.../core/resource/JdbcConnectionResourceImpl.java | 10 +--
.../resource/LinesFromFileStringsResourceImpl.java | 8 +-
.../core/resource/StringMapResourceImpl.java | 11 ++-
.../core/sentence/EndOfSentenceScannerImpl.java | 4 +-
.../core/sentence/SentenceDetectorCtakes.java | 36 +++------
.../java/org/apache/ctakes/core/util/FSUtil.java | 18 ++---
.../java/org/apache/ctakes/core/util/JCasUtil.java | 4 +-
.../org/apache/ctakes/core/util/ListFactory.java | 3 +-
.../org/apache/ctakes/core/util/ListIterable.java | 4 +-
.../org/apache/ctakes/core/util/ParamUtil.java | 6 +-
.../ctakes/core/util/external/SystemUtil.java | 5 +-
.../core/ae/SentenceDetectorAnnotatorTest.java | 16 ++--
.../core/ae/SimpleSegmentAnnotatorTests.java | 18 ++---
.../ctakes/core/ae/TestCDASegmentAnnotator.java | 1 -
.../ctakes/core/ae/TokenizerAnnotatorPTBTests.java | 16 +---
.../core/ci/HyphenTextModifierImplTests.java | 8 +-
.../scripts/groovy/cTAKES_clinical_pipeline.groovy | 42 +++-------
.../ctakes/core/scripts/groovy/run_cTAKES.groovy | 3 -
.../ae/CoreferenceChainCoNLLWriter.java | 26 +++----
.../coreference/ae/EventCoreferenceAnnotator.java | 42 ++--------
.../coreference/ae/MipacqMarkableCreator.java | 14 ++--
.../coreference/ae/MipacqMarkableExpander.java | 8 +-
.../ae/MipacqMarkablePairGenerator.java | 19 ++---
.../coreference/ae/PatientScoringWriter.java | 1 -
.../coreference/ae/PersonChainAnnotator.java | 6 +-
.../ae/features/AttributeFeatureExtractor.java | 14 ++--
.../ae/features/CorefSyntaxFeatureExtractor.java | 6 +-
.../ae/features/DistSemFeatureExtractor.java | 16 ++--
.../ae/features/DistanceFeatureExtractor.java | 8 +-
.../ae/features/SalienceFeatureExtractor.java | 6 +-
.../ae/features/SectionFeatureExtractor.java | 6 +-
.../features/StringMatchingFeatureExtractor.java | 10 +--
.../ae/features/TemporalFeatureExtractor.java | 6 +-
.../ae/features/TokenFeatureExtractor.java | 8 +-
.../MentionClusterAgreementFeaturesExtractor.java | 15 ++--
.../MentionClusterAttributeFeaturesExtractor.java | 21 ++---
.../MentionClusterAttributeVectorExtractor.java | 4 +-
.../cluster/MentionClusterDepHeadExtractor.java | 4 +-
.../cluster/MentionClusterDistSemExtractor.java | 10 +--
.../MentionClusterDistanceFeaturesExtractor.java | 6 +-
.../MentionClusterMentionFeaturesExtractor.java | 20 ++---
.../MentionClusterSalienceFeaturesExtractor.java | 6 +-
.../MentionClusterSectionFeaturesExtractor.java | 10 +--
...tionClusterSemTypeDepPrefsFeatureExtractor.java | 10 +--
.../MentionClusterStackFeaturesExtractor.java | 6 +-
.../MentionClusterStringFeaturesExtractor.java | 17 +---
.../MentionClusterUMLSFeatureExtractor.java | 15 ++--
.../salience/ClinicalFeatureExtractor.java | 6 +-
.../salience/GrammaticalRoleFeatureExtractor.java | 6 +-
.../salience/MorphosyntacticFeatureExtractor.java | 6 +-
.../SemanticEnvironmentFeatureExtractor.java | 12 +--
.../coreference/ae/pairing/AnnotationPairer.java | 4 +-
.../ae/pairing/cluster/PreviousDocumentPairer.java | 1 -
.../coreference/data/PrintMimicMarkables.java | 8 +-
.../eval/EvaluationOfMarkableSalience.java | 14 +---
.../coreference/extractors/ContinuousBag.java | 14 ++--
.../extractors/ContinuousTextExtractor.java | 13 +---
.../training/LinearKernelMatrixWriter.java | 16 ++--
.../treekernel/training/RowFillerThread.java | 6 +-
.../treekernel/training/TreeKernelTrainer.java | 10 +--
.../coreference/util/AbstractClassifier.java | 11 +--
.../util/AnaphoricityAttributeCalculator.java | 15 ++--
.../coreference/util/AnnotOffsetComparator.java | 3 +-
.../ctakes/coreference/util/AnnotationCounter.java | 4 +-
.../coreference/util/AnnotationSelector.java | 16 ++--
.../coreference/util/AttributeCalculator.java | 10 +--
.../coreference/util/ClusterMentionFetcher.java | 2 -
.../ctakes/coreference/util/FSIteratorToList.java | 5 +-
.../coreference/util/GoldStandardLabeler.java | 14 ++--
.../coreference/util/HobbsTreeNavigator.java | 16 ++--
.../ctakes/coreference/util/MarkableDepUtils.java | 7 +-
.../ctakes/coreference/util/MarkableTreeUtils.java | 11 ++-
.../ctakes/coreference/util/MarkableUtilities.java | 16 +---
.../coreference/util/PairAttributeCalculator.java | 4 +-
.../ctakes/coreference/util/SvmVectorCreator.java | 17 ++--
.../util/SyntaxAttributeCalculator.java | 27 ++++---
.../ctakes/coreference/util/ThymeCasOrderer.java | 1 -
.../ctakes/coreference/eval/helpers/SpanTest.java | 5 +-
.../parser/ae/shared/SRLSharedModel.java | 11 ++-
.../parser/ae/shared/SRLSharedParserModel.java | 3 +-
.../parser/ae/shared/SRLSharedPredictionModel.java | 3 +-
.../parser/ae/shared/SRLSharedRoleModel.java | 3 +-
.../parser/ae/util/WriteClearNLPDescriptors.java | 10 +--
.../dependency/parser/util/AnnotationDepUtils.java | 15 ++--
.../dependency/parser/util/DependencyPath.java | 4 +-
.../dependency/parser/util/DependencyRegex.java | 7 +-
.../ctakes/dependency/parser/util/SRLUtility.java | 5 +-
.../ae/util/TestClearNLPAnalysisEngines.java | 2 -
.../AlikeSubsumingAnnotationCreator.java | 2 +-
.../lookup2/util/tool/DictionaryComparator.java | 5 +-
.../lookup2/util/tool/DictionaryCuiCounter.java | 5 +-
.../dictionary/lookup2/util/DummyAnnotator.java | 5 +-
...reateAssertionLuceneIndexFromDelimitedFile.java | 31 +++-----
.../lookup/ae/AssertionCuePhraseConsumerImpl.java | 18 ++---
.../lookup/ae/BaseLookupConsumerImpl.java | 2 -
.../dictionary/lookup/ae/DebugConsumerImpl.java | 7 +-
.../lookup/ae/DictionaryLookupAnnotator.java | 14 +---
.../lookup/ae/DirectLookupInitializerImpl.java | 2 +-
.../lookup/ae/LookupAnnotationToJCasAdapter.java | 6 +-
.../dictionary/lookup/ae/LookupConsumer.java | 4 +-
.../dictionary/lookup/ae/LookupInitializer.java | 8 +-
.../dictionary/lookup/ae/LookupParseUtilities.java | 21 ++---
.../lookup/ae/NamedEntityLookupConsumerImpl.java | 9 +--
.../lookup/ae/UmlsDictionaryLookupAnnotator.java | 7 +-
.../lookup/ae/UmlsToSnomedConsumerImpl.java | 9 +--
.../lookup/algorithms/DirectPassThroughImpl.java | 8 +-
.../filter/TruncateCollectionFilterImpl.java | 6 +-
.../dictionary/lookup/jdbc/JdbcDictionaryImpl.java | 17 ++--
.../lookup/lucene/LuceneDictionaryImpl.java | 1 -
.../lucene/LuceneDocumentMetaDataHitImpl.java | 12 +--
.../lookup/phrasebuilder/PhraseBuilder.java | 4 +-
.../phrasebuilder/VariantPhraseBuilderImpl.java | 5 +-
.../lookup/strtable/StringTableDictionaryImpl.java | 8 +-
.../strtable/StringTableRowMetaDataHitImpl.java | 7 +-
.../lookup/vo/LookupAnnotationToTokAdapter.java | 4 +-
.../org/apache/ctakes/drugner/DrugMention.java | 36 ++-------
.../drugner/ae/impl/NegContextInitializerImpl.java | 10 +--
.../drugner/cc/ConsumeNamedEntityRecordModel.java | 57 ++++----------
.../conditions/ContainsSetTextValueCondition.java | 5 +-
.../conditions/DecimalStrengthStatusCondition.java | 3 +-
.../fsm/elements/conditions/DosageCondition.java | 3 +-
.../conditions/DrugChangeStatusCondition.java | 3 +-
.../fsm/elements/conditions/FormCondition.java | 3 +-
.../fsm/elements/conditions/FractionCondition.java | 3 +-
.../conditions/FractionStrengthCondition.java | 3 +-
.../conditions/FrequencyUnitCondition.java | 3 +-
.../elements/conditions/RangeDosageCondition.java | 3 +-
.../conditions/RangeStrengthCondition.java | 3 +-
.../fsm/elements/conditions/RouteCondition.java | 3 +-
.../fsm/elements/conditions/StrengthCondition.java | 3 +-
.../conditions/StrengthUnitCombinedCondition.java | 3 +-
.../elements/conditions/StrengthUnitCondition.java | 3 +-
.../fsm/elements/conditions/TimeCondition.java | 3 +-
.../fsm/machines/elements/DecimalStrengthFSM.java | 14 +---
.../drugner/fsm/machines/elements/DosagesFSM.java | 24 ++----
.../fsm/machines/elements/DrugChangeStatusFSM.java | 22 ++----
.../drugner/fsm/machines/elements/DurationFSM.java | 16 ++--
.../drugner/fsm/machines/elements/FormFSM.java | 16 ++--
.../fsm/machines/elements/FractionStrengthFSM.java | 16 ++--
.../fsm/machines/elements/FrequencyFSM.java | 22 ++----
.../fsm/machines/elements/FrequencyUnitFSM.java | 26 ++-----
.../fsm/machines/elements/RangeStrengthFSM.java | 22 ++----
.../drugner/fsm/machines/elements/RouteFSM.java | 22 ++----
.../drugner/fsm/machines/elements/StrengthFSM.java | 21 ++---
.../fsm/machines/elements/StrengthUnitFSM.java | 14 +---
.../fsm/machines/util/HyphenatedDrugFSM.java | 16 ++--
.../drugner/fsm/machines/util/NegIndicatorFSM.java | 16 ++--
.../drugner/fsm/machines/util/NonIndicatorFSM.java | 16 ++--
.../fsm/machines/util/StatusIndicatorFSM.java | 16 ++--
.../fsm/machines/util/SubSectionIndicatorFSM.java | 16 ++--
.../fsm/machines/util/SuffixFrequencyFSM.java | 16 ++--
.../fsm/machines/util/SuffixStrengthFSM.java | 16 ++--
.../apache/ctakes/examples/ae/BodySideFinder.java | 2 -
.../ctakes/examples/ae/ConfigParameterExample.java | 8 +-
.../apache/ctakes/examples/cc/TokenSpanWriter.java | 6 +-
.../ctakes/examples/ctakes_cnlpt_py/setup.py | 2 +
.../src/ctakes_cnlpt/ae/doctimerel_delegator.py | 11 +--
.../src/ctakes_cnlpt/ae/negation_delegator.py | 9 ++-
.../src/ctakes_cnlpt/ae/temporal_delegator.py | 11 +--
.../src/ctakes_cnlpt/negation_pipeline.py | 3 +-
.../ctakes/gui/pipeline/bit/PipeBitFinder.java | 1 -
.../org/apache/ctakes/lvg/ae/LvgAnnotator.java | 30 ++------
.../ctakes/lvg/ae/LvgBaseTokenAnnotator.java | 19 ++---
.../ctakes/lvg/resource/LvgCmdApiResourceImpl.java | 6 +-
.../apache/ctakes/necontexts/ContextAnalyzer.java | 4 +-
.../ctakes/necontexts/ContextAnalyzerAdapter.java | 4 +-
.../org/apache/ctakes/necontexts/ContextHit.java | 4 +-
.../necontexts/NamedEntityContextAnalyzer.java | 8 +-
.../necontexts/NamedEntityContextHitConsumer.java | 3 +-
.../negation/NegationContextAnalyzer.java | 6 +-
.../negation/NegationContextHitConsumer.java | 7 +-
.../necontexts/status/StatusContextAnalyzer.java | 8 +-
.../status/StatusContextHitConsumer.java | 7 +-
.../ctakes/necontexts/ContextAnnotatorTests.java | 14 +---
.../ctakes/necontexts/NegationAnnotatorTests.java | 11 ++-
.../ctakes/necontexts/StatusAnnotatorTests.java | 11 ++-
.../org/apache/ctakes/pbj/ctakes_pbj_py/setup.py | 2 +
.../src/ctakes_pbj/component/pbj_sender.py | 4 +-
.../examples/sentence_printer_pipeline.py | 3 +-
.../ctakes_pbj/examples/word_finder_pipeline.py | 4 +-
.../src/ctakes_pbj/pbj_tools/stomp_receiver.py | 5 +-
.../org/apache/ctakes/postagger/POSTagger.java | 11 ++-
.../ctakes/postagger/TagDictionaryCreator.java | 8 +-
.../org/apache/ctakes/postagger/test/CpeTests.java | 8 +-
.../test/OpenNLPPOSCollectionReaderTests.java | 15 ++--
.../ctakes/postagger/test/POSTaggerTests.java | 12 +--
.../postagger/test/TagDictionaryCreatorTests.java | 10 +--
.../preprocessor/ClinicalNotePreProcessor.java | 14 ++--
.../org/apache/ctakes/preprocessor/DTDloader.java | 9 +--
.../ctakes/preprocessor/DocumentMetaData.java | 6 +-
.../ctakes/preprocessor/test/TestDriver.java | 14 ++--
.../preprocessor/ClinicalNotePreProcessorTest.java | 15 +---
.../ctakes/core/ae/LabValueFinderTester.java | 22 ++----
.../regression/test/RegressionPipelineTest.java | 5 +-
.../ae/DegreeOfRelationExtractorAnnotator.java | 7 +-
.../ae/IdentifiedAnnotationExpander.java | 17 ++--
.../ae/LocationOfRelationExtractorAnnotator.java | 13 ++--
.../ManagesTreatsRelationExtractorAnnotator.java | 13 +---
.../ManifestationOfRelationExtractorAnnotator.java | 6 +-
.../ae/ModifierExtractorAnnotator.java | 6 +-
.../ae/RelationExtractorAnnotator.java | 21 +----
.../relationextractor/ae/baselines/Utils.java | 12 +--
.../ae/features/ArgumentOrderFeatureExtractor.java | 6 +-
.../ae/features/DependencyParseUtils.java | 11 ++-
.../features/DependencyPathFeaturesExtractor.java | 8 +-
.../features/DependencyTreeFeaturesExtractor.java | 6 +-
.../ae/features/EmbeddingFeatureExtractor.java | 10 +--
.../ae/features/EntitySpanFeatureExtractor.java | 6 +-
.../ae/features/FlatTreeFeatureExtractor.java | 6 +-
.../ae/features/NamedEntityFeaturesExtractor.java | 8 +-
.../ae/features/PETFeatureExtractor.java | 6 +-
.../ae/features/PartOfSpeechFeaturesExtractor.java | 6 +-
.../ae/features/PhraseChunkingExtractor.java | 6 +-
.../ae/features/PrepositionFeatureExtractor.java | 10 +--
.../ae/features/PunctuationFeatureExtractor.java | 6 +-
.../ae/features/RelationFeaturesExtractor.java | 5 +-
.../ae/features/TokenFeaturesExtractor.java | 20 ++---
.../ae/features/TreeFragmentFeatureExtractor.java | 14 ++--
.../ae/features/WordNetFeatureExtractor.java | 9 +--
.../ae/features/WordNetUtils.java | 16 ++--
.../data/GoldAnnotationAnalysisPipeline.java | 8 +-
.../data/GoldAnnotationStatsCalculator.java | 13 ++--
.../ctakes/relationextractor/data/Splitter.java | 6 +-
.../ctakes/relationextractor/data/Stats.java | 18 ++---
.../data/analysis/EventAndEntityViewer.java | 9 +--
.../data/analysis/GoldRelationViewer.java | 13 +---
.../relationextractor/data/analysis/Utils.java | 19 +++--
.../eval/ModifierExtractorEvaluation.java | 2 -
.../relationextractor/eval/ParameterSettings.java | 7 +-
.../eval/PrintRelationStatistics.java | 13 ++--
.../eval/RelationExtractorEvaluation.java | 41 ++--------
.../ctakes/relationextractor/eval/SHARPXMI.java | 4 +-
.../relationextractor/knowtator/RelationInfo.java | 4 +-
.../relationextractor/knowtator/XMLReader.java | 6 +-
.../AnatomicalSiteListExtractorPipeline.java | 15 ++--
.../metastasis/MetastasisAnaforaXMLReader.java | 15 ++--
.../pipelines/RelationAnnotationViewer.java | 9 +--
.../pipelines/RelationExtractorConsumer.java | 11 ++-
.../RelationExtractorPipelineSingleCas.java | 6 +-
.../pipelines/RelationExtractorTrain.java | 15 ++--
.../SelectiveRelationAnnotationViewer.java | 12 +--
.../pipelines/TreeFeatureConsumer.java | 22 +++---
.../ae/NamedEntityFeaturesExtractorTest.java | 8 +-
.../ae/RelationExtractorAnnotatorsTest.java | 14 ++--
.../ctakes/sideeffect/ae/PSESentenceAnnotator.java | 17 ++--
.../ae/SESentenceClassifierAnnotator.java | 18 ++---
.../org/apache/ctakes/sideeffect/util/SEUtil.java | 19 ++---
.../smokingstatus/MLutil/GenerateTrainingData.java | 17 +---
.../smokingstatus/ae/ClassifiableEntries.java | 40 ++++------
.../ae/KuRuleBasedClassifierAnnotator.java | 25 +++---
.../ae/PcsClassifierAnnotator_libsvm.java | 28 +++----
.../smokingstatus/ae/ResolutionAnnotator.java | 30 +++-----
.../ctakes/smokingstatus/ae/SentenceAdjuster.java | 13 +---
.../cc/RecordResolutionCasConsumer.java | 7 +-
.../ae/NonSmokerNamedEntityLookupConsumerImpl.java | 22 +++---
.../ae/SmokerNamedEntityLookupConsumerImpl.java | 22 +++---
...UnknownSmokerNamedEntityLookupConsumerImpl.java | 22 +++---
.../patientLevel/PatientLevelSmokingStatus.java | 7 +-
.../filler/ae/TemplateFillerAnnotator.java | 47 +++--------
.../ae/CrossSentenceTemporalRelationAnnotator.java | 8 +-
.../temporal/ae/DeepPheAnaforaXMLReader.java | 11 ++-
.../ctakes/temporal/ae/DocTimeRelAnnotator.java | 1 -
.../temporal/ae/DocTimeRelBertRestAnnotator.java | 3 -
.../temporal/ae/EventAdmissionTimeAnnotator.java | 30 ++------
.../temporal/ae/EventDischargeTimeAnnotator.java | 30 ++------
.../ctakes/temporal/ae/EventEventCNNAnnotator.java | 10 +--
.../ae/EventEventCRFRelationAnnotator.java | 24 ++----
.../ae/EventEventI2B2RelationAnnotator.java | 45 ++---------
.../EventEventRelationGoldContainerAnnotator.java | 55 ++-----------
.../ae/EventEventRelationSeedBasedAnnotator.java | 53 ++-----------
.../ctakes/temporal/ae/EventTimeCNNAnnotator.java | 10 +--
.../ae/EventTimeI2B2RelationAnnotator.java | 43 +++--------
.../ae/EventTimeSelfRelationAnnotator.java | 53 +++----------
.../temporal/ae/EventToClearTKEventAnnotator.java | 6 +-
.../ctakes/temporal/ae/I2B2TemporalXMLReader.java | 18 ++---
.../ctakes/temporal/ae/MetaTimeAnnotator.java | 20 ++---
.../temporal/ae/NEPredicateEventAnnotator.java | 8 +-
.../ae/NeuralEventTimeSelfRelationAnnotator.java | 50 ++----------
.../ctakes/temporal/ae/THYMEAnaforaXMLReader.java | 26 +++----
.../temporal/ae/THYMEKnowtatorXMLReader.java | 23 +++---
.../temporal/ae/THYMEQAAnaforaXMLReader.java | 23 +++---
.../ctakes/temporal/ae/THYMETreebankReader.java | 33 +++-----
.../temporal/ae/ThymePatientViewAnnotator.java | 16 ++--
.../apache/ctakes/temporal/ae/TimeAnnotator.java | 18 ++---
.../temporal/ae/TimexAdmissionTimeAnnotator.java | 23 ++----
.../temporal/ae/TimexDischargeTimeAnnotator.java | 22 ++----
.../temporal/ae/TimexToClearTKTimexAnnotator.java | 6 +-
.../ae/WithinSentenceBeforeRelationAnnotator.java | 14 +---
.../F1BaselineEventTimeRelationAnnotator.java | 22 ++----
...recisionBaselineEventTimeRelationAnnotator.java | 22 ++----
.../RecallBaselineEventEventRelationAnnotator.java | 12 +--
.../RecallBaselineEventTimeRelationAnnotator.java | 22 ++----
.../TimidBaselineEventTimeRelationAnnotator.java | 23 +++---
.../temporal/ae/baselines/TreeHeightBaseline.java | 8 +-
.../feature/CheckSpecialWordRelationExtractor.java | 14 ++--
.../temporal/ae/feature/ChunkingExtractor.java | 5 +-
.../temporal/ae/feature/ClosestVerbExtractor.java | 5 +-
.../ConjunctionRelationFeaturesExtractor.java | 8 +-
.../ae/feature/ContinuousTextExtractor.java | 13 +---
.../ae/feature/CoordinateFeaturesExtractor.java | 8 +-
.../ae/feature/CoveredTextToValuesExtractor.java | 19 +++--
.../ae/feature/DateAndMeasurementExtractor.java | 10 +--
.../ae/feature/DependencyFeatureExtractor.java | 12 +--
.../temporal/ae/feature/DependencyParseUtils.java | 10 +--
.../feature/DependencyPathFeaturesExtractor.java | 8 +-
.../ae/feature/DependingVerbsFeatureExtractor.java | 8 +-
.../DeterminerRelationFeaturesExtractor.java | 7 +-
.../ae/feature/DocTimeRelFeatureExtractor.java | 6 +-
.../ae/feature/EmptyFeaturesExtractor.java | 4 +-
.../ae/feature/EventArgumentPropertyExtractor.java | 10 +--
.../ae/feature/EventPositionFeatureExtractor.java | 14 ++--
.../EventPositionRelationFeaturesExtractor.java | 13 ++--
.../EventTimeRelationsFeaturesExtractor.java | 7 +-
.../ae/feature/FramesetCategoryExtractor.java | 17 ++--
.../IdentifiedAnnotationFeatureExtractor.java | 19 ++---
.../temporal/ae/feature/ListFeaturesExtractor.java | 11 ++-
.../feature/NearbyVerbTenseRelationExtractor.java | 12 +--
.../ae/feature/NearbyVerbTenseXExtractor.java | 11 ++-
.../ae/feature/NearestFlagFeatureExtractor.java | 10 +--
.../NoOtherETPuntInBetweenFeaturesExtractor.java | 8 +-
...umberOfEventTimeBetweenCandidatesExtractor.java | 10 +--
.../NumberOfEventsInTheSameSentenceExtractor.java | 13 ++--
.../temporal/ae/feature/ParseFeatureExtractor.java | 6 +-
.../ae/feature/ParseSpanFeatureExtractor.java | 6 +-
.../ae/feature/PredicateArgumentExtractor.java | 13 ++--
.../feature/RelationEmbeddingFeatureExtractor.java | 10 +--
...RelationSyntacticEmbeddingFeatureExtractor.java | 14 ++--
.../ae/feature/SRLRelationFeaturesExtractor.java | 13 +---
.../ae/feature/SectionHeaderExtractor.java | 11 ++-
.../ae/feature/SectionHeaderRelationExtractor.java | 13 ++--
.../SpecialAnnotationRelationExtractor.java | 19 ++---
.../feature/SyntacticParentFeatureExtractor.java | 5 +-
.../feature/TemporalAttributeFeatureExtractor.java | 8 +-
.../TemporalAttributeForMixEventTimeExtractor.java | 8 +-
.../ae/feature/TemporalPETFlatExtractor.java | 8 +-
.../temporal/ae/feature/TimeWordTypeExtractor.java | 22 ++----
.../ctakes/temporal/ae/feature/TimeXExtractor.java | 14 +---
.../TimeXPropertyRelationFeaturesExtractor.java | 11 ++-
.../ae/feature/TimeXRelationFeaturesExtractor.java | 19 ++---
.../ae/feature/TokenPropertyFeaturesExtractor.java | 15 ++--
.../feature/UMLSBasedTokenFeaturesExtractor.java | 24 ++----
.../temporal/ae/feature/UmlsFeatureExtractor.java | 11 +--
.../ae/feature/UmlsSingleFeatureExtractor.java | 7 +-
.../feature/UnexpandedTokenFeaturesExtractor.java | 20 ++---
.../DurationDistributionFeatureExtractor.java | 15 ++--
.../DurationEventEventFeatureExtractor.java | 15 ++--
.../DurationEventTimeFeatureExtractor.java | 17 ++--
.../DurationExpectationFeatureExtractor.java | 15 ++--
.../duration/DurationTimeUnitFeatureExtractor.java | 12 ++-
.../selection/BinaryAlphaFeatureSelection.java | 23 ++----
.../ae/feature/selection/Chi2FeatureSelection.java | 23 ++----
.../ae/feature/selection/FeatureSelection.java | 17 ++--
.../MutualInformationFeatureSelection.java | 28 ++-----
.../selection/OddsRatioFeatureSelection.java | 21 ++---
.../selection/ZscoreNormalizationExtractor.java | 18 +----
.../treekernel/DependencySingleTreeExtractor.java | 6 +-
.../EventTimeFlatTreeFeatureExtractor.java | 9 +--
.../treekernel/SyntaticSingleTreeExtractor.java | 6 +-
.../ae/feature/treekernel/TemporalFTExtractor.java | 6 +-
.../feature/treekernel/TemporalPETExtractor.java | 8 +-
.../feature/treekernel/TemporalPathExtractor.java | 6 +-
.../ctakes/temporal/cc/EventTimeAnaforaWriter.java | 13 +++-
.../analysis/EventContextAnalysisPipeline.java | 23 +++---
.../data/analysis/EventPrinterPipeline.java | 28 +++----
.../temporal/data/analysis/GoldRelationViewer.java | 19 ++---
.../analysis/PrintFailedTimeNormalizations.java | 19 ++---
.../data/analysis/PrintNonrelatedEvents.java | 15 ++--
.../PrintNormalizedTemporalExpressions.java | 8 +-
.../analysis/RelationContextViewerPipeline.java | 19 ++---
.../analysis/TimexTreeAlignmentStatistics.java | 15 ++--
.../duration/EventDurationDistribution.java | 40 ++++------
.../ExtractDurationsUsingContainsRelation.java | 31 +++-----
.../PreserveCertainEventEventRelationsInGold.java | 15 ++--
.../PreserveCertainEventTimeRelationsInGold.java | 17 ++--
.../duration/PreserveCertainEventsInGold.java | 15 ++--
.../PreserveUMLSEventEventRelationsInGold.java | 7 +-
.../PreserveUMLSEventTimeRelationsInGold.java | 7 +-
.../org/apache/ctakes/temporal/duration/Utils.java | 52 +++++--------
.../eval/EvaluationOfAnnotationSpans_ImplBase.java | 24 ++----
.../eval/EvaluationOfClearTKEventProperties.java | 2 +-
.../eval/EvaluationOfClearTKEventSpans.java | 11 ++-
.../eval/EvaluationOfClearTKRelations.java | 21 ++---
.../eval/EvaluationOfClearTKTimeSpans.java | 11 ++-
.../eval/EvaluationOfEventDocTimeRelDeepPhe.java | 2 +-
.../eval/EvaluationOfEventEventRelations.java | 22 ++----
.../temporal/eval/EvaluationOfEventProperties.java | 2 +-
.../temporal/eval/EvaluationOfEventSpans.java | 15 ++--
.../EvaluationOfMetaTimeExpressionExtractor.java | 25 +++---
.../eval/EvaluationOfNEPredicateEventSpans.java | 15 ++--
.../EvaluationOfTemporalRelations_ImplBase.java | 21 +++--
.../temporal/eval/EvaluationOfTimeSpans.java | 39 ++++------
.../ctakes/temporal/eval/PrintRelations.java | 20 ++---
.../temporal/eval/RemoveTreeAlignedMentions.java | 12 +--
.../org/apache/ctakes/temporal/eval/THYMEData.java | 4 +-
.../keras/KerasStringFeatureDataWriter.java | 4 +-
.../keras/KerasStringOutcomeClassifier.java | 5 +-
.../keras/KerasStringOutcomeClassifierBuilder.java | 11 ++-
.../keras/KerasStringOutcomeDataWriter.java | 7 +-
.../keras/ScriptStringFeatureDataWriter.java | 9 +--
.../keras/ScriptStringOutcomeClassifier.java | 12 +--
.../ScriptStringOutcomeClassifierBuilder.java | 12 +--
.../keras/ScriptStringOutcomeDataWriter.java | 8 +-
.../nn/ae/EventEventPosBasedAnnotator.java | 9 +--
.../nn/ae/EventEventPositionBasedAnnotator.java | 9 +--
.../nn/ae/EventEventTokenAndBIOBasedAnnotator.java | 9 +--
.../nn/ae/EventEventTokenAndPosBasedAnnotator.java | 9 +--
.../nn/ae/EventEventTokenBasedAnnotator.java | 19 +----
.../temporal/nn/ae/EventTimePosBasedAnnotator.java | 9 +--
.../nn/ae/EventTimePositionBasedAnnotator.java | 9 +--
.../nn/ae/EventTimeTokenAndBIOBasedAnnotator.java | 10 +--
.../nn/ae/EventTimeTokenAndPosBasedAnnotator.java | 10 +--
.../nn/ae/EventTimeTokenBasedAnnotator.java | 19 +----
.../temporal/nn/ae/WindowBasedAnnotator.java | 16 ++--
.../temporal/nn/data/ArgContextProvider.java | 8 +-
.../ctakes/temporal/nn/data/DtrRelPrinter.java | 22 +++---
.../nn/data/EventEventAllPairRelPrinter.java | 21 ++---
.../nn/data/EventEventRelPositionPrinter.java | 21 ++---
.../temporal/nn/data/EventEventRelPrinter.java | 22 ++----
.../nn/data/EventTimeRelPositionPrinter.java | 22 ++----
.../temporal/nn/data/EventTimeRelPrinter.java | 22 ++----
.../ctakes/temporal/nn/data/GoldEventPrinter.java | 21 +++--
.../nn/data/GoldEventPrinterWithLabels.java | 21 +++--
.../nn/eval/EvaluationOfNeuralJointRelations.java | 48 ++++--------
.../temporal/pipelines/EventPrintingPipeline.java | 15 ++--
.../TemporalExtractionPipeline_ImplBase.java | 5 +-
.../temporal/utils/AnnotationIdCollection.java | 9 +--
.../temporal/utils/CheckKnowtatorAnnotations.java | 13 ++--
.../temporal/utils/RunCorpusDiagnostics.java | 15 ++--
.../apache/ctakes/temporal/utils/SMOTEplus.java | 12 +--
.../ctakes/temporal/utils/TLinkTypeArray2.java | 16 +---
.../apache/ctakes/temporal/utils/TlinkType.java | 9 +--
.../temporal/ae/BackwardsTimeAnnotatorTest.java | 14 ++--
.../ae/ContextualModalityAnnotatorTest.java | 8 +-
.../ctakes/temporal/ae/EventAnnotatorTest.java | 14 ++--
.../ae/EventEventRelationAnnotatorTest.java | 7 +-
.../ae/EventTimeRelationAnnotatorTest.java | 7 +-
.../ctakes/temporal/scripts/keras/cleartk_io.py | 3 +-
.../ctakes/temporal/scripts/keras/dataset.py | 4 +-
.../ctakes/temporal/scripts/keras/dima-predict.py | 7 +-
.../scripts/keras/et_RCNN_train-and-package.py | 6 --
.../ctakes/temporal/scripts/keras/et_cleartk_io.py | 3 +-
.../scripts/keras/et_dimaCNN_train-and-package.py | 6 --
.../temporal/scripts/keras/et_neural_testCNN.py | 10 ++-
.../scripts/keras/et_neural_train-and-package.py | 3 -
.../keras/et_resnet_func2_train-and-package.py | 10 +--
.../ctakes/temporal/scripts/keras/keras-predict.py | 7 +-
.../ctakes/temporal/scripts/keras/nn_models.py | 7 +-
.../ctakes/temporal/scripts/keras/rCNN-predict.py | 9 +--
.../temporal/scripts/keras/resnet-predict.py | 7 +-
.../ctakes/temporal/scripts/nn/cleartk_io.py | 3 +-
.../ctakes/temporal/scripts/nn/cnn_classify.py | 7 +-
.../temporal/scripts/nn/cnn_classify_hybrid.py | 7 +-
.../temporal/scripts/nn/cnn_classify_position.py | 7 +-
.../apache/ctakes/temporal/scripts/nn/cnn_train.py | 4 -
.../ctakes/temporal/scripts/nn/cnn_train_hybrid.py | 4 -
.../temporal/scripts/nn/cnn_train_position.py | 4 -
.../apache/ctakes/temporal/scripts/nn/dataset.py | 4 +-
.../ctakes/temporal/scripts/nn/dataset_hybrid.py | 6 +-
.../ctakes/temporal/scripts/nn/dataset_position.py | 7 +-
.../ctakes/temporal/scripts/nn/et_cleartk_io.py | 3 +-
.../ctakes/temporal/scripts/nn/lstm_classify.py | 7 +-
.../temporal/scripts/nn/lstm_classify_hybrid.py | 7 +-
.../ctakes/temporal/scripts/nn/lstm_train.py | 6 +-
.../temporal/scripts/nn/lstm_train_hybrid.py | 4 -
.../apache/ctakes/temporal/scripts/nn/nn_models.py | 7 +-
ctakes-tiny-rest/pom.xml | 5 ++
.../ctakes/utils/distsem/WordEmbeddings.java | 6 +-
.../ctakes/utils/distsem/WordVectorReader.java | 6 +-
.../org/apache/ctakes/utils/kernel/PolyKernel.java | 5 +-
.../apache/ctakes/utils/struct/CounterTreeMap.java | 1 -
.../org/apache/ctakes/utils/test/TestUtil.java | 12 +--
.../ctakes/utils/wiki/TestCosineSimilarity.java | 6 +-
.../org/apache/ctakes/utils/wiki/WikiIndex.java | 13 ++--
.../ctakes/utils/xcas_comparison/Compare.java | 5 +-
.../apache/ctakes/utils/xcas_comparison/Const.java | 4 +-
.../utils/xcas_comparison/XcasAnnotation.java | 5 +-
.../ctakes/utils/xcas_comparison/XcasDiff.java | 7 +-
.../ctakes/utils/xcas_comparison/XcasFile.java | 3 +-
.../utils/xcas_comparison/XcasProcessor.java | 15 ++--
.../org/apache/ctakes/rest/filter/CORSFilter.java | 9 ++-
.../org/apache/ctakes/rest/util/JCasFormatter.java | 3 -
.../org/apache/ctakes/rest/util/XMLParser.java | 7 +-
.../ctakes/ytex/tools/DBAnnotationViewerMain.java | 78 +++++--------------
.../org/apache/ctakes/ytex/tools/ExportCAS.java | 10 +--
.../java/org/apache/ctakes/ytex/tools/RunCPE.java | 8 +-
.../docanalyzer/DBAnnotationViewerDialog.java | 62 ++++-----------
.../ctakes/ytex/uima/ApplicationContextHolder.java | 10 +--
.../ctakes/ytex/uima/DBCollectionReader.java | 2 +-
.../ctakes/ytex/uima/annotators/DBConsumer.java | 16 ++--
.../ctakes/ytex/uima/annotators/DateAnnotator.java | 9 +--
.../uima/annotators/MetaMapToCTakesAnnotator.java | 10 +--
.../uima/annotators/NamedEntityRegexAnnotator.java | 12 +--
.../ytex/uima/annotators/NegexAnnotator.java | 30 +++-----
.../uima/annotators/SegmentRegexAnnotator.java | 14 +---
.../annotators/SenseDisambiguatorAnnotator.java | 13 +---
.../ytex/uima/annotators/SentenceDetector.java | 24 +++---
.../ctakes/ytex/uima/dao/NamedEntityRegexDao.java | 4 +-
.../ytex/uima/dao/NamedEntityRegexDaoImpl.java | 4 +-
.../ctakes/ytex/uima/dao/SegmentRegexDao.java | 4 +-
.../ctakes/ytex/uima/dao/SegmentRegexDaoImpl.java | 4 +-
.../ae/StemmedLookupAnnotationToJCasAdapter.java | 6 +-
.../ytex/uima/mapper/DocumentMapperService.java | 4 +-
.../uima/mapper/DocumentMapperServiceImpl.java | 46 +++--------
.../ctakes/ytex/uima/mapper/ISO8601Converter.java | 8 +-
.../InitableJdbcConnectionResourceImpl.java | 10 +--
.../org/apache/ctakes/ytex/uima/TestUtils.java | 14 ++--
.../uima/annotators/DBCollectionReaderTest.java | 6 +-
.../ytex/uima/annotators/DBConsumerTest.java | 10 +--
.../annotators/DictionaryLookupAnnotatorTest.java | 12 +--
.../ytex/uima/annotators/NamedEntityRegexTest.java | 10 +--
.../ytex/uima/annotators/SegmentRegexTest.java | 16 ++--
.../ytex/uima/annotators/SentenceDetectorTest.java | 10 +--
.../uima/annotators/SparseDataExporterTest.java | 12 +--
.../ctakes/ytex/web/search/ConceptLookupBean.java | 16 ++--
.../ytex/web/search/ConceptSearchServiceImpl.java | 17 ++--
.../ytex/web/search/DocumentSearchServiceImpl.java | 17 ++--
.../ctakes/ytex/web/search/DocumentViewBean.java | 9 +--
.../ytex/web/search/FullTextDocumentViewBean.java | 4 +-
.../ctakes/ytex/web/search/FullTextSearchBean.java | 3 +-
.../ctakes/ytex/web/search/SemanticSearchBean.java | 16 ++--
.../ctakes/ytex/web/search/SemanticSimBean.java | 21 ++---
.../ytex/ws/ConceptSimilarityRestService.java | 5 +-
.../ytex/ws/ConceptSimilarityWebService.java | 7 +-
.../ytex/ws/ConceptSimilarityWebServiceImpl.java | 17 ++--
.../src/main/webapp/WEB-INF/faces-config.xml | 5 +-
.../WEB-INF/inc-templates/commonLayout.xhtml | 9 +--
ctakes-ytex-web/src/main/webapp/about.xhtml | 9 +--
.../src/main/webapp/metricCheckboxes.xhtml | 6 +-
.../src/main/webapp/semanticSearch.xhtml | 10 +--
ctakes-ytex-web/src/main/webapp/semanticSim.xhtml | 12 ++-
.../src/main/webapp/semanticSimMulti.xhtml | 11 +--
ctakes-ytex-web/src/main/webapp/viewDocument.xhtml | 9 +--
ctakes-ytex/pom.xml | 22 ++++++
ctakes-ytex/scripts/build-classpath.xml | 2 +-
.../scripts/data/examples/fracture_demo.xml | 2 +-
ctakes-ytex/scripts/data/ref_uima_type.xml | 2 +-
ctakes-ytex/scripts/data/snomedct/sct2_concept.xml | 2 +-
.../scripts/data/snomedct/sct2_description.xml | 2 +-
.../scripts/data/snomedct/sct2_relationship.xml | 2 +-
.../scripts/data/snomedct/sct2f_concept.xml | 2 +-
.../scripts/data/snomedct/sct2f_description.xml | 2 +-
.../scripts/data/snomedct/sct2f_relationship.xml | 2 +-
ctakes-ytex/scripts/data/stopword.xml | 2 +-
ctakes-ytex/scripts/data/umls/AMBIGLUI.xml | 2 +-
ctakes-ytex/scripts/data/umls/AMBIGSUI.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRAUI.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRCOC.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRCOLS.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRCONSO.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRCUI.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRDEF.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRDOC.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRFILES.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRHIER.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRHIST.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRMAP.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRRANK.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRREL.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRSAB.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRSAT.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRSMAP.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRSTY.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRXNS_ENG.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRXNW_ENG.xml | 2 +-
ctakes-ytex/scripts/data/umls/MRXW_ENG.xml | 2 +-
ctakes-ytex/scripts/data/umls/SRDEF.xml | 2 +-
ctakes-ytex/scripts/data/umls/SRFIL.xml | 2 +-
ctakes-ytex/scripts/data/umls/SRFLD.xml | 2 +-
ctakes-ytex/scripts/data/umls/SRSTR.xml | 2 +-
ctakes-ytex/scripts/data/umls/SRSTRE1.xml | 2 +-
ctakes-ytex/scripts/data/umls/SRSTRE2.xml | 2 +-
ctakes-ytex/scripts/data/umls/umls_aui_fword.xml | 2 +-
.../scripts/data/umls/v_snomed_fword_lookup.xml | 2 +-
.../main/java/org/apache/ctakes/jdl/AppJdl.java | 13 ++--
.../main/java/org/apache/ctakes/jdl/AppMain.java | 7 +-
.../org/apache/ctakes/jdl/common/FileUtil.java | 4 +-
.../apache/ctakes/jdl/data/base/JdlConnection.java | 7 +-
.../apache/ctakes/jdl/data/loader/CsvLoader.java | 22 ++----
.../org/apache/ctakes/jdl/data/loader/Loader.java | 4 +-
.../apache/ctakes/jdl/data/loader/XmlLoader.java | 9 +--
.../org/apache/ctakes/jdl/data/xml/DomParser.java | 9 +--
.../org/apache/ctakes/jdl/data/xml/DomUtil.java | 21 ++---
.../org/apache/ctakes/jdl/data/xml/SaxParser.java | 13 ++--
.../org/apache/ctakes/jdl/data/xml/SchemaUtil.java | 14 ++--
.../org/apache/ctakes/jdl/data/xml/Validation.java | 16 ++--
.../jdl/data/xml/jaxb/ObjectFactoryBind.java | 7 +-
.../jdl/data/xml/jaxb/ObjectFactoryUtil.java | 6 +-
.../org/apache/ctakes/ytex/KernelLauncher.java | 10 +--
.../ctakes/ytex/R/RGramMatrixExporterImpl.java | 20 ++---
.../java/org/apache/ctakes/ytex/dao/DBUtil.java | 6 +-
.../ytex/kernel/AbstractBagOfWordsExporter.java | 26 +++----
.../apache/ctakes/ytex/kernel/BagOfWordsData.java | 7 +-
.../kernel/BaseClassifierEvaluationParser.java | 26 +++----
.../ytex/kernel/BaseSparseDataFormatter.java | 13 +---
.../ctakes/ytex/kernel/ClassifierEvalUtil.java | 12 +--
.../ytex/kernel/ClassifierEvaluationImporter.java | 14 +---
.../apache/ctakes/ytex/kernel/CytoscapeHelper.java | 4 +-
.../ctakes/ytex/kernel/CytoscapeHelperImpl.java | 24 ++----
.../org/apache/ctakes/ytex/kernel/FileUtil.java | 8 +-
.../ctakes/ytex/kernel/FoldGeneratorImpl.java | 26 +------
.../ytex/kernel/ImputedFeatureEvaluator.java | 4 +-
.../ytex/kernel/ImputedFeatureEvaluatorImpl.java | 41 +++-------
.../ytex/kernel/InfoContentEvaluatorImpl.java | 25 ++----
.../ytex/kernel/IntrinsicInfoContentEvaluator.java | 4 +-
.../kernel/IntrinsicInfoContentEvaluatorImpl.java | 22 ++----
.../org/apache/ctakes/ytex/kernel/KernelUtil.java | 9 +--
.../apache/ctakes/ytex/kernel/KernelUtilImpl.java | 37 +++------
.../apache/ctakes/ytex/kernel/RRFtoWideTab.java | 10 +--
.../ctakes/ytex/kernel/SVMLinFormatterFactory.java | 19 ++---
.../org/apache/ctakes/ytex/kernel/SparseData.java | 7 +-
.../ctakes/ytex/kernel/SparseDataExporterImpl.java | 28 ++-----
.../ctakes/ytex/kernel/SvmlinEvaluationParser.java | 18 +----
.../ytex/kernel/dao/ClassifierEvaluationDao.java | 10 +--
.../kernel/dao/ClassifierEvaluationDaoImpl.java | 17 +---
.../apache/ctakes/ytex/kernel/dao/ConceptDao.java | 4 +-
.../ctakes/ytex/kernel/dao/ConceptDaoImpl.java | 49 ++++--------
.../ytex/kernel/dao/KernelEvaluationDao.java | 4 +-
.../ytex/kernel/dao/KernelEvaluationDaoImpl.java | 4 +-
.../ctakes/ytex/kernel/dao/SortedSetUserType.java | 14 ++--
.../ytex/kernel/dao/StringArrayUserType.java | 19 ++---
.../ctakes/ytex/kernel/evaluator/CacheKernel.java | 1 -
.../kernel/evaluator/CorpusKernelEvaluator.java | 4 +-
.../evaluator/CorpusKernelEvaluatorImpl.java | 32 +++-----
.../kernel/evaluator/MethodCachingInterceptor.java | 5 +-
.../ctakes/ytex/kernel/evaluator/NormKernel.java | 1 -
.../ytex/kernel/evaluator/ProductKernel.java | 6 +-
.../ytex/kernel/evaluator/SemanticSimKernel.java | 12 ++-
.../ytex/kernel/evaluator/SemanticTypeKernel.java | 10 +--
.../evaluator/SymmetricPairCacheKeyGenerator.java | 4 +-
.../ctakes/ytex/kernel/evaluator/TreePrinter.java | 6 +-
.../evaluator/WeightedPolynomialMixingKernel.java | 4 +-
.../ytex/kernel/metric/BaseSimilarityMetric.java | 2 -
.../ctakes/ytex/kernel/metric/ConceptPair.java | 3 +-
.../ytex/kernel/metric/ConceptPairSimilarity.java | 5 +-
.../kernel/metric/ConceptSimilarityService.java | 4 +-
.../metric/ConceptSimilarityServiceImpl.java | 35 +--------
.../apache/ctakes/ytex/kernel/metric/LCSPath.java | 5 +-
.../ctakes/ytex/kernel/metric/LinMetric.java | 4 +-
.../ctakes/ytex/kernel/metric/PageRankMetric.java | 4 +-
.../ctakes/ytex/kernel/metric/SimilarityInfo.java | 7 +-
.../kernel/model/ClassifierEvaluationIRStat.java | 4 +-
.../apache/ctakes/ytex/kernel/model/ConcRel.java | 16 +---
.../ytex/kernel/model/CrossValidationFold.java | 4 +-
.../ytex/kernel/model/FeatureEvaluation.java | 4 +-
.../ctakes/ytex/kernel/model/KernelEvaluation.java | 4 +-
.../ytex/kernel/pagerank/PageRankService.java | 4 +-
.../ytex/kernel/pagerank/PageRankServiceImpl.java | 18 +----
.../ytex/kernel/tree/InstanceTreeBuilderImpl.java | 20 +----
.../ytex/kernel/wsd/WordSenseDisambiguator.java | 4 +-
.../kernel/wsd/WordSenseDisambiguatorImpl.java | 14 +---
.../ctakes/ytex/libsvm/LibSVMFormatterFactory.java | 19 +----
.../ytex/libsvm/LibSVMGramMatrixExporterImpl.java | 30 ++------
.../apache/ctakes/ytex/libsvm/LibSVMParser.java | 10 +--
.../apache/ctakes/ytex/libsvm/LibSVMUtilImpl.java | 15 ++--
.../ctakes/ytex/semil/SemiLEvaluationParser.java | 21 ++---
.../ctakes/ytex/semil/SemiLFormatterFactory.java | 18 +----
.../ytex/sparsematrix/InstanceDataExporter.java | 4 +-
.../sparsematrix/InstanceDataExporterImpl.java | 10 +--
.../sparsematrix/SparseMatrixFormatterFactory.java | 12 +--
.../ctakes/ytex/svmlight/SGTFormatterFactory.java | 10 +--
.../ytex/svmlight/SVMLightFormatterFactory.java | 25 ++----
.../ctakes/ytex/svmlight/SVMLightParser.java | 15 ++--
.../org/apache/ctakes/ytex/umls/dao/UMLSDao.java | 4 +-
.../apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java | 15 ++--
.../ytex/weka/DocumentResultInstanceImporter.java | 4 +-
.../apache/ctakes/ytex/weka/ExportBagOfWords.java | 4 +-
.../apache/ctakes/ytex/weka/ExportGramMatrix.java | 4 +-
.../ctakes/ytex/weka/GramMatrixExporterImpl.java | 25 ++----
.../apache/ctakes/ytex/weka/ImportWekaResults.java | 19 +----
.../ytex/weka/WekaAttributeEvaluatorImpl.java | 28 ++-----
.../ctakes/ytex/weka/WekaBagOfWordsExporter.java | 6 +-
.../ytex/weka/WekaBagOfWordsExporterImpl.java | 23 ++----
.../ctakes/ytex/weka/WekaFormatterFactory.java | 21 ++---
.../ctakes/ytex/weka/WekaResultsImporterImpl.java | 12 +--
.../org/apache/ctakes/ytex/beans-datasource.xml | 8 +-
.../org/apache/ctakes/ytex/beans-kernel-sim.xml | 8 +-
.../org/apache/ctakes/ytex/beans-kernel.hbm.xml | 8 +-
.../org/apache/ctakes/ytex/beans-kernel.xml | 8 +-
.../org/apache/ctakes/ytex/uima/beans-uima-dao.xml | 8 +-
.../apache/ctakes/ytex/uima/beans-uima-mapper.xml | 8 +-
.../org/apache/ctakes/ytex/uima/beans-uima.hbm.xml | 8 +-
.../apache/ctakes/ytex/web/beans-kernel-simweb.xml | 8 +-
.../org/apache/ctakes/ytex/web/beans-web.xml | 8 +-
.../java/org/apache/ctakes/jdl/AppJdlTest.java | 21 +++--
.../java/org/apache/ctakes/jdl/AppMainTest.java | 23 +++---
.../org/apache/ctakes/jdl/common/FileUtilTest.java | 16 ++--
.../org/apache/ctakes/jdl/common/PropFileTest.java | 15 ++--
.../ctakes/jdl/common/PropertiesFileTest.java | 15 ++--
.../apache/ctakes/jdl/common/SingletonTest.java | 9 +--
.../ctakes/jdl/data/base/JdlConnectionTest.java | 19 ++---
.../ctakes/jdl/data/loader/CsvLoaderTest.java | 17 ++--
.../ctakes/jdl/data/loader/XmlLoaderTest.java | 15 ++--
.../apache/ctakes/jdl/data/xml/DomParserTest.java | 7 +-
.../apache/ctakes/jdl/data/xml/DomUtilTest.java | 14 ++--
.../apache/ctakes/jdl/data/xml/ValidationTest.java | 19 ++---
.../jdl/data/xml/jaxb/ObjectFactoryBindTest.java | 16 ++--
.../jdl/data/xml/jaxb/ObjectFactoryUtilTest.java | 14 ++--
.../org/apache/ctakes/jdl/test/PropFileMaps.java | 4 +-
.../java/org/apache/ctakes/jdl/test/SqlJdl.java | 4 +-
.../org/apache/ctakes/ytex/ConceptDaoTest.java | 17 ++--
.../apache/ctakes/ytex/umls/dao/UMLSDaoTest.java | 4 +-
ctakes-ytex/src/test/resources/conn.xml | 2 +-
ctakes-ytex/src/test/resources/load1csv.xml | 2 +-
ctakes-ytex/src/test/resources/load1xml.xml | 2 +-
ctakes-ytex/src/test/resources/load2csv.xml | 2 +-
ctakes-ytex/src/test/resources/load2xml.xml | 2 +-
pom.xml | 2 +
851 files changed, 3566 insertions(+), 6390 deletions(-)
