Path	Lines of Code
ctakes-ytex/scripts/build-classpath.xml	2
ctakes-ytex/scripts/build-nonasf.xml	2
ctakes-ytex/scripts/build-setup.xml	2
ctakes-ytex/scripts/data/hsql/kernel/create_tables.sql	228
ctakes-ytex/scripts/data/hsql/kernel/drop_tables.sql	21
ctakes-ytex/scripts/data/hsql/kernel/ic_copy.template.sql	14
ctakes-ytex/scripts/data/hsql/kernel/ic_create.sql	7
ctakes-ytex/scripts/data/hsql/uima/create_document.sql	180
ctakes-ytex/scripts/data/hsql/uima/create_reference.sql	38
ctakes-ytex/scripts/data/hsql/uima/create_view.sql	43
ctakes-ytex/scripts/data/hsql/uima/drop_document.sql	28
ctakes-ytex/scripts/data/hsql/uima/drop_reference.sql	6
ctakes-ytex/scripts/data/hsql/uima/drop_view.sql	8
ctakes-ytex/scripts/data/hsql/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/hsql/umls/create_indices.sql	2
ctakes-ytex/scripts/data/hsql/umls/create_tables.sql	7
ctakes-ytex/scripts/data/hsql/umls/create_view.sql	8
ctakes-ytex/scripts/data/hsql/umls/drop_tables.sql	1
ctakes-ytex/scripts/data/hsql/umls/drop_view.sql	2
ctakes-ytex/scripts/data/hsql/umls/import_umls.sql	31
ctakes-ytex/scripts/data/hsql/umls/index_umls.sql	10
ctakes-ytex/scripts/data/hsql/umls/index_view.sql	3
ctakes-ytex/scripts/data/hsql/umls/insert_view.sql	26
ctakes-ytex/scripts/data/mssql/esld/abs/create_abstraction.sql	109
ctakes-ytex/scripts/data/mssql/esld/abs/create_sp.sql	20
ctakes-ytex/scripts/data/mssql/esld/abs/drop_abstraction.sql	5
ctakes-ytex/scripts/data/mssql/esld/create_document.sql	1
ctakes-ytex/scripts/data/mssql/esld/create_view.sql	60
ctakes-ytex/scripts/data/mssql/esld/insert_reference.sql	40
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_ascites.sql	53
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_livermass.sql	87
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_radiology.sql	243
ctakes-ytex/scripts/data/mssql/esld/postprocessing/classify_varices.sql	87
ctakes-ytex/scripts/data/mssql/esld/postprocessing/create_view.sql	50
ctakes-ytex/scripts/data/mssql/esld/postprocessing/delete_analysis_batch.sql	3
ctakes-ytex/scripts/data/mssql/esld/postprocessing/insert_radiology_review.sql	11
ctakes-ytex/scripts/data/mssql/esld/postprocessing/link_documents.sql	34
ctakes-ytex/scripts/data/mssql/esld/postprocessing/mark_duplicates.sql	40
ctakes-ytex/scripts/data/mssql/esld/postprocessing/score_report.sql	100
ctakes-ytex/scripts/data/mssql/esld/postprocessing/score_report_all.sql	94
ctakes-ytex/scripts/data/mssql/kernel/create_tables.sql	217
ctakes-ytex/scripts/data/mssql/kernel/drop_tables.sql	63
ctakes-ytex/scripts/data/mssql/uima/create_document.sql	215
ctakes-ytex/scripts/data/mssql/uima/create_reference.sql	40
ctakes-ytex/scripts/data/mssql/uima/create_view.sql	50
ctakes-ytex/scripts/data/mssql/uima/drop_document.sql	75
ctakes-ytex/scripts/data/mssql/uima/drop_reference.sql	18
ctakes-ytex/scripts/data/mssql/uima/drop_view.sql	12
ctakes-ytex/scripts/data/mssql/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/mssql/umls/create_indices.sql	2
ctakes-ytex/scripts/data/mssql/umls/create_tables.sql	7
ctakes-ytex/scripts/data/mssql/umls/create_view.sql	9
ctakes-ytex/scripts/data/mssql/umls/drop_tables.sql	3
ctakes-ytex/scripts/data/mssql/umls/drop_view.sql	6
ctakes-ytex/scripts/data/mssql/umls/import_umls.sql	30
ctakes-ytex/scripts/data/mssql/umls/index_umls.sql	9
ctakes-ytex/scripts/data/mssql/umls/index_view.sql	2
ctakes-ytex/scripts/data/mssql/umls/insert_view.sql	28
ctakes-ytex/scripts/data/mssql/umls/mssql_drop.sql	159
ctakes-ytex/scripts/data/mssql/umls/mssql_indexes.sql	70
ctakes-ytex/scripts/data/mssql/umls/mssql_net_tables.sql	42
ctakes-ytex/scripts/data/mssql/umls/mssql_tables.sql	422
ctakes-ytex/scripts/data/mysql/kernel/create_tables.sql	211
ctakes-ytex/scripts/data/mysql/kernel/drop_tables.sql	21
ctakes-ytex/scripts/data/mysql/kernel/ic_copy.template.sql	14
ctakes-ytex/scripts/data/mysql/kernel/ic_create.sql	7
ctakes-ytex/scripts/data/mysql/snomedct/create_tables.sql	36
ctakes-ytex/scripts/data/mysql/snomedct/create_tables_full.sql	37
ctakes-ytex/scripts/data/mysql/snomedct/index_tables.sql	8
ctakes-ytex/scripts/data/mysql/snomedct/index_tables_full.sql	8
ctakes-ytex/scripts/data/mysql/uima/create_document.sql	198
ctakes-ytex/scripts/data/mysql/uima/create_reference.sql	44
ctakes-ytex/scripts/data/mysql/uima/create_view.sql	43
ctakes-ytex/scripts/data/mysql/uima/delete_orphan.sql	72
ctakes-ytex/scripts/data/mysql/uima/drop_document.sql	28
ctakes-ytex/scripts/data/mysql/uima/drop_reference.sql	6
ctakes-ytex/scripts/data/mysql/uima/drop_view.sql	8
ctakes-ytex/scripts/data/mysql/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/mysql/umls/create_indices.sql	2
ctakes-ytex/scripts/data/mysql/umls/create_tables.sql	7
ctakes-ytex/scripts/data/mysql/umls/create_view.sql	8
ctakes-ytex/scripts/data/mysql/umls/drop_tables.sql	1
ctakes-ytex/scripts/data/mysql/umls/drop_view.sql	2
ctakes-ytex/scripts/data/mysql/umls/import_umls.sql	30
ctakes-ytex/scripts/data/mysql/umls/index_umls.sql	10
ctakes-ytex/scripts/data/mysql/umls/index_view.sql	3
ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql	26
ctakes-ytex/scripts/data/mysql/util/update_anno_contain.sql	21
ctakes-ytex/scripts/data/orcl/kernel/create_tables.sql	32
ctakes-ytex/scripts/data/orcl/kernel/create_tables_trg.sql	21
ctakes-ytex/scripts/data/orcl/kernel/drop_tables.sql	15
ctakes-ytex/scripts/data/orcl/uima/create_document.sql	226
ctakes-ytex/scripts/data/orcl/uima/create_document_trg.sql	28
ctakes-ytex/scripts/data/orcl/uima/create_reference.sql	53
ctakes-ytex/scripts/data/orcl/uima/create_reference_trg.sql	14
ctakes-ytex/scripts/data/orcl/uima/create_view.sql	47
ctakes-ytex/scripts/data/orcl/uima/drop_document.sql	47
ctakes-ytex/scripts/data/orcl/uima/drop_reference.sql	12
ctakes-ytex/scripts/data/orcl/uima/drop_view.sql	4
ctakes-ytex/scripts/data/orcl/uima/fracture_demo.sql	1
ctakes-ytex/scripts/data/orcl/umls/create_indices.sql	2
ctakes-ytex/scripts/data/orcl/umls/create_tables.sql	7
ctakes-ytex/scripts/data/orcl/umls/create_view.sql	9
ctakes-ytex/scripts/data/orcl/umls/drop_tables.sql	3
ctakes-ytex/scripts/data/orcl/umls/drop_view.sql	5
ctakes-ytex/scripts/data/orcl/umls/import_umls.sql	28
ctakes-ytex/scripts/data/orcl/umls/index_umls.sql	16
ctakes-ytex/scripts/data/orcl/umls/index_view.sql	3
ctakes-ytex/scripts/data/orcl/umls/insert_view.template.sql	26
ctakes-ytex/scripts/data/ref_uima_type.xml	9
ctakes-ytex/scripts/data/snomedct/sct2_concept.xml	11
ctakes-ytex/scripts/data/snomedct/sct2_description.xml	17
ctakes-ytex/scripts/data/snomedct/sct2_relationship.xml	16
ctakes-ytex/scripts/data/snomedct/sct2f_concept.xml	11
ctakes-ytex/scripts/data/snomedct/sct2f_description.xml	17
ctakes-ytex/scripts/data/snomedct/sct2f_relationship.xml	16
ctakes-ytex/scripts/data/stopword.xml	7
ctakes-ytex/scripts/data/umls/AMBIGLUI.xml	8
ctakes-ytex/scripts/data/umls/AMBIGSUI.xml	8
ctakes-ytex/scripts/data/umls/MRAUI.xml	15
ctakes-ytex/scripts/data/umls/MRCOC.xml	15
ctakes-ytex/scripts/data/umls/MRCOLS.xml	14
ctakes-ytex/scripts/data/umls/MRCONSO.xml	24
ctakes-ytex/scripts/data/umls/MRCUI.xml	13
ctakes-ytex/scripts/data/umls/MRDEF.xml	14
ctakes-ytex/scripts/data/umls/MRDOC.xml	10
ctakes-ytex/scripts/data/umls/MRFILES.xml	12
ctakes-ytex/scripts/data/umls/MRHIER.xml	15
ctakes-ytex/scripts/data/umls/MRHIST.xml	15
ctakes-ytex/scripts/data/umls/MRMAP.xml	32
ctakes-ytex/scripts/data/umls/MRRANK.xml	10
ctakes-ytex/scripts/data/umls/MRREL.xml	22
ctakes-ytex/scripts/data/umls/MRSAB.xml	31
ctakes-ytex/scripts/data/umls/MRSAT.xml	19
ctakes-ytex/scripts/data/umls/MRSMAP.xml	17
ctakes-ytex/scripts/data/umls/MRSTY.xml	12
ctakes-ytex/scripts/data/umls/MRXNS_ENG.xml	11
ctakes-ytex/scripts/data/umls/MRXNW_ENG.xml	11
ctakes-ytex/scripts/data/umls/MRXW_ENG.xml	11
ctakes-ytex/scripts/data/umls/SRDEF.xml	16
ctakes-ytex/scripts/data/umls/SRFIL.xml	12
ctakes-ytex/scripts/data/umls/SRFLD.xml	10
ctakes-ytex/scripts/data/umls/SRSTR.xml	10
ctakes-ytex/scripts/data/umls/SRSTRE1.xml	9
ctakes-ytex/scripts/data/umls/SRSTRE2.xml	9
ctakes-ytex/scripts/data/umls/umls_aui_fword.xml	11
ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.xml	12
ctakes-ytex/src/assemble/dist.xml	25
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/App.java	8
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/AppJdl.java	76
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/AppMain.java	44
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/FileUtil.java	24
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/PropFile.java	29
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/PropertiesFile.java	27
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/Singleton.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/common/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/base/JdlConnection.java	66
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/base/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/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/loader/package-info.java	1
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/jdl/data/xml/Validation.java	80
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/jaxb/ObjectFactoryBind.java	41
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/jaxb/ObjectFactoryUtil.java	63
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/jaxb/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/data/xml/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/jdl/package-info.java	1
ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHelper.java	33
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/KernelLauncher.java	145
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/R/RGramMatrixExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/R/RGramMatrixExporterImpl.java	146
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/dao/DBUtil.java	78
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/AbstractBagOfWordsExporter.java	158
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BagOfWordsData.java	70
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BagOfWordsDecorator.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BagOfWordsExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BaseClassifierEvaluationParser.java	278
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/BaseSparseDataFormatter.java	135
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvalUtil.java	328
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationImporter.java	79
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationParser.java	28
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationResult.java	31
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ClassifierEvaluationResults.java	45
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/CytoscapeHelper.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/CytoscapeHelperImpl.java	205
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/FileUtil.java	185
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/FoldGenerator.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/FoldGeneratorImpl.java	233
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IRMetrics.java	70
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ImputedFeatureEvaluator.java	20
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/ImputedFeatureEvaluatorImpl.java	757
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/InfoContentEvaluator.java	8
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/InfoContentEvaluatorImpl.java	143
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/InstanceData.java	50
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluator.java	11
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java	315
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/KernelContextHolder.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/KernelUtil.java	29
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/KernelUtilImpl.java	320
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/OrderedPair.java	45
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/Pair.java	40
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/RRFtoWideTab.java	45
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SVMLinFormatterFactory.java	140
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SimSvcContextHolder.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseData.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporter.java	22
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataExporterImpl.java	283
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataFormatter.java	25
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SparseDataFormatterFactory.java	4
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/SvmlinEvaluationParser.java	129
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ClassifierEvaluationDao.java	58
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ClassifierEvaluationDaoImpl.java	300
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDao.java	10
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java	386
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/KernelEvaluationDao.java	20
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/KernelEvaluationDaoImpl.java	135
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/SortedSetUserType.java	76
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/StringArrayUserType.java	81
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/AttributeProductKernel.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CacheKernel.java	52
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CacheKeyGenerator.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/ConvolutionKernel.java	43
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CorpusKernelEvaluator.java	11
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/CorpusKernelEvaluatorImpl.java	404
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/EqualityKernel.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/Kernel.java	4
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/LinKernel.java	8
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/MethodCachingInterceptor.java	64
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/NamedEntityNegationKernel.java	24
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/NodeAttributeKernel.java	31
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/NormKernel.java	79
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/ProductKernel.java	32
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SemanticSimKernel.java	111
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SemanticTypeKernel.java	257
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SumKernel.java	19
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/SymmetricPairCacheKeyGenerator.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/TreePrinter.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/evaluator/WeightedPolynomialMixingKernel.java	71
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/BaseSimilarityMetric.java	51
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptInfo.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptPair.java	71
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptPairSimilarity.java	37
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityService.java	48
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityServiceImpl.java	648
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicLCHMetric.java	23
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicPathMetric.java	21
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicRadaMetric.java	21
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/JaccardMetric.java	18
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LCHMetric.java	22
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LCSPath.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LinMetric.java	42
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/PageRankMetric.java	17
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/PathMetric.java	17
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/RadaMetric.java	22
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/SimilarityInfo.java	67
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/SimilarityMetric.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/SokalSneathMetric.java	18
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/WuPalmerMetric.java	23
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.java	92
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluationIRStat.java	127
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ClassifierInstanceEvaluation.java	50
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ConcRel.java	334
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ConceptGraph.java	51
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/CrossValidationFold.java	69
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/CrossValidationFoldInstance.java	50
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/FeatureEvaluation.java	73
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/FeatureParentChild.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/FeatureRank.java	98
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/KernelEvaluation.java	55
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/KernelEvaluationInstance.java	70
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/ObjPair.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/SVMClassifierEvaluation.java	53
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/model/SemiLClassifierEvaluation.java	60
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/pagerank/PageRankService.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/pagerank/PageRankServiceImpl.java	315
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/InstanceTreeBuilder.java	10
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/InstanceTreeBuilderImpl.java	150
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/Node.java	69
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/NodeKey.java	40
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/NodeMappingInfo.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/QueryMappingInfo.java	26
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/tree/TreeMappingInfo.java	43
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/wsd/WordSenseDisambiguator.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/wsd/WordSenseDisambiguatorImpl.java	124
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMFormatterFactory.java	115
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMGramMatrixExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMGramMatrixExporterImpl.java	215
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMParser.java	202
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMUtil.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/libsvm/LibSVMUtilImpl.java	59
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/semil/SemiLEvaluationParser.java	148
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/semil/SemiLFormatterFactory.java	147
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/sparsematrix/InstanceDataExporter.java	14
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/sparsematrix/InstanceDataExporterImpl.java	101
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/sparsematrix/SparseMatrixFormatterFactory.java	101
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/svmlight/SGTFormatterFactory.java	47
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/svmlight/SVMLightFormatterFactory.java	123
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/svmlight/SVMLightParser.java	113
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java	16
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java	97
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/MRCONSO.java	157
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/MRREL.java	74
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/MRSTY.java	83
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/model/UmlsAuiFirstWord.java	52
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/DocumentResultInstanceImporter.java	32
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ExportBagOfWords.java	11
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ExportGramMatrix.java	15
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/GramMatrixExporter.java	6
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/GramMatrixExporterImpl.java	191
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/ImportWekaResults.java	128
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaAttributeEvaluator.java	10
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaAttributeEvaluatorImpl.java	198
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaBagOfWordsExporter.java	12
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaBagOfWordsExporterImpl.java	203
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaFormatterFactory.java	172
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaResultInstanceImporter.java	7
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaResultsImporter.java	13
ctakes-ytex/src/main/java/org/apache/ctakes/ytex/weka/WekaResultsImporterImpl.java	122
ctakes-ytex/src/main/resources/ehcache.xml	6
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml	73
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml	55
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-kernel.hbm.xml	18
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/beans-kernel.xml	292
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.template.xml	4
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml	4
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.template.xml	4
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml	37
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml	38
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml	16
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernel/model/ClassifierEvaluation.hbm.xml	298
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernel/model/KernelEvaluation.hbm.xml	63
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml	14
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml	15
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml	17
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-dao.xml	20
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima-mapper.xml	115
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/beans-uima.hbm.xml	21
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/model/Document.hbm.xml	57
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/model/NamedEntityRegex.hbm.xml	16
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/uima/model/SegmentRegex.hbm.xml	14
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/umls/model/FWord.hbm.xml	37
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml	43
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml	34
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-security.xml	29
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-web.xml	25
ctakes-ytex/src/main/resources/org/apache/ctakes/ytex/web/beans-ws.xml	24