Path	Lines of Code
ctakes-core/desc/analysis_engine/AggregateAE.xml	59
ctakes-core/desc/analysis_engine/AggregateTemplateFiller.xml	58
ctakes-core/desc/analysis_engine/BsvRegexSectionizer.xml	54
ctakes-core/desc/analysis_engine/CDASegmentAnnotator.xml	51
ctakes-core/desc/analysis_engine/CopyAnnotator.xml	91
ctakes-core/desc/analysis_engine/FilterAnnotator.xml	29
ctakes-core/desc/analysis_engine/NullAnnotator.xml	26
ctakes-core/desc/analysis_engine/OverlapAnnotator.xml	130
ctakes-core/desc/analysis_engine/PiperFileAggregate.xml	38
ctakes-core/desc/analysis_engine/PiperFileRunEngine.xml	49
ctakes-core/desc/analysis_engine/SHARPKnowtatorXMLReader.xml	60
ctakes-core/desc/analysis_engine/SectionFilter.xml	51
ctakes-core/desc/analysis_engine/SectionSegmentAnnotator.xml	82
ctakes-core/desc/analysis_engine/SentenceDetectorAggregate.xml	42
ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml	60
ctakes-core/desc/analysis_engine/SentenceDetectorAnnotatorBIO.xml	2572
ctakes-core/desc/analysis_engine/SentencesAndTokensAggregate.xml	59
ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml	44
ctakes-core/desc/analysis_engine/SimpleSegmentWithTagsAnnotator.xml	52
ctakes-core/desc/analysis_engine/TemplateFillerAnnotator.xml	24
ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml	56
ctakes-core/desc/analysis_engine/TokenizerAnnotatorVersion1.xml	91
ctakes-core/desc/analysis_engine/TokensAndSentencesTAE.xml	45
ctakes-core/desc/cas_consumer/EmbeddedXmlCasConsumer.xml	61
ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml	52
ctakes-core/desc/cas_consumer/FilesInDirectoryCasConsumer.example.xml	36
ctakes-core/desc/cas_consumer/HtmlTableCasConsumer.xml	65
ctakes-core/desc/cas_consumer/JdbcCasConsumer.xml	148
ctakes-core/desc/cas_consumer/JdbcWriterTemplate.xml	142
ctakes-core/desc/cas_consumer/NormalizedFilesInDirectoryCasConsumer.example.xml	40
ctakes-core/desc/cas_consumer/PrettyTextWriter.xml	46
ctakes-core/desc/cas_consumer/PropertyTextWriter.xml	44
ctakes-core/desc/cas_consumer/SentenceTokensPrinter.xml	42
ctakes-core/desc/cas_consumer/TokenFreqCasConsumer.xml	38
ctakes-core/desc/cas_consumer/TokenOffsetsCasConsumer.example.xml	50
ctakes-core/desc/cas_consumer/XCasWriterCasConsumer.xml	46
ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.xml	44
ctakes-core/desc/cas_initializer/NseCasInitializer.xml	47
ctakes-core/desc/cas_initializer/XCasReaderCasInitializer.xml	33
ctakes-core/desc/collection_processing_engine/PiperFileCPE.xml	23
ctakes-core/desc/collection_processing_engine/SentenceDetectorCPE.xml	58
ctakes-core/desc/collection_processing_engine/SentencesAndTokensCPE.xml	58
ctakes-core/desc/collection_reader/FilesInDirectoryCollectionCyclicalReads.xml	84
ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml	72
ctakes-core/desc/collection_reader/JdbcCollectionReader.example.xml	191
ctakes-core/desc/collection_reader/LinesFromFileCollectionReader.xml	85
ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml	46
ctakes-core/src/main/java/org/apache/ctakes/core/ae/AbstractCommandRunner.java	95
ctakes-core/src/main/java/org/apache/ctakes/core/ae/BsvRegexSectionizer.java	79
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CDASegmentAnnotator.java	150
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java	98
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CopyAnnotator.java	106
ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java	100
ctakes-core/src/main/java/org/apache/ctakes/core/ae/DocumentIdPrinterAnalysisEngine.java	26
ctakes-core/src/main/java/org/apache/ctakes/core/ae/EolSentenceFixer.java	113
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ExitForcer.java	54
ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java	52
ctakes-core/src/main/java/org/apache/ctakes/core/ae/LabValueFinder.java	311
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListAnnotator.java	258
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListEntryNegator.java	84
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListParagraphFixer.java	71
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ListSentenceFixer.java	70
ctakes-core/src/main/java/org/apache/ctakes/core/ae/MrsDrSentenceJoiner.java	84
ctakes-core/src/main/java/org/apache/ctakes/core/ae/NamedEngine.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/ae/NullAnnotator.java	17
ctakes-core/src/main/java/org/apache/ctakes/core/ae/OverlapAnnotator.java	328
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphAnnotator.java	156
ctakes-core/src/main/java/org/apache/ctakes/core/ae/ParagraphSentenceFixer.java	88
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PausableFileLoggerAE.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PiperFileRunEngine.java	129
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonPipper.java	65
ctakes-core/src/main/java/org/apache/ctakes/core/ae/PythonRunner.java	136
ctakes-core/src/main/java/org/apache/ctakes/core/ae/RegexSectionizer.java	312
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java	1329
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SectionSegmentAnnotator.java	79
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetector.java	222
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorBIO.java	330
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotator.java	49
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SimpleSegmentWithTagsAnnotator.java	94
ctakes-core/src/main/java/org/apache/ctakes/core/ae/StartFinishLogger.java	109
ctakes-core/src/main/java/org/apache/ctakes/core/ae/SubjectSectionFixer.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java	235
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenConverter.java	167
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotator.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTB.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/ae/UmlsEnvironmentConfiguration.java	27
ctakes-core/src/main/java/org/apache/ctakes/core/ae/inert/PausableAE.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractFileWriter.java	125
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJCasFileWriter.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractJdbcWriter.java	177
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractOutputFileWriter.java	4
ctakes-core/src/main/java/org/apache/ctakes/core/cc/AbstractTableFileWriter.java	183
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CASConsumerTestDriver.java	43
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CasConsumer.java	61
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiCountFileWriter.java	120
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiListFileWriter.java	89
ctakes-core/src/main/java/org/apache/ctakes/core/cc/CuiLookupLister.java	42
ctakes-core/src/main/java/org/apache/ctakes/core/cc/FileTreeXmiWriter.java	46
ctakes-core/src/main/java/org/apache/ctakes/core/cc/FilesInDirectoryCasConsumer.java	55
ctakes-core/src/main/java/org/apache/ctakes/core/cc/HtmlTableCasConsumer.java	293
ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java	204
ctakes-core/src/main/java/org/apache/ctakes/core/cc/MedicationTableFileWriter.java	127
ctakes-core/src/main/java/org/apache/ctakes/core/cc/NonTerminalConsumer.java	7
ctakes-core/src/main/java/org/apache/ctakes/core/cc/NormalizedFilesInDirectoryCasConsumer.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/cc/SemanticTableFileWriter.java	159
ctakes-core/src/main/java/org/apache/ctakes/core/cc/SentenceTokensPrinter.java	119
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TextSpanWriter.java	112
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenFreqCasConsumer.java	102
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenOffsetsCasConsumer.java	68
ctakes-core/src/main/java/org/apache/ctakes/core/cc/TokenTableFileWriter.java	35
ctakes-core/src/main/java/org/apache/ctakes/core/cc/XMISerializer.java	144
ctakes-core/src/main/java/org/apache/ctakes/core/cc/XmiWriterCasConsumerCtakes.java	149
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/HtmlTextWriter.java	1223
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/JsWriter.java	57
ctakes-core/src/main/java/org/apache/ctakes/core/cc/html/SemanticMarkup.java	52
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/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/jdbc/db/JdbcDb.java	30
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/BooleanField.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/FloatField.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/JdbcField.java	8
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/TextField.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/i2b2/I2b2Db.java	32
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/ObservationFactRow.java	133
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/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/table/AbstractJdbcTable.java	52
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/JdbcTable.java	44
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/cell/AbstractItemCell.java	12
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/DefaultBaseItemCell.java	37
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/ItemCell.java	9
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/UmlsItemCell.java	5
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/HtmlTextWriter.java	1105
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/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/row/DefaultItemRow.java	65
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/property/plaintext/PropertyTextWriter.java	210
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/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/ci/TextModifier.java	5
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/ContinuousTextExtractor.java	67
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/FollowingWithPadding.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/MaxContext.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/MinContext.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/PrecedingWithPadding.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/cleartk/SumContext.java	56
ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetector.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeSentenceDetectorBio.java	72
ctakes-core/src/main/java/org/apache/ctakes/core/concurrent/ThreadSafeWrapper.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/config/ConfigParameterConstants.java	20
ctakes-core/src/main/java/org/apache/ctakes/core/cpe/CmdLineCpeRunner.java	111
ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java	562
ctakes-core/src/main/java/org/apache/ctakes/core/cr/FileTreeReader.java	105
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/JCasBuilder.java	219
ctakes-core/src/main/java/org/apache/ctakes/core/cr/JdbcCollectionReader.java	260
ctakes-core/src/main/java/org/apache/ctakes/core/cr/LinesFromFileCollectionReader.java	134
ctakes-core/src/main/java/org/apache/ctakes/core/cr/LuceneCollectionReader.java	102
ctakes-core/src/main/java/org/apache/ctakes/core/cr/TextReader.java	57
ctakes-core/src/main/java/org/apache/ctakes/core/cr/XMIReader.java	59
ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiCollectionReaderCtakes.java	75
ctakes-core/src/main/java/org/apache/ctakes/core/cr/XmiTreeReader.java	26
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/DecryptorWrapper.java	23
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/PassThroughDecryptor.java	10
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/CharacterTokenAdapter.java	17
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/DecimalTokenAdapter.java	30
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/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/SymbolTokenAdapter.java	10
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/WordTokenAdapter.java	44
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/adapters/package.html	5
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/DayNightWordCondition.java	20
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/DecimalCondition.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/DecimalValueCondition.java	19
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/HourMinuteCondition.java	43
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/IntegerRangeCondition.java	21
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/NegateCondition.java	12
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/PunctuationValueCondition.java	19
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/RomanNumeralCondition.java	12
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/TextSetCondition.java	25
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/WordSetCondition.java	25
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/condition/WordValueCondition.java	27
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/FSM.java	7
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/machine/FractionFSM.java	121
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/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/RangeFSM.java	129
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/TimeFSM.java	95
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/DateToken.java	6
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/MeasurementToken.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/fsm/output/NegationIndicator.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/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/TimeToken.java	6
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/token/BaseToken.java	5
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/ContractionToken.java	3
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/EolToken.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/NumberToken.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/SymbolToken.java	3
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/WordToken.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/token/adapter/CharacterTokenAdapter.java	14
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/IntegerTokenAdapter.java	37
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/WordTokenAdapter.java	41
ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorAnnotation.java	97
ctakes-core/src/main/java/org/apache/ctakes/core/knowtator/KnowtatorXMLParser.java	193
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/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/OffsetComparator.java	19
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/Tokenizer.java	443
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/TokenizerPTB.java	781
ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientConsumer.java	70
ctakes-core/src/main/java/org/apache/ctakes/core/patient/AbstractPatientFileWriter.java	51
ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteCollector.java	21
ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientNoteStore.java	297
ctakes-core/src/main/java/org/apache/ctakes/core/patient/PatientViewUtil.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionals.java	234
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CliOptionalsHandler.java	159
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/CuiCollector.java	85
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/EntityCollector.java	108
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/GenerateSentenceBIODescriptors.java	19
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfo.java	75
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitInfoUtil.java	124
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipeBitLocator.java	209
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PipelineBuilder.java	245
ctakes-core/src/main/java/org/apache/ctakes/core/pipeline/PiperFileReader.java	432
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/StandardCliOptions.java	73
ctakes-core/src/main/java/org/apache/ctakes/core/resource/FileLocator.java	307
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/FileResourceImpl.java	39
ctakes-core/src/main/java/org/apache/ctakes/core/resource/JdbcConnectionResource.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/LinesFromFileStringsResourceImpl.java	43
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/StringIntegerMapResource.java	6
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringIntegerMapResourceImpl.java	65
ctakes-core/src/main/java/org/apache/ctakes/core/resource/StringMapResource.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/StringsResource.java	5
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/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/sentence/SentenceSpan.java	68
ctakes-core/src/main/java/org/apache/ctakes/core/util/BannerWriter.java	53
ctakes-core/src/main/java/org/apache/ctakes/core/util/CalendarUtil.java	214
ctakes-core/src/main/java/org/apache/ctakes/core/util/CtakesFileNamer.java	39
ctakes-core/src/main/java/org/apache/ctakes/core/util/DateParser.java	85
ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentIDAnnotationUtil.java	26
ctakes-core/src/main/java/org/apache/ctakes/core/util/DocumentSection.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/util/DotLogger.java	16
ctakes-core/src/main/java/org/apache/ctakes/core/util/EssentialAnnotationUtil.java	57
ctakes-core/src/main/java/org/apache/ctakes/core/util/FSUtil.java	86
ctakes-core/src/main/java/org/apache/ctakes/core/util/FinishedLogger.java	30
ctakes-core/src/main/java/org/apache/ctakes/core/util/JCasUtil.java	23
ctakes-core/src/main/java/org/apache/ctakes/core/util/ListFactory.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/util/ListIterable.java	30
ctakes-core/src/main/java/org/apache/ctakes/core/util/Mapper.java	21
ctakes-core/src/main/java/org/apache/ctakes/core/util/MutableUimaContext.java	168
ctakes-core/src/main/java/org/apache/ctakes/core/util/NumberedSuffixComparator.java	70
ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java	181
ctakes-core/src/main/java/org/apache/ctakes/core/util/Pair.java	35
ctakes-core/src/main/java/org/apache/ctakes/core/util/ParamUtil.java	36
ctakes-core/src/main/java/org/apache/ctakes/core/util/PropertyAeFactory.java	197
ctakes-core/src/main/java/org/apache/ctakes/core/util/RelationArgumentUtil.java	207
ctakes-core/src/main/java/org/apache/ctakes/core/util/SHARPKnowtatorXMLDefaults.java	10
ctakes-core/src/main/java/org/apache/ctakes/core/util/SourceMetadataUtil.java	60
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/annotation/ConceptBuilder.java	86
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/IdentifiedAnnotationBuilder.java	226
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/OntologyConceptUtil.java	359
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/SemanticTui.java	241
ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/WordTokenUtil.java	23
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/CollectionCreator.java	6
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/CollectionMap.java	15
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/collection/HashSetMap.java	107
ctakes-core/src/main/java/org/apache/ctakes/core/util/collection/ImmutableCollectionMap.java	102
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/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/SourceMetadataUtil.java	106
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySectionBuilder.java	41
ctakes-core/src/main/java/org/apache/ctakes/core/util/doc/TextBySentenceBuilder.java	76
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/regex/RegexSpanFinder.java	92
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/TimeoutMatcher.java	73
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/textspan/DefaultTextSpan.java	47
ctakes-core/src/main/java/org/apache/ctakes/core/util/textspan/TextSpan.java	8
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/main/resources/org/apache/ctakes/core/train/sentdetect/sample_sd_included.mod	85
ctakes-core/src/user/resources/org/apache/ctakes/core/list/DefaultListRegex.bsv	11
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/sections/DefaultSectionRegex.bsv	84
ctakes-core/src/user/resources/org/apache/ctakes/core/sections/NaaccrXmlSections.bsv	7
ctakes-core/src/user/resources/org/apache/ctakes/core/sections/SameLineSectionRegex.bsv	87