Index (Gene ID Mapper 2.5.0 API)

A B C D E F G H I J K L M N O P Q R S T U V W
All Classes All Packages

A

A - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
A() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A: Never called.
A(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A: Internal - constructor used by generator
A(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A
A(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A
A_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
A_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A_Type: initialize variables to correspond with Cas Type and Features
accept(File, String) - Method in class de.julielab.genemapper.utils.ExtensionFileFilter
ACCollector - Class in de.julielab.genemapper.utils.dict: Deprecated.
Check if this class is used anywhere (resource scripts?)
AcronymPipe - Class in de.julielab.genemapper.filtering.families
AcronymPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.AcronymPipe
AcronymTextCoverWriter - Class in de.julielab.genemapper.evaluation.tools
AcronymTextCoverWriter() - Constructor for class de.julielab.genemapper.evaluation.tools.AcronymTextCoverWriter
ADD_DESC - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ADD_GENERIF - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ADD_INTERACTIONS - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ADD_NAME_TYPES - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ADD_SUMMARY - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
addAcronymForm(ResolvedCompositeGeneName) - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName
addDocumentLevelGeneAnnotations(GeneDocument, Multimap<String, String>) - Static method in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
addEntity2SynonymsJaroWinklerScores(Map<String, Collection<GeneName>>, Map<String, Multimap<String, String>>, boolean, Map<String, Map<String, Double>>, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker: Performs Jaro-Winkler string similarity scoring between the gene names in the document and the database synonyms of the gene IDs found by those gene names.
addEntity2SynonymsLuceneScores(Map<String, Collection<GeneName>>, String, Map<String, Map<String, Double>>, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker: Obtains lucene scores for all gene names in the document.
addFeaturesForGeneMention(Token, GeneDocument, GeneMention, BioLemmatizer) - Method in class de.julielab.genemapper.filtering.families.LastWordPipe
addNameLevelUnificationStrategy(DypsisMappingCore.NameLevelUnificationStrategy...) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData: Deprecated.
addSynonym2ContextItemsScores(Map<String, Collection<GeneName>>, Map<String, Map<String, Double>>, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker: For each gene ID occurring in the document, this method uses all textual occurrences associated with this ID and formulates a query of it.
addSynonyms(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector
addTokenizedOutput(StringBuilder, JCoReAnnotationIndexMerger, JCoReOverlapAnnotationIndex<Organism>) - Method in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
addUntokenizedOutput(JCas, StringBuilder, Sentence) - Method in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
AnchorDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus
AnchorDisambiguationStep() - Constructor for class de.julielab.genemapper.mappingcores.quercus.AnchorDisambiguationStep
APP_NAME - Static variable in class de.julielab.genemapper.GeneMapper
APPROX_MATCH - Static variable in class de.julielab.genemapper.Configuration
APPROX_SCORER_TYPE - Static variable in class de.julielab.genemapper.Configuration
AppUtils - Class in de.julielab.genemapper.apps
assignContextScore(MentionDisambiguationData) - Method in interface de.julielab.genemapper.disambig.ContextRanker
assignContextScore(MentionDisambiguationData) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
available() - Method in class de.julielab.genemapper.utils.ReaderInputStream
avgDiffCorrect - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
avgDiffWrong - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
avgRatioCorrect - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
avgRatioWrong - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker

B

batchProcessComplete() - Method in class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
BC2Evaluation - Class in de.julielab.genemapper.hpo
BC2Evaluation() - Constructor for class de.julielab.genemapper.hpo.BC2Evaluation
BC3CorpusEvaluation - Class in de.julielab.genemapper.hpo
BC3CorpusEvaluation() - Constructor for class de.julielab.genemapper.hpo.BC3CorpusEvaluation
Be - Class in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer: Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Be - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Be() - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be: Never called.
Be() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be: Never called.
Be(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be: Internal - constructor used by generator
Be(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be: Internal - constructor used by generator
Be(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be
Be(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be
Be(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be
Be(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be
Be_Type - Class in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer: Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Be_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Be_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be_Type: initialize variables to correspond with Cas Type and Features
Be_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be_Type: initialize variables to correspond with Cas Type and Features
BioThesaurusFilterDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus: Removes IDs for which the respective candidate synonym stems from the BioThesaurus as long as other options are available.
BioThesaurusFilterDisambiguationStep() - Constructor for class de.julielab.genemapper.mappingcores.quercus.BioThesaurusFilterDisambiguationStep
BioThesaurusIproClassMerger - Class in de.julielab.genemapper.utils.dict
blacklist_pattern - Static variable in class de.julielab.genemapper.filtering.UnspecificNameFilter
BTMatcher - Class in de.julielab.genemapper.utils.dict
buildDijkstraTree(String) - Method in class de.julielab.genemapper.WikipediaCategoryManager

C

calculateScore(HpoInstance, Parameters, int, int, int, int, HpoRoute.Metric, int) - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
calculateScore(HpoInstance, Parameters, int, int, int, int, HpoRoute.Metric, int) - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
calculateScore(HpoInstance, Parameters, int, int, int, int, HpoRoute.Metric, int) - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
CANDIDATE_SETTER_PARAMS - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
CandidateRetrievalOptimizationRoute - Class in de.julielab.genemapper.hpo
CandidateRetrievalOptimizationRoute(Configuration) - Constructor for class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
checkSpeciesAssigner() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore: Performs a null check for the DypsisMappingCore.speciesAssigner and throws an exception if it is not present.
ChemicalSuffix - Class in de.julielab.genemapper.filtering.families: Taken from GNormPlus code: Wei, C.
ChemicalSuffix() - Constructor for class de.julielab.genemapper.filtering.families.ChemicalSuffix
ChunkTypePipe - Class in de.julielab.genemapper.filtering
ChunkTypePipe(String) - Constructor for class de.julielab.genemapper.filtering.ChunkTypePipe
classifySentencePairs(List<String>, List<String>) - Method in class de.julielab.genemapper.classification.TransformerClassifier
clear() - Method in interface de.julielab.genemapper.disambig.ContextRanker
clear() - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
clear() - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker: Sets the internal state to null.
clear() - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
clear() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
clear() - Method in interface de.julielab.genemapper.mappingcores.MappingCore
clear() - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
clearLexicalRankingModel() - Method in class de.julielab.genemapper.GeneMapper
clearSemanticRankingModel() - Method in class de.julielab.genemapper.GeneMapper
clipAsterisksFromGeneNames(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector: Call BEFORE selecting genes.
close() - Method in class de.julielab.genemapper.utils.ReaderInputStream
ClosedParenthesis - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
ClosedParenthesis() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis: Never called.
ClosedParenthesis(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis: Internal - constructor used by generator
ClosedParenthesis(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis
ClosedParenthesis(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis
ClosedParenthesis_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
ClosedParenthesis_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis_Type: initialize variables to correspond with Cas Type and Features
collectCandidateDisambiguationScores(GeneDocument, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
collectionProcessComplete() - Method in class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
collectionProcessComplete() - Method in class de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter
collectionProcessComplete() - Method in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
collectionProcessComplete() - Method in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
collectMatchingCandidates(Set<String>, List<SynHit>, List<String>) - Static method in class de.julielab.genemapper.apps.AppUtils: Retrieves the taxonomy IDs that have the synonym of the first candidate
Column - Class in de.julielab.genemapper.utils.dict
COMPONENT_ID - Static variable in class de.julielab.genemapper.uima.GeneMapperAnnotator
CompositeMentionTokenizer - Class in de.julielab.genemapper.composites: Special tokenization for composite concept resolution.
CompositeMentionTokenizer() - Constructor for class de.julielab.genemapper.composites.CompositeMentionTokenizer
CompositePatternResolver - Class in de.julielab.genemapper.composites: This is the base class for composite gene name resolution classes.
CompositePatternResolver() - Constructor for class de.julielab.genemapper.composites.CompositePatternResolver
CompositeToken - Class in de.julielab.genemapper.composites: This class represents the individual tokens of the composite gene mention tokenization.
CompositeToken(String, int, int, boolean, boolean) - Constructor for class de.julielab.genemapper.composites.CompositeToken
concatenate(String[], String[]) - Static method in class de.julielab.genemapper.filtering.StringHelper: Concatenates to string arrays into one.

The new array will have length array1.length + array2.length and contain, from elements 0 to array1.length-1, the elements of the original array1 first, then, starting from array1.length, the elements of original array2.
CONFIG_QUERCUS - Static variable in class de.julielab.genemapper.hpo.GnHpoServer
CONFIG_WITH_SA_AND_LUCENE_SETTINGS - Static variable in class de.julielab.genemapper.hpo.GnHpoServer
CONFIG_WITH_SA_SETTINGS - Static variable in class de.julielab.genemapper.hpo.GnHpoServer
Configuration - Class in de.julielab.genemapper
Configuration() - Constructor for class de.julielab.genemapper.Configuration
Configuration(Configuration) - Constructor for class de.julielab.genemapper.Configuration
Configuration(File) - Constructor for class de.julielab.genemapper.Configuration
Configuration(String...) - Constructor for class de.julielab.genemapper.Configuration
configure() - Method in class de.julielab.genemapper.ioc.GeneMappingModule
configure() - Method in class de.julielab.genemapper.ioc.WikipediaModule
containsAny(Collection<SynHit>) - Method in class de.julielab.genemapper.SynHitSet
CONTEXT_INDEX - Static variable in class de.julielab.genemapper.Configuration
CONTEXT_ITEMS_INDEX - Static variable in class de.julielab.genemapper.Configuration
CONTEXT_WINDOW_SIZE - Static variable in class de.julielab.genemapper.uima.GeneMapperAnnotator
ContextEmbeddingPipe - Class in de.julielab.genemapper.filtering.families
ContextEmbeddingPipe() - Constructor for class de.julielab.genemapper.filtering.families.ContextEmbeddingPipe
ContextGenerator - Class in de.julielab.genemapper.index
ContextGenerator(String, String) - Constructor for class de.julielab.genemapper.index.ContextGenerator: constructor which creates semantic context index in the specified directory on the disk file paths are hard-coded due to size issues
contextHash - Variable in class de.julielab.genemapper.disambig.ContextScoreCacheKey
ContextIndexFieldNames - Class in de.julielab.genemapper.index
ContextIndexFieldNames() - Constructor for class de.julielab.genemapper.index.ContextIndexFieldNames
ContextItemRecordsIndex - Class in de.julielab.genemapper.disambig: Deprecated.
in favor of ContextItemsIndex
ContextItemRecordsIndex(Configuration) - Constructor for class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
ContextItemsCacheKey - Class in de.julielab.genemapper
ContextItemsCacheKey(String, String) - Constructor for class de.julielab.genemapper.ContextItemsCacheKey
ContextItemsIndex - Class in de.julielab.genemapper.disambig
ContextItemsIndex(CacheService, Configuration) - Constructor for class de.julielab.genemapper.disambig.ContextItemsIndex
ContextPosPipe - Class in de.julielab.genemapper.filtering
ContextPosPipe - Class in de.julielab.genemapper.filtering.families
ContextPosPipe(String, int, boolean) - Constructor for class de.julielab.genemapper.filtering.ContextPosPipe
ContextPosPipe(String, int, boolean) - Constructor for class de.julielab.genemapper.filtering.families.ContextPosPipe
ContextRanker - Interface in de.julielab.genemapper.disambig
ContextScoreCacheKey - Class in de.julielab.genemapper.disambig
ContextScoreCacheKey(Collection<String>, byte[], String, boolean) - Constructor for class de.julielab.genemapper.disambig.ContextScoreCacheKey
ContextUtils - Class in de.julielab.genemapper.utils
ContextUtils() - Constructor for class de.julielab.genemapper.utils.ContextUtils
correct - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
createClassificationInstances(GeneDocument, Map<String, Map<String, Double>>, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
createGeneDocument(JCas, Map<String, Matcher>, Function<EntityMention, Pair<String, BooleanQuery>>, Parameters) - Method in class de.julielab.genemapper.genemodel.GeneDocumentFactory: Creates a document by setting all required information from the jCas.
createGuiceInjector(Configuration) - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
createGuiceInjector(Configuration) - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
createGuiceInjector(Configuration) - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
createInstanceList(Stream<GeneDocument>) - Method in class de.julielab.genemapper.filtering.InstanceListCreator
createInstanceList(Stream<GeneDocument>, Alphabet, Alphabet) - Method in class de.julielab.genemapper.filtering.families.InstanceListCreator
createInstanceList(Stream<GeneDocument>, Configuration) - Method in class de.julielab.genemapper.filtering.families.InstanceListCreator
createPipes() - Method in class de.julielab.genemapper.filtering.InstanceListCreator
createPipes(Configuration) - Method in class de.julielab.genemapper.filtering.families.InstanceListCreator

D

Dash - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Dash() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash: Never called.
Dash(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash: Internal - constructor used by generator
Dash(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash
Dash(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash
Dash_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Dash_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash_Type: initialize variables to correspond with Cas Type and Features
dcg(double[]) - Static method in class de.julielab.genemapper.utils.NDCG
dcg(double[], int) - Static method in class de.julielab.genemapper.utils.NDCG
de.julielab.genemapper - package de.julielab.genemapper
de.julielab.genemapper.apps - package de.julielab.genemapper.apps
de.julielab.genemapper.classification - package de.julielab.genemapper.classification
de.julielab.genemapper.composites - package de.julielab.genemapper.composites
de.julielab.genemapper.disambig - package de.julielab.genemapper.disambig
de.julielab.genemapper.disambig.wikipedia - package de.julielab.genemapper.disambig.wikipedia
de.julielab.genemapper.evaluation - package de.julielab.genemapper.evaluation
de.julielab.genemapper.evaluation.tools - package de.julielab.genemapper.evaluation.tools
de.julielab.genemapper.filtering - package de.julielab.genemapper.filtering
de.julielab.genemapper.filtering.families - package de.julielab.genemapper.filtering.families
de.julielab.genemapper.genemodel - package de.julielab.genemapper.genemodel
de.julielab.genemapper.hpo - package de.julielab.genemapper.hpo
de.julielab.genemapper.index - package de.julielab.genemapper.index
de.julielab.genemapper.ioc - package de.julielab.genemapper.ioc
de.julielab.genemapper.mappingcores - package de.julielab.genemapper.mappingcores
de.julielab.genemapper.mappingcores.quercus - package de.julielab.genemapper.mappingcores.quercus
de.julielab.genemapper.uima - package de.julielab.genemapper.uima
de.julielab.genemapper.utils - package de.julielab.genemapper.utils
de.julielab.genemapper.utils.dict - package de.julielab.genemapper.utils.dict
de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction - package de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
de.julielab.jcore.ae.genemapper.desc.FamilyResolution - package de.julielab.jcore.ae.genemapper.desc.FamilyResolution
de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer - package de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration - package de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration
de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion - package de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing - package de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Det - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Det - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Det() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det: Never called.
Det() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det: Never called.
Det(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det: Internal - constructor used by generator
Det(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det: Internal - constructor used by generator
Det(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det
Det(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det
Det(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det
Det(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det
Det_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Det_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Det_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det_Type: initialize variables to correspond with Cas Type and Features
Det_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det_Type: initialize variables to correspond with Cas Type and Features
DictionaryClusterCleaner - Class in de.julielab.genemapper.utils.dict
disambiguate(GeneDocument) - Method in class de.julielab.genemapper.mappingcores.QuercusDisambiguation
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.AnchorDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.BioThesaurusFilterDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.GeneRecordQueryDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.OfficialSymbolPromotionDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in interface de.julielab.genemapper.mappingcores.quercus.QuercusDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.SemanticIndexDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.TestDisambiguationStep
disambiguate(GeneMention, SynHit) - Method in class de.julielab.genemapper.mappingcores.quercus.UnderspecifiedNameDisambiguationStep
disambiguateByMapLocations(GeneDocument, Parameters) - Static method in class de.julielab.genemapper.disambig.DypsisMapLocationDisambiguator
doContextRanking(DocumentDisambiguationData, Parameters) - Method in interface de.julielab.genemapper.disambig.ContextRanker
doContextRanking(DocumentDisambiguationData, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
DocResult - Class in de.julielab.genemapper.evaluation.tools
DocResult() - Constructor for class de.julielab.genemapper.evaluation.tools.DocResult
DocResult(int, int, int) - Constructor for class de.julielab.genemapper.evaluation.tools.DocResult
DocumentDisambiguationData - Interface in de.julielab.genemapper.disambig
docWise - Variable in class de.julielab.genemapper.evaluation.tools.MentionAndDocResult
doDisambiguation(SynHit, Query, double) - Method in class de.julielab.genemapper.mappingcores.quercus.SemanticIndexDisambiguationStep
doDisambiguation(List<SynHit>, Query) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex: does semantic disambiguation, takes best one
doDisambiguation(List<SynHit>, Query, double) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex: does semantic disambiguation, takes best one if its semantic score is above or equals minScore threshold
doit(GeneDocument) - Method in class de.julielab.genemapper.filtering.families.RuleBasedFamilyAssigner
doit(Collection<GeneDocument>) - Method in class de.julielab.genemapper.filtering.families.RuleBasedFamilyAssigner
Domain - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Domain() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain: Never called.
Domain(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain: Internal - constructor used by generator
Domain(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain
Domain(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain
Domain_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Domain_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain_Type: initialize variables to correspond with Cas Type and Features
DomainCue - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
DomainCue() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue: Never called.
DomainCue(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue: Internal - constructor used by generator
DomainCue(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue
DomainCue(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue
DomainCue_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
DomainCue_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue_Type: initialize variables to correspond with Cas Type and Features
doSeparateDisambiguation(ArrayList<SynHit>, String, double) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex: does semantic disambiguation on each SynHit separately, takes best one if its semantic score is above or equals minScore threshold
DypsisCandidateRanker - Class in de.julielab.genemapper.mappingcores: Uses machine learning methods to create features for the mapping candidates of a gene mention.
DypsisCandidateRanker(Configuration, CandidateRetrieval, CacheService) - Constructor for class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
DypsisCandidateRejector - Class in de.julielab.genemapper.disambig
DypsisCandidateRejector() - Constructor for class de.julielab.genemapper.disambig.DypsisCandidateRejector
DypsisCandidateSetter - Class in de.julielab.genemapper.mappingcores
DypsisCandidateSetter(Configuration, CandidateRetrieval, NameCentricRetrieval, DypsisCandidateRanker, GeneOrthologs) - Constructor for class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
DypsisContextRanker - Class in de.julielab.genemapper.disambig
DypsisContextRanker(Configuration, CandidateRetrieval, ContextItemsIndex, CacheService) - Constructor for class de.julielab.genemapper.disambig.DypsisContextRanker
DypsisDocumentDisambiguationData - Class in de.julielab.genemapper.disambig
DypsisDocumentDisambiguationData() - Constructor for class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
DypsisGeneSelector - Class in de.julielab.genemapper.mappingcores
DypsisGeneSelector() - Constructor for class de.julielab.genemapper.mappingcores.DypsisGeneSelector
DypsisGeneSetHomogenizator - Class in de.julielab.genemapper.disambig
DypsisGeneSetHomogenizator() - Constructor for class de.julielab.genemapper.disambig.DypsisGeneSetHomogenizator
DypsisMapLocationDisambiguator - Class in de.julielab.genemapper.disambig
DypsisMapLocationDisambiguator() - Constructor for class de.julielab.genemapper.disambig.DypsisMapLocationDisambiguator
DypsisMappingCore - Class in de.julielab.genemapper.mappingcores: This mapping core is named after the Dypsis lutescens, "Goldfruchtpalme" is is supposed to augment the older YukkaMappingCore with a document oriented integrity approach.
DypsisMappingCore(TermNormalizer, CandidateRetrieval, DypsisCandidateSetter, WikipediaEntityClassDecisionBear, GeneCompositeNameResolver, GeneSpeciesAssigner, SpeciesAssignmentFilter) - Constructor for class de.julielab.genemapper.mappingcores.DypsisMappingCore
DypsisMappingCore.NameLevelUnificationStrategy - Enum in de.julielab.genemapper.mappingcores
DypsisRankingMerger - Class in de.julielab.genemapper.disambig
DypsisRankingMerger() - Constructor for class de.julielab.genemapper.disambig.DypsisRankingMerger

E

EgSummaryEntity - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
EgSummaryEntity() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity: Never called.
EgSummaryEntity(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity: Internal - constructor used by generator
EgSummaryEntity(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity
EgSummaryEntity(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity
EgSummaryEntity_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
EgSummaryEntity_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity_Type: initialize variables to correspond with Cas Type and Features
EGSummaryStructureAnnotator - Class in de.julielab.genemapper.uima
EGSummaryStructureAnnotator() - Constructor for class de.julielab.genemapper.uima.EGSummaryStructureAnnotator
EmbeddedAcronymPatternResolver - Class in de.julielab.genemapper.composites
EmbeddedAcronymPatternResolver() - Constructor for class de.julielab.genemapper.composites.EmbeddedAcronymPatternResolver
EmbeddingsWithTokensConnectionAnnotator - Class in de.julielab.genemapper.uima
EmbeddingsWithTokensConnectionAnnotator() - Constructor for class de.julielab.genemapper.uima.EmbeddingsWithTokensConnectionAnnotator
ENTITIES - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
Entity - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Entity() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity: Never called.
Entity(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity: Internal - constructor used by generator
Entity(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity
Entity(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity
ENTITY_MAPPING_TYPES - Static variable in class de.julielab.genemapper.uima.GeneMapperAnnotator
Entity_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Entity_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity_Type: initialize variables to correspond with Cas Type and Features
EntityChunk - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
EntityChunk() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk: Never called.
EntityChunk(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk: Internal - constructor used by generator
EntityChunk(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk
EntityChunk(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk
EntityChunk_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
EntityChunk_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk_Type: initialize variables to correspond with Cas Type and Features
ENTITYCHUNKS - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
EntrezGeneUniProtLexcionCreator - Class in de.julielab.genemapper.utils.dict
EntrezGeneUniProtLexcionCreator() - Constructor for class de.julielab.genemapper.utils.dict.EntrezGeneUniProtLexcionCreator
EnumerationResolver - Class in de.julielab.genemapper.composites: For simple enumerations like NK-2, NK-3 and NK-3 receptor (those are three different entities).
EnumerationResolver() - Constructor for class de.julielab.genemapper.composites.EnumerationResolver
equals(Object) - Method in class de.julielab.genemapper.ContextItemsCacheKey
equals(Object) - Method in class de.julielab.genemapper.disambig.ContextScoreCacheKey
equalsIgnorePlural(String, String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Simple method for testing if two string are equal even if they vary in an ending 's'.
escapeString(String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Escapes certain characters in a string so that it can be used inside a regular expression.
EVAL_ON_HUMAN_ONLY - Static variable in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
evaluate(File, File, MLGeneFilter, File) - Static method in class de.julielab.genemapper.filtering.MLGeneFilter
evaluate(String, Multimap<String, String>, Multimap<String, GeneMention>, Function<SynHit, Double>) - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator: Writes the TAP input file from the given gold and predicted data and runs the TAP evaluation script via TAPEvaluator.evaluate(String, File, File)-
evaluate(String, File, File) - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator: Carries out the evaluation on the tapInputFile.
EXACT_MATCH - Static variable in class de.julielab.genemapper.Configuration
EXACT_SCORER_TYPE - Static variable in class de.julielab.genemapper.Configuration
EXCLUDE_FP_GM - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ExperimentsPipe - Class in de.julielab.genemapper.filtering
ExperimentsPipe() - Constructor for class de.julielab.genemapper.filtering.ExperimentsPipe
ExtendedProtein - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
ExtendedProtein() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein: Never called.
ExtendedProtein(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein: Internal - constructor used by generator
ExtendedProtein(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein
ExtendedProtein(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein
ExtendedProtein_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
ExtendedProtein_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein_Type: initialize variables to correspond with Cas Type and Features
ExtendedProteinsMerger - Class in de.julielab.genemapper.uima
ExtendedProteinsMerger() - Constructor for class de.julielab.genemapper.uima.ExtendedProteinsMerger
ExtensionFileFilter - Class in de.julielab.genemapper.utils
ExtensionFileFilter(String) - Constructor for class de.julielab.genemapper.utils.ExtensionFileFilter

F

Family - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Family - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Family() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family: Never called.
Family() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family: Never called.
Family(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family: Internal - constructor used by generator
Family(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family: Internal - constructor used by generator
Family(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family
Family(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family
Family(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family
Family(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family
Family_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Family_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Family_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family_Type: initialize variables to correspond with Cas Type and Features
Family_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family_Type: initialize variables to correspond with Cas Type and Features
FamilyAcronym - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyAcronym - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyAcronym() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym: Never called.
FamilyAcronym() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym: Never called.
FamilyAcronym(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym: Internal - constructor used by generator
FamilyAcronym(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym: Internal - constructor used by generator
FamilyAcronym(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym
FamilyAcronym(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym
FamilyAcronym(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym
FamilyAcronym(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym
FamilyAcronym_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyAcronym_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyAcronym_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type: initialize variables to correspond with Cas Type and Features
FamilyAcronym_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type: initialize variables to correspond with Cas Type and Features
FamilyConfidencePipe - Class in de.julielab.genemapper.filtering.families
FamilyConfidencePipe() - Constructor for class de.julielab.genemapper.filtering.families.FamilyConfidencePipe
FamilyCue - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyCue - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyCue - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyCue() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue: Never called.
FamilyCue() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue: Never called.
FamilyCue() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue: Never called.
FamilyCue(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue: Internal - constructor used by generator
FamilyCue(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue: Internal - constructor used by generator
FamilyCue(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue: Internal - constructor used by generator
FamilyCue(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue
FamilyCue(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue
FamilyCue(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue
FamilyCue(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue
FamilyCue(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue
FamilyCue(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue
FamilyCue_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyCue_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyCue_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyCue_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue_Type: initialize variables to correspond with Cas Type and Features
FamilyCue_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue_Type: initialize variables to correspond with Cas Type and Features
FamilyCue_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue_Type: initialize variables to correspond with Cas Type and Features
FamilyGenegroupProbabilityPipe - Class in de.julielab.genemapper.filtering.families
FamilyGenegroupProbabilityPipe() - Constructor for class de.julielab.genemapper.filtering.families.FamilyGenegroupProbabilityPipe
FamilyIndicator - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyIndicator() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator: Never called.
FamilyIndicator(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator: Internal - constructor used by generator
FamilyIndicator(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator
FamilyIndicator(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator
FamilyIndicator_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyIndicator_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator_Type: initialize variables to correspond with Cas Type and Features
FamilyMatchPipe - Class in de.julielab.genemapper.filtering.families
FamilyMatchPipe(Parameters) - Constructor for class de.julielab.genemapper.filtering.families.FamilyMatchPipe
FamilyStopword - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
FamilyStopword() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword: Never called.
FamilyStopword(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword: Internal - constructor used by generator
FamilyStopword(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword
FamilyStopword(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword
FamilyStopword_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
FamilyStopword_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword_Type: initialize variables to correspond with Cas Type and Features
FamilyUtils - Class in de.julielab.genemapper.filtering.families
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of_Type
featOkTst - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle_Type
field - Variable in class de.julielab.genemapper.disambig.ContextScoreCacheKey
FIELD_ACTIVITY_REGULATION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_CHROMOSOME - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames: Note that this field is used differently by some context index generators.
FIELD_CONTEXT_ITEM - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_DESCRIPTION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_DESIGNATION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_DEVELOPMENTAL_STAGE - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_DISEASE - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_DOMAIN - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_FUNCTION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_GENERIF - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_INDUCTION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_INTERACTION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_ITEM_TYPE - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_KEYWORD - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_MAP_LOCATION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_MISCELLANEOUS - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_PATHWAY - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_SIMILARITY - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_SUBCELLULAR_LOCATION - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_SUBUNIT - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_SUMMARY - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_SYNONYMS_BOW - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_SYNONYMS_EXACT - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_TISSUE - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
FIELD_TISSUE_SPECIFICITY - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
filter(GeneDocument) - Method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Removes all recognized gene names that are made up entirely of unspecific keywords or where names point to something else than a gene name, e.g.
filter(Stream<GeneDocument>) - Method in class de.julielab.genemapper.filtering.MLGeneFilter: The genes of al documents must have already have been selected.
FILTER_CONFIG - Static variable in class de.julielab.genemapper.hpo.BC2Evaluation
FILTER_CONFIG - Static variable in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
FILTER_CONFIG - Static variable in class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
FILTER_CONFIG_WITH_SPECIES_ASSIGNER - Static variable in class de.julielab.genemapper.hpo.BC3CorpusEvaluation
filterLog - Static variable in class de.julielab.genemapper.mappingcores.DypsisMappingCore
filterStopwords(Stream<String>) - Static method in class de.julielab.genemapper.utils.ContextUtils
FIXED_TAX_ID - Static variable in class de.julielab.genemapper.Configuration: When this parameter is set, the provided value will be used as tax ID for all gene mentions.
FlairCompositeMentionTagger - Class in de.julielab.genemapper.composites
FlairCompositeMentionTagger(CacheService, Configuration) - Constructor for class de.julielab.genemapper.composites.FlairCompositeMentionTagger
fuse(List<List<SynHit>>) - Method in class de.julielab.genemapper.disambig.RRFSynHitListFusion
fuse(List<List<SynHit>>) - Method in interface de.julielab.genemapper.disambig.SynHitListFusion

G

GAZETTEER_FIRST - de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy
GENE_RECORD_INDEX - Static variable in class de.julielab.genemapper.Configuration
GENE_RECORD_ORIGINAL_NAMES_INDEX - Static variable in class de.julielab.genemapper.Configuration
GeneCompositeNameResolver - Class in de.julielab.genemapper.composites
GeneCompositeNameResolver(FlairCompositeMentionTagger, Configuration) - Constructor for class de.julielab.genemapper.composites.GeneCompositeNameResolver
GeneConfigurationDependentPipe - Interface in de.julielab.genemapper.filtering.families: Some pipes access resources whose path are given in the gene configuration and which cannot be stored on disc when saving the model.
GeneDocumentFactory - Class in de.julielab.genemapper.genemodel
GeneDocumentFactory(Configuration, GeneSpeciesAssigner, TermNormalizer) - Constructor for class de.julielab.genemapper.genemodel.GeneDocumentFactory
GeneId - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
GeneId() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId: Never called.
GeneId(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId: Internal - constructor used by generator
GeneId(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId
GeneId(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId
GeneId_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
GeneId_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId_Type: initialize variables to correspond with Cas Type and Features
GeneIdCorrectnessRenderer - Class in de.julielab.genemapper.evaluation
GeneIdCorrectnessRenderer() - Constructor for class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
GenelistByTaxonomyFilter - Class in de.julielab.genemapper.evaluation.tools: Reads a gene list (the second field must be the gene ID) and writes out the same file but filtered for a specific taxonomy ID.
GenelistByTaxonomyFilter() - Constructor for class de.julielab.genemapper.evaluation.tools.GenelistByTaxonomyFilter
GenelistIdUpdater - Class in de.julielab.genemapper.evaluation.tools: Reads a gene list and writes the same list where for each gene ID is checked if it has been replaced in NCBI Gene.
GenelistIdUpdater() - Constructor for class de.julielab.genemapper.evaluation.tools.GenelistIdUpdater
GenelistTaxonomyPredictor - Class in de.julielab.genemapper.evaluation.tools: Reads annotation data that includes genes, organisms, sentences, chunks and possibly more and predicts a taxonomy ID for each gene mention.
GenelistTaxonomyPredictor() - Constructor for class de.julielab.genemapper.evaluation.tools.GenelistTaxonomyPredictor
GenelistToTaxonomyListConverter - Class in de.julielab.genemapper.evaluation.tools: Reads a gene list (the second field must be the gene ID) and writes out the same file but with the gene IDs replaced by the taxonomy ID of the respective gene.
GenelistToTaxonomyListConverter() - Constructor for class de.julielab.genemapper.evaluation.tools.GenelistToTaxonomyListConverter
GeneMapper - Class in de.julielab.genemapper
GeneMapper(Configuration, MappingCore) - Constructor for class de.julielab.genemapper.GeneMapper
GeneMapperAnnotator - Class in de.julielab.genemapper.uima
GeneMapperAnnotator() - Constructor for class de.julielab.genemapper.uima.GeneMapperAnnotator
GeneMapperException - Exception in de.julielab.genemapper.utils
GeneMapperException() - Constructor for exception de.julielab.genemapper.utils.GeneMapperException
GeneMapperException(String) - Constructor for exception de.julielab.genemapper.utils.GeneMapperException
GeneMapperException(String, Throwable) - Constructor for exception de.julielab.genemapper.utils.GeneMapperException
GeneMapperException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.genemapper.utils.GeneMapperException
GeneMapperException(Throwable) - Constructor for exception de.julielab.genemapper.utils.GeneMapperException
GeneMapperInitializationException - Exception in de.julielab.genemapper.utils
GeneMapperInitializationException() - Constructor for exception de.julielab.genemapper.utils.GeneMapperInitializationException
GeneMapperInitializationException(String) - Constructor for exception de.julielab.genemapper.utils.GeneMapperInitializationException
GeneMapperInitializationException(String, Throwable) - Constructor for exception de.julielab.genemapper.utils.GeneMapperInitializationException
GeneMapperInitializationException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.genemapper.utils.GeneMapperInitializationException
GeneMapperInitializationException(Throwable) - Constructor for exception de.julielab.genemapper.utils.GeneMapperInitializationException
GeneMapperRuntimeException - Exception in de.julielab.genemapper.utils
GeneMapperRuntimeException() - Constructor for exception de.julielab.genemapper.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(String) - Constructor for exception de.julielab.genemapper.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(String, Throwable) - Constructor for exception de.julielab.genemapper.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.genemapper.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(Throwable) - Constructor for exception de.julielab.genemapper.utils.GeneMapperRuntimeException
GeneMappingModule - Class in de.julielab.genemapper.ioc
GeneMappingModule(Configuration) - Constructor for class de.julielab.genemapper.ioc.GeneMappingModule
GeneMappingOptimizationRoute - Class in de.julielab.genemapper.hpo
GeneMappingOptimizationRoute(Configuration) - Constructor for class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
GeneMention2Token - Class in de.julielab.genemapper.filtering.families
GeneMention2Token() - Constructor for class de.julielab.genemapper.filtering.families.GeneMention2Token
GeneMentionFamilyFeatureSetter - Class in de.julielab.genemapper.filtering.families: Experimental.
GeneMentionFamilyFeatureSetter() - Constructor for class de.julielab.genemapper.filtering.families.GeneMentionFamilyFeatureSetter
GeneMentionFilter - Class in de.julielab.genemapper
GeneMentionFilter() - Constructor for class de.julielab.genemapper.GeneMentionFilter
GeneMentionTaxIdCountWriter - Class in de.julielab.genemapper.uima
GeneMentionTaxIdCountWriter() - Constructor for class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
GeneNameToAmbiguousIdsMapper - Class in de.julielab.genemapper.apps: This class takes a list of gene names and a taxonomy ID.
GeneNameToAmbiguousIdsMapper() - Constructor for class de.julielab.genemapper.apps.GeneNameToAmbiguousIdsMapper
GeneRecordQueryDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus
GeneRecordQueryDisambiguationStep(CandidateRetrieval) - Constructor for class de.julielab.genemapper.mappingcores.quercus.GeneRecordQueryDisambiguationStep
GeneSequence2SingleGene - Class in de.julielab.genemapper.filtering: For non-sequence filtering, we will have a single gene per GeneSet in the GeneDocument passed to GeneSet2GeneSequence which should be the very first pipe to be employed in each pipe sequence.
GeneSequence2SingleGene() - Constructor for class de.julielab.genemapper.filtering.GeneSequence2SingleGene
GeneSet2GeneSequence - Class in de.julielab.genemapper.filtering
GeneSet2GeneSequence() - Constructor for class de.julielab.genemapper.filtering.GeneSet2GeneSequence
GeneSet2Token - Class in de.julielab.genemapper.filtering.families
GeneSet2Token() - Constructor for class de.julielab.genemapper.filtering.families.GeneSet2Token
GenesetsOptimizationRoute - Class in de.julielab.genemapper.hpo
GenesetsOptimizationRoute(Configuration) - Constructor for class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
GeneSynonymEmbeddingCentroidWriter - Class in de.julielab.genemapper.uima
GeneSynonymEmbeddingCentroidWriter() - Constructor for class de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter
GeneToProteinConverter - Class in de.julielab.genemapper.uima
GeneToProteinConverter() - Constructor for class de.julielab.genemapper.uima.GeneToProteinConverter
GET_GENE_MAPPING_SCORE - Static variable in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
GET_GENESET_SCORE - Static variable in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
GET_MENTION_SEARCH_SCORE - Static variable in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getAcronymForms() - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName: Returns the acronym variant of this gene name, if it was embedded into the long form for this mention.
getActiveCorpora() - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getActiveCorpora() - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
getActiveCorpora() - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
getAnnotations(JCas, Annotation, Class<T>) - Static method in class de.julielab.genemapper.utils.UIMAUtils: This method returns all annotations (in order) that are inside a "window" annotation of a particular kind.
getBegin() - Method in class de.julielab.genemapper.composites.CompositeToken
getBegin() - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName
getBestMatchingScore() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
getBestMatchingTitle() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
getCandidateForTaxId(List<SynHit>, String) - Static method in class de.julielab.genemapper.apps.AppUtils: Sets the given taxonomy ID to the top candidate and returns it.
getCandidateQueryString(SynHit, CandidateRetrieval) - Static method in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils: Creates a single string describing the given gene database candidate.
getCandidateRetrieval() - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
getCandidateRetrieval() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
getCandidateRetrieval() - Method in interface de.julielab.genemapper.mappingcores.MappingCore
getCandidateRetrieval() - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
getCandidateSetter() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
getCategoriesForCategory(String) - Method in class de.julielab.genemapper.WikipediaCategoryManager
getCategoriesForPage(String) - Method in class de.julielab.genemapper.WikipediaCategoryManager
getColumn() - Method in class de.julielab.genemapper.utils.dict.Column
getCommonTokens(Collection<String>) - Method in class de.julielab.genemapper.mappingcores.quercus.TestDisambiguationStep
getConfidence() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputLine
getConfiguration() - Method in class de.julielab.genemapper.GeneMapper
getConfigurationPath() - Method in class de.julielab.genemapper.hpo.BC2Evaluation
getConfigurationPath() - Method in class de.julielab.genemapper.hpo.BC3CorpusEvaluation
getConfigurationPath() - Method in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
getConfigurationPath() - Method in class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
getContainingAnnotation(JCas, Annotation, Class<T>) - Static method in class de.julielab.genemapper.utils.UIMAUtils: This method finds the smallest annotation of containingType that begins before or at the same character as the focusAnnotation and ends after or at the same character as the focusAnnotation.
getContext(String) - Method in class de.julielab.genemapper.index.ContextGenerator: Builds the semantic context for a given Gene ID
getContextForSynHits(SynHit, Query) - Method in class de.julielab.genemapper.mappingcores.quercus.SemanticIndexDisambiguationStep
getContextForSynHits(List<SynHit>, Map<String, SynHit>, Query) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex
getContextItems(ContextItemsCacheKey) - Method in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
getContextItems(ContextItemsCacheKey) - Method in class de.julielab.genemapper.disambig.ContextItemsIndex
getContextItems(String, String) - Method in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
getContextItems(String, String) - Method in class de.julielab.genemapper.disambig.ContextItemsIndex
getContextItemScores(Collection<String>, BooleanQuery, String, boolean) - Method in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
getContextItemScores(Collection<String>, BooleanQuery, String, boolean) - Method in class de.julielab.genemapper.disambig.ContextItemsIndex
getContextItemsIndex() - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
getContextItemsSearcher() - Method in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
getContextItemsSearcher() - Method in class de.julielab.genemapper.disambig.ContextItemsIndex
getContextualRanking() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
getContextualRanking() - Method in interface de.julielab.genemapper.mappingcores.MappingCore
getContextualRanking() - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
getCorrectGenesInCandidateList() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getCounter() - Method in class de.julielab.genemapper.utils.dict.RefCounter
getDefaultMetric() - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getDefaultMetric() - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
getDefaultMetric() - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
getDevSamplingFrequency() - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getDevSamplingFrequency() - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
getDevSamplingFrequency() - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
getDisambiguationClassifier() - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
getDisambiguationRanker() - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
getDocument() - Method in interface de.julielab.genemapper.disambig.DocumentDisambiguationData
getDocument() - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
getEnd() - Method in class de.julielab.genemapper.composites.CompositeToken
getEnd() - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName
getEntities() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
getEpq() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
getEpqThresholdMatcher() - Static method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
getEvaluationEndpoint() - Method in class de.julielab.genemapper.hpo.BC2Evaluation
getEvaluationEndpoint() - Method in class de.julielab.genemapper.hpo.BC3CorpusEvaluation
getEvaluationEndpoint() - Method in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
getEvaluationEndpoint() - Method in class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
getFilter() - Method in class de.julielab.genemapper.utils.dict.Column
getFn() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
getFp() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
getFrequencies(String) - Method in class de.julielab.genemapper.utils.dict.BTMatcher: Mines given text for all listed synonyms and counts their occurrences.
getFscore() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
getGeneDocument() - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
getGeneId() - Method in class de.julielab.genemapper.ContextItemsCacheKey
getGeneId() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family: getter for geneId - gets geneId
getGeneId() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym: getter for geneId - gets geneId
getGeneId() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym: getter for geneId - gets geneId
getGeneId() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym: getter for geneId - gets geneId
getGeneId(int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family_Type
getGeneId(int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
getGeneId(int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym_Type
getGeneId(int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
getGmMarkedDocumentText(GeneMention, int, boolean, boolean) - Static method in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
getIndexField() - Method in class de.julielab.genemapper.ContextItemsCacheKey
getInstances() - Method in class de.julielab.genemapper.hpo.BC2Evaluation
getInstances() - Method in class de.julielab.genemapper.hpo.BC3CorpusEvaluation
getInstances() - Method in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
getInstances() - Method in class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
getIntraTaxAmbiguousContextItemScores(SynHit, BooleanQuery, String, boolean) - Method in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
getIntraTaxAmbiguousContextItemScores(SynHit, BooleanQuery, String, boolean) - Method in class de.julielab.genemapper.disambig.ContextItemsIndex
getListname() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputList
getListname() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultList
getListname() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
getListresult() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultList
getLongform() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym: getter for longform - gets longform
getLongform() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym: getter for longform - gets longform
getLongform(int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
getLongform(int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
getMappingCore() - Method in class de.julielab.genemapper.GeneMapper
getMatchStyle() - Method in class de.julielab.genemapper.utils.dict.Column
getMaxAgglomerationCandidates() - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
getMention() - Method in interface de.julielab.genemapper.disambig.MentionDisambiguationData
getMentionedWikipediaEntities() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
getModelParameters() - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
getModelParameters() - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
getModelPath() - Method in class de.julielab.genemapper.classification.TransformerClassifier
getName() - Method in class de.julielab.genemapper.composites.CompositePatternResolver
getNameLevelUnificationStrategies() - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
getNumApprxGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumApprxGoldOverlappingMentions() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCandidateSearches() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectApprxTop10WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectApprxTop15WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectApprxTop3WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectApprxTop5WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectExactTop10WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectExactTop15WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectExactTop3WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectExactTop5WithGold() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectGenesInCandidateListAfterSpeciesRestriction() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectGenesInCandidateListExactMatchFirstTry() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumCorrectGenesInOrthologsOfExactMatch() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumExactGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumExactGoldOverlappingMentions() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumExactMatchAfterSpeciesRestriction() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumExactMatchFirstTry() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumGenes() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getNumSplits() - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getNumSplits() - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
getNumSplits() - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
getOriginalExactMatches(GeneMention, Parameters, List<SynHit>) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
getParameters() - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
getPort() - Method in class de.julielab.genemapper.hpo.BC2Evaluation
getPort() - Method in class de.julielab.genemapper.hpo.BC3CorpusEvaluation
getPort() - Method in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
getPort() - Method in class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
getPrecision() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
getRecall() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
getRelevance() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputLine
getReport() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getResolutionComponent() - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName
getRouteEndpoint() - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getRouteEndpoint() - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
getRouteEndpoint() - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
getScore() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity: The Lucene score of this Wikipedia page with respect to the searched entity string.
getSemanticIndex() - Method in interface de.julielab.genemapper.disambig.ContextRanker
getSemanticIndex() - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
getSemanticIndexSearcher() - Method in class de.julielab.genemapper.disambig.SemanticContextIndex
getSemanticRerankingFeatureInstance(GeneDocument, Map<String, Map<String, Double>>, LabelAlphabet, int, GeneMention, SynHit, Map<String, FeatureVector>, Pipe, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker: Create a single disambiguation instance for the given candidate database entry relative to the GeneMention gm.
getShortestPath(String, String) - Method in class de.julielab.genemapper.WikipediaCategoryManager: A little Dijkstra to find the shortest path of categories from a Wikipedia page to the given category.
getShortestPathToDijkstraTreeRoot(String, Set<String>) - Method in class de.julielab.genemapper.WikipediaCategoryManager
getStats() - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
getStemmingStream(String) - Static method in class de.julielab.genemapper.utils.ContextUtils
getSynonymGeneRifScoresForTaxIds(SynHit, Set<String>) - Method in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
getSynonymGeneRifScoresForTaxIds(SynHit, Set<String>) - Method in class de.julielab.genemapper.disambig.ContextItemsIndex
getTag() - Method in class de.julielab.genemapper.composites.CompositeToken
getTagging() - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName
getTap() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
getTaskName() - Method in class de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute
getTaskName() - Method in class de.julielab.genemapper.hpo.GeneMappingOptimizationRoute
getTaskName() - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
getTermNormalizer() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
getTermNormalizer() - Method in interface de.julielab.genemapper.mappingcores.MappingCore
getTermNormalizer() - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
getText() - Method in class de.julielab.genemapper.composites.CompositeToken
getThreshold() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
getTitle() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
getTotalNumberCandidates() - Method in class de.julielab.genemapper.evaluation.tools.Stats
getTp() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of
getTypeIndexID() - Method in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle
getUniRefs() - Method in class de.julielab.genemapper.utils.dict.RefCounter
GnHpoServer - Class in de.julielab.genemapper.hpo
GnHpoServer(int) - Constructor for class de.julielab.genemapper.hpo.GnHpoServer
GNormPlusBC2GNTrainEntityFiltering - Class in de.julielab.genemapper.evaluation
GNormPlusBC2GNTrainEntityFiltering() - Constructor for class de.julielab.genemapper.evaluation.GNormPlusBC2GNTrainEntityFiltering
GNormPlusBC2TestRoute - Class in de.julielab.genemapper.hpo
GNormPlusBC2TestRoute(Configuration) - Constructor for class de.julielab.genemapper.hpo.GNormPlusBC2TestRoute
GNormPlusCorpusEvaluation - Class in de.julielab.genemapper.hpo
GNormPlusCorpusEvaluation() - Constructor for class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
Greek - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Greek() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek: Never called.
Greek(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek: Internal - constructor used by generator
Greek(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek
Greek(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek
Greek_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Greek_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek_Type: initialize variables to correspond with Cas Type and Features

H

hashCode() - Method in class de.julielab.genemapper.ContextItemsCacheKey
hashCode() - Method in class de.julielab.genemapper.disambig.ContextScoreCacheKey
HASUNSPECTITLE - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
homogenize(GeneDocument, Parameters) - Static method in class de.julielab.genemapper.disambig.DypsisGeneSetHomogenizator

I

ids - Variable in class de.julielab.genemapper.disambig.ContextScoreCacheKey
incAmbiguousApprxBestCandidateHasCorrectIdSelected() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incAmbiguousBestCandidateHasCorrectIdSelected() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incAmbiguousExactBestCandidateHasCorrectIdSelected() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incApprxBestCandidateHasCorrectId() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incApprxBestCandidateWithCorrectIdIsAmbiguous() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incApprxCorrectlyDisambiguated() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incBestApprxCandidateHasCorrectTaxId() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incBestCandidateHasCorrectId() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incBestCandidateHasCorrectTaxId() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incBestCandidateWithCorrectIdIsAmbiguous() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incBestExactCandidateHasCorrectTaxId() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGeneIdAfterRelaxed1(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGeneIdAfterRelaxed2(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGeneIdAfterRelaxed3(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGeneIdInApprxBestCandidates() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGeneIdInBestCandidates() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGeneIdInExactBestCandidates() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGenesInCandidateList() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectGenesInCandidateList(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incCorrectlyDisambiguated() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incDisambiguated() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incExactBestCandidateHasCorrectId() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incExactBestCandidateWithCorrectIdIsAmbiguous() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incExactCorrectlyDisambiguated() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incExactMatchFirstTryIfTrue(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incMissedMentions() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNoCorrectAfterExactSearch(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNoCorrectAfterRelaxed1(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNoCorrectAfterRelaxed2(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNoCorrectAfterRelaxed3(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNotGoldOverlappingMatchType(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumAmbiguous() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumApprxAmbiguous() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumApprxGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumApprxGoldOverlappingGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCandidateSearches() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCertainAndWrong() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectApprxHightestMentionScoreGeneId(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectApprxMatchesTop10(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectApprxMatchesTop15(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectApprxMatchesTop3(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectApprxMatchesTop5(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectExactHightestMentionScoreGeneId(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectExactMatchesTop10(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectExactMatchesTop15(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectExactMatchesTop3(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectExactMatchesTop5(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectFirstGeneId(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectGenesInCandidateListAfterSpeciesRestrictionIfTrue(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectGenesInCandidateListExactMatchFirstTry() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectGenesInCandidateListExactMatchFirstTryIfTrue(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectGenesInOrthologsOfExactMatchIfTrue(boolean, boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectHighestMentionScoreGeneId(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectInInitialSearchNotInOrthologs(boolean, boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumCorrectMajorityGeneId(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumExactAmbiguous() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumExactGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumExactGoldOverlappingGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumExactMatchAfterSpeciesRestrictionIfTrue(Boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumExcactMatchWithOrthologResolution(boolean) - Method in class de.julielab.genemapper.evaluation.tools.Stats: Exact matches which didn't have an entry for the given tax ID but did have an ortholog for this tax ID
incNumFpMentions() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumGenes() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumGoldOverlappingGenesRecognized() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumPerfectMatchFirstTry() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumUncertainAndCorrect() - Method in class de.julielab.genemapper.evaluation.tools.Stats
incNumUncertainAndWrong() - Method in class de.julielab.genemapper.evaluation.tools.Stats
increment() - Method in class de.julielab.genemapper.utils.dict.RefCounter
incrementCountsForCoveredOrganisms(String, Annotation, Consumer<GeneMentionTaxIdCountWriter.GeneOccurrenceCount>, Set<GeneMentionTaxIdCountWriter.GeneNameTaxPair>, JCoReTreeMapAnnotationIndex<Long, Organism>, Map<GeneMentionTaxIdCountWriter.GeneNameTaxPair, GeneMentionTaxIdCountWriter.GeneOccurrenceCount>) - Method in class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
incTotalNumberCandidates(int) - Method in class de.julielab.genemapper.evaluation.tools.Stats
incUnambiguousCorrectGeneInBestCandidates() - Method in class de.julielab.genemapper.evaluation.tools.Stats
IndexIdWriter - Class in de.julielab.genemapper.evaluation.tools
IndexIdWriter() - Constructor for class de.julielab.genemapper.evaluation.tools.IndexIdWriter
initialize(Configuration) - Method in interface de.julielab.genemapper.filtering.families.GeneConfigurationDependentPipe
initialize(Configuration) - Method in class de.julielab.genemapper.filtering.families.SymbolPrefixPipe
initialize(UimaContext) - Method in class de.julielab.genemapper.uima.GeneMapperAnnotator: initialization of GeneMapper: load the index, get some parameters
initialize(UimaContext) - Method in class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
initialize(UimaContext) - Method in class de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter
initialize(UimaContext) - Method in class de.julielab.genemapper.uima.ProteinConsistencyTagger
initialize(UimaContext) - Method in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
initialize(UimaContext) - Method in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
InstanceListCreator - Class in de.julielab.genemapper.filtering.families
InstanceListCreator - Class in de.julielab.genemapper.filtering
InstanceListCreator() - Constructor for class de.julielab.genemapper.filtering.families.InstanceListCreator
InstanceListCreator(boolean) - Constructor for class de.julielab.genemapper.filtering.InstanceListCreator
InteractiveCandidateFinder - Class in de.julielab.genemapper.apps
InteractiveCandidateFinder() - Constructor for class de.julielab.genemapper.apps.InteractiveCandidateFinder
InteractiveNameCentricCandidateFinder - Class in de.julielab.genemapper.apps
InteractiveNameCentricCandidateFinder() - Constructor for class de.julielab.genemapper.apps.InteractiveNameCentricCandidateFinder
InteractiveSpellingChecker - Class in de.julielab.genemapper.evaluation.tools
InteractiveSpellingChecker() - Constructor for class de.julielab.genemapper.evaluation.tools.InteractiveSpellingChecker
InteractiveWikipediaPageRetrieval - Class in de.julielab.genemapper.apps
InteractiveWikipediaPageRetrieval() - Constructor for class de.julielab.genemapper.apps.InteractiveWikipediaPageRetrieval
intersectionFilter(GeneDocument, TermNormalizer, boolean) - Static method in class de.julielab.genemapper.GeneMentionFilter: Must be done after all genes have received their candidates.
IOUtils - Class in de.julielab.genemapper.utils
IOUtils() - Constructor for class de.julielab.genemapper.utils.IOUtils
isAminoAcid(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Checks if the given term matches an amino acid, using three-letter code (Ala) and full names (Alanine, alanines).
IsAPipe - Class in de.julielab.genemapper.filtering.families
IsAPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.IsAPipe
isCellLine(String, String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Returns true if the name is followed by a keyword indicating that this name is a cell line.
isChromosome(String, String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Checks if the given name found in a sentence refers to a (human!) chromosome:
it should have at least a chromosome number and arm (13p), maybe also bands (13p.23), and the name should also appear next to the word 'chromosome'
isDiseaseName(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Returns true if the name represents a disease name.
isEligible(String) - Method in class de.julielab.genemapper.composites.CompositePatternResolver: Checks the gene name for eligibility with regards to the original gene name string.
isEligible(String) - Method in class de.julielab.genemapper.composites.EmbeddedAcronymPatternResolver
isEligible(String) - Method in class de.julielab.genemapper.composites.EnumerationResolver
isEligible(String) - Method in class de.julielab.genemapper.composites.NumberElipseEnumerationPatternResolver
isEligible(String) - Method in class de.julielab.genemapper.composites.PatternResolutionChain
isEligible(String) - Method in class de.julielab.genemapper.composites.SlashDashAlternativePatternResolver
isEligible(String) - Method in class de.julielab.genemapper.composites.TwoPartedRangePatternResolver
IsFamilyPipe - Class in de.julielab.genemapper.filtering.families
IsFamilyPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.IsFamilyPipe
isLeftWs() - Method in class de.julielab.genemapper.composites.CompositeToken
isNegativePair(String, String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Some gene names refer to the actual gene only in very few cases.
isPlural() - Method in class de.julielab.genemapper.composites.CompositeToken
isRightWs() - Method in class de.julielab.genemapper.composites.CompositeToken
isSpecies(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Naive implementation: checks if the name refers to a species.
isSpecifier(String) - Static method in class de.julielab.genemapper.filtering.families.FamilyUtils
isTissueCellCompartment(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter
isTitleHasUnspecificArticle() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
isTitleMentionedInPlural() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
isUnspecific(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter
isUnspecific(String, HashSet<Integer>) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Decides whether a proposed gene name is too unspecific: mainly checks for compound names that do not have any reference concering the exact identity of a protein.
isUnspecificAbbreviation(String, String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter
isUnspecificAbbreviation(String, String, HashSet<Integer>) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter
isUnspecificSingleWord(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Checks a gene name against a list of single word, case sensitive words that are pretty much always false positives: "aim", "fat", "up".
isUnspecificSingleWordCaseInsensitive(String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter

J

JCasConverter - Class in de.julielab.genemapper.evaluation.tools
JCasConverter() - Constructor for class de.julielab.genemapper.evaluation.tools.JCasConverter
JJ - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
JJ() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ: Never called.
JJ(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ: Internal - constructor used by generator
JJ(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ
JJ(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ
JJ_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
JJ_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ_Type: initialize variables to correspond with Cas Type and Features
JNET_FIRST - de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy
JNET_ONLY - de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy
joinIntegerSet(Set<Integer>, String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Puts all elements of a set into a single delimited string.
joinStringArray(String[], String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Joins the entries in a String array into a single String.
joinStringList(List<String>, String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Joins the entries in a String list into a single String.
joinStringSet(Set<String>, String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Puts all elements of a set into a single delimited string.

K

keepDiseaseName(String, String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter: Returns true if this disease name is mentioned together with a locus or genes/proteins in this sentence.
KEY_MAX_FAMILY_MATCH_SCORE - Static variable in class de.julielab.genemapper.Configuration
KEY_MIN_FAMILY_MATCH_SCORE - Static variable in class de.julielab.genemapper.Configuration

L

LastWordPipe - Class in de.julielab.genemapper.filtering.families
LastWordPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.LastWordPipe
LastWordPipe(String, boolean) - Constructor for class de.julielab.genemapper.filtering.families.LastWordPipe
leftWordBoundary - Static variable in class de.julielab.genemapper.filtering.UnspecificNameFilter: characters that appear on the left side of a proper word: white space, bracket starts, ..
LEGACY_INDEX_SUPPORT - Static variable in class de.julielab.genemapper.GeneMapper
Line - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Line() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line: Never called.
Line(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line: Internal - constructor used by generator
Line(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line
Line(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line
Line_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Line_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line_Type: initialize variables to correspond with Cas Type and Features
load(File) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
loadCandidateSetter(File) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
loadFieldValue - Variable in class de.julielab.genemapper.disambig.ContextScoreCacheKey
loadLexicalCandidateRankingModel(Configuration) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
loadModel(File) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
loadModel(InputStream) - Method in class de.julielab.genemapper.filtering.MLGeneFilter
loadModel(InputStream) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
loadParameters(File) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
LONGER_FIRST - de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy
LOOKUP_CONTEXT_FIELD - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
LOOKUP_ID_FIELD - Static variable in class de.julielab.genemapper.index.ContextIndexFieldNames
lookupEntityType(GeneMention) - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntityClassDecisionBear
LowerCaseBoWPipe - Class in de.julielab.genemapper.filtering.families
LowerCaseBoWPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.LowerCaseBoWPipe
LowerCasePipe - Class in de.julielab.genemapper.filtering
LowerCasePipe(String) - Constructor for class de.julielab.genemapper.filtering.LowerCasePipe
LUCENE_CONFIG - Static variable in class de.julielab.genemapper.hpo.BC2Evaluation
LUCENE_CONFIG - Static variable in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation

M

main(String[]) - Static method in class de.julielab.genemapper.apps.GeneNameToAmbiguousIdsMapper
main(String[]) - Static method in class de.julielab.genemapper.apps.InteractiveCandidateFinder
main(String[]) - Static method in class de.julielab.genemapper.apps.InteractiveNameCentricCandidateFinder
main(String[]) - Static method in class de.julielab.genemapper.apps.InteractiveWikipediaPageRetrieval
main(String[]) - Static method in class de.julielab.genemapper.apps.SmacRunRepeater
main(String[]) - Static method in class de.julielab.genemapper.classification.TransformerClassifier
main(String[]) - Static method in class de.julielab.genemapper.disambig.wikipedia.WikipediaIndexReader
main(String[]) - Static method in class de.julielab.genemapper.evaluation.GNormPlusBC2GNTrainEntityFiltering
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.AcronymTextCoverWriter
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.GenelistByTaxonomyFilter
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.GenelistIdUpdater
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.GenelistTaxonomyPredictor
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.GenelistToTaxonomyListConverter
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.IndexIdWriter
main(String[]) - Static method in class de.julielab.genemapper.evaluation.tools.InteractiveSpellingChecker
main(String[]) - Static method in class de.julielab.genemapper.evaluation.WikipediaClassLookupDevelopment
main(String[]) - Static method in class de.julielab.genemapper.filtering.MLGeneFilter
main(String[]) - Static method in class de.julielab.genemapper.filtering.StringHelper
main(String[]) - Static method in class de.julielab.genemapper.hpo.BC2Evaluation
main(String[]) - Static method in class de.julielab.genemapper.hpo.BC3CorpusEvaluation
main(String[]) - Static method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
main(String[]) - Static method in class de.julielab.genemapper.hpo.GnHpoServer
main(String[]) - Static method in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
main(String[]) - Static method in class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
main(String[]) - Static method in class de.julielab.genemapper.hpo.PrintBestSmacConfiguration
main(String[]) - Static method in class de.julielab.genemapper.utils.dict.ACCollector: Deprecated.
main(String[]) - Static method in class de.julielab.genemapper.utils.dict.BioThesaurusIproClassMerger
main(String[]) - Static method in class de.julielab.genemapper.utils.dict.BTMatcher: to execute the BTMatcher start it with the following command-line arguments: arg0: thesaurusFile arg1: directory of text files or single file arg2: output file
main(String[]) - Static method in class de.julielab.genemapper.utils.dict.DictionaryClusterCleaner
main(String[]) - Static method in class de.julielab.genemapper.utils.dict.EntrezGeneUniProtLexcionCreator
main(String[]) - Static method in class de.julielab.genemapper.utils.dict.ThesaurusCleaner: to execute the thesaurus cleaner start it with the following command-line arguments: arg0: selectionFile arg1: thesaurusFile arg2: outputFile
main(String[]) - Static method in class de.julielab.genemapper.WikipediaCategoryManager
makeContext(JCas, int, EntityMention) - Static method in class de.julielab.genemapper.utils.ContextUtils
makeContextQuery(String) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex
makeContextQuery(String) - Static method in class de.julielab.genemapper.utils.ContextUtils: builds the Lucene context query a given text
makeContextQuery(String, String) - Static method in class de.julielab.genemapper.utils.ContextUtils: builds the Lucene context query a given text
makeContextQuery(JCas) - Static method in class de.julielab.genemapper.utils.ContextUtils: makes the context query.
makeContextQuery(JCas, int, EntityMention) - Static method in class de.julielab.genemapper.utils.ContextUtils: makes the context query.
makeContextTokens(String) - Static method in class de.julielab.genemapper.utils.ContextUtils
makeContextTokenString(String) - Static method in class de.julielab.genemapper.utils.ContextUtils
makeContextTypes(String) - Static method in class de.julielab.genemapper.utils.ContextUtils
makeQuery(String[], Query) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex
makeQuery(String, BooleanQuery) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex
makeQuery(List<String>, Query) - Method in class de.julielab.genemapper.mappingcores.quercus.SemanticIndexDisambiguationStep
makeSeparateQuery(String, String) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex: generates a boolean query from the context and a single ids: the id has to match and the context is combined by OR.
makeTapInputLists(String, Multimap<String, String>, Multimap<String, GeneMention>, Function<SynHit, Double>) - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator: Creates a representation of TAP input lists.
map(GeneDocument) - Method in class de.julielab.genemapper.GeneMapper
map(GeneDocument) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore: Maps the gene mentions in the passed document to database IDs.
map(GeneDocument) - Method in interface de.julielab.genemapper.mappingcores.MappingCore
map(GeneDocument) - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
map(GeneDocument, Parameters) - Method in class de.julielab.genemapper.GeneMapper
map(GeneDocument, Parameters, Stats) - Method in class de.julielab.genemapper.GeneMapper
map(GeneDocument, Parameters, Stats) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
map(GeneDocument, Parameters, Stats) - Method in interface de.julielab.genemapper.mappingcores.MappingCore
map(GeneDocument, Parameters, Stats) - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
map(GeneDocument, Stats) - Method in class de.julielab.genemapper.GeneMapper
map(GeneMention) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
map(GeneMention) - Method in interface de.julielab.genemapper.mappingcores.MappingCore
map(GeneMention) - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
map(GeneMention, BooleanQuery, String) - Method in class de.julielab.genemapper.GeneMapper: Actual mapping method.
map(String, BooleanQuery) - Method in class de.julielab.genemapper.GeneMapper: A wrapper to the main mapping function.
map(String, BooleanQuery, String) - Method in class de.julielab.genemapper.GeneMapper: Convenience method mostly used for tests.
MAPPER_CONFIG_FILE - Static variable in class de.julielab.genemapper.uima.GeneMapperAnnotator
MAPPING_CORE - Static variable in class de.julielab.genemapper.Configuration: Deprecated.
Not a configurable property any more but bound in the MappingModule
MappingCore - Interface in de.julielab.genemapper.mappingcores
mapSentences2Ranges(JCas) - Static method in class de.julielab.genemapper.evaluation.tools.JCasConverter
mapTopN(String, int) - Method in class de.julielab.genemapper.GeneMapper: This mapping returns a list of SynHits.
matches(String) - Method in class de.julielab.genemapper.composites.CompositePatternResolver: Requires the completed composite tagging via FlairCompositeMentionTagger and returns true if the respective subclass handles the given case.
matches(String) - Method in class de.julielab.genemapper.composites.EmbeddedAcronymPatternResolver
matches(String) - Method in class de.julielab.genemapper.composites.EnumerationResolver
matches(String) - Method in class de.julielab.genemapper.composites.NumberElipseEnumerationPatternResolver
matches(String) - Method in class de.julielab.genemapper.composites.PatternResolutionChain
matches(String) - Method in class de.julielab.genemapper.composites.SlashDashAlternativePatternResolver
matches(String) - Method in class de.julielab.genemapper.composites.TwoPartedRangePatternResolver
MAX_DOC_CONTEXT_SIZE - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ME_CONFIG - Static variable in class de.julielab.genemapper.hpo.BC2Evaluation
ME_CONFIG - Static variable in class de.julielab.genemapper.hpo.GNormPlusCorpusEvaluation
MENTION_INDEX - Static variable in class de.julielab.genemapper.Configuration
MentionAndDocResult - Class in de.julielab.genemapper.evaluation.tools
MentionAndDocResult(DocResult, DocResult) - Constructor for class de.julielab.genemapper.evaluation.tools.MentionAndDocResult
MentionDisambiguationData - Interface in de.julielab.genemapper.disambig
MENTIONED_PAGE_TITLES - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields: Titles of other Wikipedia pages found in an entity chunk of the current page.
MentionEnvironmentPipe - Class in de.julielab.genemapper.filtering.families
MentionEnvironmentPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.MentionEnvironmentPipe
MentionPrefixPipe - Class in de.julielab.genemapper.filtering.families: This pipe adds a feature indicated whether the given gene name is a prefix of another gene in the same document.
MentionPrefixPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.MentionPrefixPipe
MentionTypeHint - Class in de.julielab.genemapper.filtering.families: Taken from GNormPlus code: Wei, C.
MentionTypeHint() - Constructor for class de.julielab.genemapper.filtering.families.MentionTypeHint
mentionWise - Variable in class de.julielab.genemapper.evaluation.tools.MentionAndDocResult
mergeContinuousGeneAnnotations(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector: Call BEFORE selecting genes.
mergeLexicalWithSemanticRanking(GeneDocument, Parameters) - Static method in class de.julielab.genemapper.disambig.DypsisRankingMerger: Sets the final result entry to the MentionMappingResult objects of the GeneMentions.
mergeParameters(Parameters) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker: Merges the stored model parameters with the externally passed parameters.
MissingConfigurationException - Exception in de.julielab.genemapper.utils
MissingConfigurationException() - Constructor for exception de.julielab.genemapper.utils.MissingConfigurationException
MissingConfigurationException(String) - Constructor for exception de.julielab.genemapper.utils.MissingConfigurationException
MissingConfigurationException(String, Throwable) - Constructor for exception de.julielab.genemapper.utils.MissingConfigurationException
MissingConfigurationException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.genemapper.utils.MissingConfigurationException
MissingConfigurationException(Throwable) - Constructor for exception de.julielab.genemapper.utils.MissingConfigurationException
MLGeneFilter - Class in de.julielab.genemapper.filtering
MLGeneFilter() - Constructor for class de.julielab.genemapper.filtering.MLGeneFilter
MOLECULAR_BIOLOGY_PATH - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
MOLECULAR_BIOLOGY_PATH_LENGTH - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
MoleculeType - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
MoleculeType() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType: Never called.
MoleculeType(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType: Internal - constructor used by generator
MoleculeType(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType
MoleculeType(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType
MoleculeType_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
MoleculeType_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType_Type: initialize variables to correspond with Cas Type and Features

N

ndcg(double[], double[], int) - Static method in class de.julielab.genemapper.utils.NDCG
ndcg(Collection<SynHit>, int) - Static method in class de.julielab.genemapper.utils.NDCG
NDCG - Class in de.julielab.genemapper.utils
NDCG() - Constructor for class de.julielab.genemapper.utils.NDCG
NER_CONFIDENCE - Static variable in class de.julielab.genemapper.RejectionConstants
NextCharPipe - Class in de.julielab.genemapper.filtering
NextCharPipe(String) - Constructor for class de.julielab.genemapper.filtering.NextCharPipe
NlmGeneCorpusEvaluation - Class in de.julielab.genemapper.hpo
NlmGeneCorpusEvaluation() - Constructor for class de.julielab.genemapper.hpo.NlmGeneCorpusEvaluation
NoDbHitsPipe - Class in de.julielab.genemapper.filtering.families: This pipe adds a feature indicated whether the given gene name is a prefix of the official symbol of the gene candidate that was retrieved for the gene name.
NoDbHitsPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.NoDbHitsPipe
NonDescriptivePipe - Class in de.julielab.genemapper.filtering.families
NonDescriptivePipe(String) - Constructor for class de.julielab.genemapper.filtering.families.NonDescriptivePipe
NonFamilyIndicator - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
NonFamilyIndicator() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator: Never called.
NonFamilyIndicator(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator: Internal - constructor used by generator
NonFamilyIndicator(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator
NonFamilyIndicator(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator
NonFamilyIndicator_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
NonFamilyIndicator_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator_Type: initialize variables to correspond with Cas Type and Features
NonGeneCue - Class in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer: Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
NonGeneCue() - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue: Never called.
NonGeneCue(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue: Internal - constructor used by generator
NonGeneCue(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue
NonGeneCue(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue
NonGeneCue_Type - Class in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer: Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
NonGeneCue_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue_Type: initialize variables to correspond with Cas Type and Features
NonGenePhrase - Class in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer: Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
NonGenePhrase() - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase: Never called.
NonGenePhrase(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase: Internal - constructor used by generator
NonGenePhrase(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase
NonGenePhrase(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase
NonGenePhrase_Type - Class in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer: Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
NonGenePhrase_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase_Type: initialize variables to correspond with Cas Type and Features
NORMALIZE_CONTEXT_GENES - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
NormalizeFeaturesForGeneSetSize - Class in de.julielab.genemapper.filtering.families
NormalizeFeaturesForGeneSetSize() - Constructor for class de.julielab.genemapper.filtering.families.NormalizeFeaturesForGeneSetSize
NounPipe - Class in de.julielab.genemapper.filtering
NounPipe(String) - Constructor for class de.julielab.genemapper.filtering.NounPipe
NumberClassPipe - Class in de.julielab.genemapper.filtering
NumberClassPipe(String, boolean) - Constructor for class de.julielab.genemapper.filtering.NumberClassPipe
NumberElipseEnumerationPatternResolver - Class in de.julielab.genemapper.composites
NumberElipseEnumerationPatternResolver() - Constructor for class de.julielab.genemapper.composites.NumberElipseEnumerationPatternResolver

O

Of - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Of - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Of() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of: Never called.
Of() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of: Never called.
Of(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of: Internal - constructor used by generator
Of(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of: Internal - constructor used by generator
Of(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of
Of(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of
Of(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of
Of(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of
Of_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Of_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Of_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of_Type: initialize variables to correspond with Cas Type and Features
Of_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of_Type: initialize variables to correspond with Cas Type and Features
OfficialSymbolPromotionDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus: If there are IDs for which the candidate synonym is the official symbol, remove all other options.
OfficialSymbolPromotionDisambiguationStep() - Constructor for class de.julielab.genemapper.mappingcores.quercus.OfficialSymbolPromotionDisambiguationStep
ONLY_APPROX_MATCHES - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
ONLY_EXACT_MATCHES - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
OrganismEnumeration - Class in de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration: Type defined in de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
OrganismEnumeration() - Constructor for class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration: Never called.
OrganismEnumeration(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration: Internal - constructor used by generator
OrganismEnumeration(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration
OrganismEnumeration(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration
OrganismEnumeration_Type - Class in de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration: Type defined in de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
OrganismEnumeration_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration_Type: initialize variables to correspond with Cas Type and Features

P

PAGE_ID - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
PARAM_ADD_CONTEXT_GENES_AS_LUCENE_RELEVANCE_SIGNAL - Static variable in class de.julielab.genemapper.Configuration
PARAM_ADD_SPECIES_PREFIX_STRIPPED_VARIANT_AS_GENENAME_ALTERNATIVE - Static variable in class de.julielab.genemapper.Configuration
PARAM_ALTERNATIVE_NAMES_SEARCH_MODE - Static variable in class de.julielab.genemapper.Configuration: One of Configuration.VALUE_CNF_RELEVANCE_SIGNAL, Configuration.VALUE_ADDITIONAL_SEARCH, Configuration.VALUE_ALL or Configuration.VALUE_NONE.
PARAM_APPROX_SINGLE_TOKEN - Static variable in class de.julielab.genemapper.RejectionConstants
PARAM_BASE_PATH - Static variable in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
PARAM_BASE_PATH - Static variable in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
PARAM_COMPOSITE_FLAIR_MODEL - Static variable in class de.julielab.genemapper.Configuration
PARAM_CONTEXT_GENE_FEATURE_GENERATION - Static variable in class de.julielab.genemapper.Configuration: How to create feature from the context genes.
PARAM_CONTRADICTING_GREEK - Static variable in class de.julielab.genemapper.RejectionConstants
PARAM_CONTRADICTING_NUMBER - Static variable in class de.julielab.genemapper.RejectionConstants
PARAM_DB_DIR - Static variable in class de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter
PARAM_DISAMBIGUATE_BY_MAP_LOCATION - Static variable in class de.julielab.genemapper.Configuration
PARAM_DISAMBIGUATE_EXACT_HITS_BY_ORIGINAL_NAME - Static variable in class de.julielab.genemapper.Configuration
PARAM_DISAMBIGUATION_LINCOMB_MAX_VALUES - Static variable in class de.julielab.genemapper.Configuration
PARAM_DISAMBIGUATION_LINCOMB_MIN_VALUES - Static variable in class de.julielab.genemapper.Configuration
PARAM_DISMAX_TIE_BREAKER - Static variable in class de.julielab.genemapper.Configuration
PARAM_DO_CONTEXTUAL_RANKING - Static variable in class de.julielab.genemapper.Configuration
PARAM_DO_FAMILY_REJECTION - Static variable in class de.julielab.genemapper.Configuration
PARAM_DO_LOW_SCORE_REJECTION - Static variable in class de.julielab.genemapper.Configuration
PARAM_DO_RRF_WITH_CANDIDATE_LISTS - Static variable in class de.julielab.genemapper.Configuration: Whether to merge all candidate lists created in candidate retrieval (gene records CNF, potentially synonym centric retrieval and ML-based re-ranking) via reciprocal rank fusion for the final candidate list.
PARAM_EXCLUDE_GENES_FOR_CONTEXT_ITEM_SCORING - Static variable in class de.julielab.genemapper.Configuration
PARAM_FILTER_OUT_METHOD - Static variable in class de.julielab.genemapper.RejectionConstants
PARAM_GENE_RECORDS_FIELD_QUERY_TYPE - Static variable in class de.julielab.genemapper.Configuration: Parameter: Which classification/ranking method to use.
PARAM_GPU_COMPOSITE_MENTIONS - Static variable in class de.julielab.genemapper.Configuration: Number of the GPU to use for the flair composite mention resolution
PARAM_GPU_TRANSFORMER_CANDIDATE_RANKING - Static variable in class de.julielab.genemapper.Configuration: Number of the GPU to use for the transformer-based candiate ranking
PARAM_GS_HOMOGENIZATION_ALLOW_CANDIDATE_TRANSFER - Static variable in class de.julielab.genemapper.Configuration: Whether we allow the transfer of candidates from accepted gene mentions to other mentions that have been rejected because they don't have candidates.
PARAM_GS_HOMOGENIZATION_BY_ABBREVIATION - Static variable in class de.julielab.genemapper.Configuration
PARAM_GS_HOMOGENIZATION_BY_LONGFORM - Static variable in class de.julielab.genemapper.Configuration
PARAM_GS_HOMOGENIZATION_METHOD - Static variable in class de.julielab.genemapper.Configuration: The method of GeneSet ID homogenization.
PARAM_GS_MAJORITY_HOMOGENIZATION_TIE_BREAKER_METHOD - Static variable in class de.julielab.genemapper.Configuration: The method to solve majority voting ties.
PARAM_GS_REJECTION_HOMOGENIZATION_METHOD - Static variable in class de.julielab.genemapper.Configuration: What to do when some genes in a gene set have been rejected and others have not? This is checked when doing gene set ID homogenization.
PARAM_INTERSECTION_FILTER - Static variable in class de.julielab.genemapper.Configuration
PARAM_LEMMAS - Static variable in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
PARAM_LEMMAS - Static variable in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
PARAM_LEX_CONTEXT_FUSE_METHOD - Static variable in class de.julielab.genemapper.Configuration
PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_APPROX - Static variable in class de.julielab.genemapper.Configuration: Must be in [0,1].
PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_EXACT - Static variable in class de.julielab.genemapper.Configuration: Must be in [0,1].
PARAM_LOWERCASING - Static variable in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
PARAM_LOWERCASING - Static variable in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING - Static variable in class de.julielab.genemapper.Configuration: Prerequisite test for Configuration.PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY: Only candidates whose Lucene score exceed the given ratio to the Lucene score of the best candidate are included in a re-ranking by original name.
PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_RERANKING - Static variable in class de.julielab.genemapper.Configuration: Similar to Configuration.PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING, this parameter sets a threshold of to be overcome for a candidate to be included in ML-based re-ranking.
PARAM_MAKE_TOKEN_WINDOW_DISTINCT - Static variable in class de.julielab.genemapper.Configuration
PARAM_MAPPING_MODE - Static variable in class de.julielab.genemapper.Configuration: One of Configuration.VALUE_GENE_MENTIONS and Configuration.VALUE_GENESETS
PARAM_MASK_ORGANISM_NAMES - Static variable in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
PARAM_MERGE_CONTINUOUS_GENE_ANNOTATIONS - Static variable in class de.julielab.genemapper.Configuration: Whether to invoke DypsisGeneSelector.mergeContinuousGeneAnnotations(GeneDocument).
PARAM_MODE - Static variable in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
PARAM_NO_TOKEN_OVERLAP - Static variable in class de.julielab.genemapper.RejectionConstants
PARAM_NORMALIZE_JARO_WINKLER_SYNONYM_SCORES - Static variable in class de.julielab.genemapper.Configuration
PARAM_NORMALIZE_LUCENE_SYNONYM_SCORES - Static variable in class de.julielab.genemapper.Configuration
PARAM_OFFSET_EXPANSION_TYPE - Static variable in class de.julielab.genemapper.uima.ProteinConsistencyTagger
PARAM_OUTPUT_PATH - Static variable in class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
PARAM_RANK_BY_SINGLE_FEATURE_VALUE - Static variable in class de.julielab.genemapper.Configuration: One of Configuration.VALUE_SEMANTIC_CONTEXT or Configuration.VALUE_NONE.
PARAM_REJECT_FAMILY_IN_NP - Static variable in class de.julielab.genemapper.Configuration
PARAM_REJECTION_FAMILY_HIT_RANK_APPROX_MATCH - Static variable in class de.julielab.genemapper.Configuration
PARAM_REJECTION_FAMILY_HIT_RANK_EXACT_MATCH - Static variable in class de.julielab.genemapper.Configuration
PARAM_REMOVE_SPECIES_PREFIXES_FOR_CANDIDATE_RETRIEVAL - Static variable in class de.julielab.genemapper.Configuration
PARAM_REPLACE_ML_MENTIONS_WITH_LONGER_GAZETTEER_MENTIONS - Static variable in class de.julielab.genemapper.Configuration: Whether to invoke DypsisGeneSelector.selectLongerGazetteerMatchesOverFlair(GeneDocument)
PARAM_SCALE_FAMILY_NAME_MATCH_SCORE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_FAMILY_NAMES_WITH_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_GENERIFS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_GENERIFS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_GENERIFS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_GENERIFS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_SUMMARIES_JARO_WINKLER - Static variable in class de.julielab.genemapper.Configuration
PARAM_SCORE_SYNONYMS_ON_SUMMARIES_LUCENE - Static variable in class de.julielab.genemapper.Configuration
PARAM_SEARCH_GM_NP_MODE - Static variable in class de.julielab.genemapper.Configuration: One of Configuration.VALUE_CNF_RELEVANCE_SIGNAL, Configuration.VALUE_ADDITIONAL_SEARCH or Configuration.VALUE_NONE.
PARAM_SEARCH_TAX_SPECIFIC_CANDIDATES_FIRST - Static variable in class de.julielab.genemapper.Configuration
PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD - Static variable in class de.julielab.genemapper.Configuration
PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY - Static variable in class de.julielab.genemapper.Configuration: Whether or not to try to disambiguate multiple exact matches with the original names.
PARAM_SORT_ML_BY_EXACT_MATCH_FIRST - Static variable in class de.julielab.genemapper.Configuration
PARAM_SPLIT_AT_SLASH - Static variable in class de.julielab.genemapper.Configuration: Whether to invoke DypsisGeneSelector.splitDashGenes(GeneDocument, CandidateRetrieval).
PARAM_STOP_CANDIDATE_SEARCH_ON_EXACT_MATCH - Static variable in class de.julielab.genemapper.Configuration
PARAM_SYNONYM_SEARCH_MODE - Static variable in class de.julielab.genemapper.Configuration: One of Configuration.VALUE_CNF_RELEVANCE_SIGNAL, Configuration.VALUE_ADDITIONAL_SEARCH or Configuration.VALUE_NONE.
PARAM_THRESHOLD_APPROX_LENGTH_DIFF_PENALTY_FACTOR - Static variable in class de.julielab.genemapper.Configuration: The approx.
PARAM_THRESHOLD_APPROX_MATCHES - Static variable in class de.julielab.genemapper.Configuration
PARAM_THRESHOLD_EXACT_MATCHES - Static variable in class de.julielab.genemapper.Configuration
PARAM_THRESHOLD_GS_REJECTION - Static variable in class de.julielab.genemapper.Configuration: Used to homogenize gene set rejection where some members have been rejected and others haven't.
PARAM_TOKEN_WINDOW_GENE_SETS_SIZE - Static variable in class de.julielab.genemapper.Configuration
PARAM_TOKENIZATION - Static variable in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
PARAM_TOKENIZATION - Static variable in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
PARAM_TOP_N_CANDIDATES_RERANKING - Static variable in class de.julielab.genemapper.Configuration: The top N candidates returned from Lucene to subject to reranking.
PARAM_TRAIN_MODE - Static variable in class de.julielab.genemapper.Configuration
PARAM_TRANSFORMER_RANKING_MODEL - Static variable in class de.julielab.genemapper.Configuration
PARAM_TRY_ORTHOLOGS - Static variable in class de.julielab.genemapper.Configuration: Whether to try ortholog genes when the primary species didn't fit
PARAM_USE_APPOSITIONS_AS_LUCENE_RELEVANCE_SIGNAL - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_APPOSITIONS_ON_GENE_CONTEXT_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_FAMILY_MATCH_EXACT_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_FAMILY_MATCH_FRACTION_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_FAMILY_MATCH_RANK_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_FAMILY_MATCH_SCORE_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GENE_FAMILY_SCORE_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GENERIF - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GNORMPLUS_CHEMICAL_SUFFIX_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GNORMPLUS_MENTION_TYPE_HINT_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GNORMPLUS_PROTEIN_SYMBOLS_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GODESC - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_GOLD_TAX - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_INTERACTION - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_JACCARD_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_JARO_WINKLER_APPROX_SCORES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_JARO_WINKLER_EXACT_SCORES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_JARO_WINKLER_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_LASTWORD_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_LEVENSHTEIN_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_LUCENE_APPROX_SCORES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_LUCENE_EXACT_SCORES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_LUCENE_SYNONYM_SET - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_NEEDLEMANWUNSCH_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_OTHER_HAS_SPECIFIER_FEATURE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_QUERY_FIELD_WEIGHTS - Static variable in class de.julielab.genemapper.Configuration: Whether to use field weights in the Lucene query to the candidate index.
PARAM_USE_SCORER_AVERAGE - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_SMITHWATERMAN_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_SUMMARY - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_TFIDF_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_TOKEN_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAM_USE_TOKEN_JARO_FEATURES - Static variable in class de.julielab.genemapper.Configuration
PARAMETER_PROTEIN_TYPE - Static variable in class de.julielab.genemapper.uima.ProteinConsistencyTagger
PatternResolutionChain - Class in de.julielab.genemapper.composites
PatternResolutionChain(CompositePatternResolver...) - Constructor for class de.julielab.genemapper.composites.PatternResolutionChain
pipe(Instance) - Method in class de.julielab.genemapper.filtering.ChunkTypePipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.ContextPosPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.ExperimentsPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.AcronymPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.ChemicalSuffix
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.ContextPosPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.FamilyConfidencePipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.FamilyGenegroupProbabilityPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.FamilyMatchPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.GeneMention2Token
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.GeneSet2Token
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.IsAPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.IsFamilyPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.LastWordPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.LowerCaseBoWPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.MentionEnvironmentPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.MentionPrefixPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.MentionTypeHint
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.NoDbHitsPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.NonDescriptivePipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.NormalizeFeaturesForGeneSetSize
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.PluralPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.PoSBoWPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.ProteinSymbols
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.SetFeatureVectorToGeneSetPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.SetInstanceSourceToGeneSetPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.SpecifierDetectionPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.SymbolPrefixPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.families.UnspecifiedPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.GeneSequence2SingleGene
pipe(Instance) - Method in class de.julielab.genemapper.filtering.GeneSet2GeneSequence
pipe(Instance) - Method in class de.julielab.genemapper.filtering.LowerCasePipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.NextCharPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.NounPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.NumberClassPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.PrevCharPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.RegExPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.TokenPrefixPipe
pipe(Instance) - Method in class de.julielab.genemapper.filtering.WordClassPipe
Plural - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Plural() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural: Never called.
Plural(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural: Internal - constructor used by generator
Plural(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural
Plural(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural
Plural_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Plural_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural_Type: initialize variables to correspond with Cas Type and Features
PluralPipe - Class in de.julielab.genemapper.filtering.families
PluralPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.PluralPipe
PoSBoWPipe - Class in de.julielab.genemapper.filtering.families
PoSBoWPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.PoSBoWPipe
preFilter(GeneDocument) - Static method in class de.julielab.genemapper.GeneMentionFilter
PREFIX_ANCHORING - Static variable in class de.julielab.genemapper.Configuration
PREFIX_CANDIDATE_FILTER - Static variable in class de.julielab.genemapper.Configuration
PREFIX_CANDIDATE_RETRIEVAL - Static variable in class de.julielab.genemapper.Configuration
PREFIX_DISAMBIGUATION - Static variable in class de.julielab.genemapper.Configuration
PREFIX_ID_HOMOGENIZATION - Static variable in class de.julielab.genemapper.Configuration
PREFIX_RECORD_CONTEXT - Static variable in class de.julielab.genemapper.Configuration
PREFIX_REJECTION - Static variable in class de.julielab.genemapper.Configuration
PREFIX_REJECTION_HOMOGENIZATION - Static variable in class de.julielab.genemapper.Configuration
PrevCharPipe - Class in de.julielab.genemapper.filtering
PrevCharPipe(String) - Constructor for class de.julielab.genemapper.filtering.PrevCharPipe
PrintBestSmacConfiguration - Class in de.julielab.genemapper.hpo
PrintBestSmacConfiguration() - Constructor for class de.julielab.genemapper.hpo.PrintBestSmacConfiguration
printInspectionFile(String, double, Map<String, Double>, HpoInstance, List<GeneDocument>) - Method in class de.julielab.genemapper.hpo.GenesetsOptimizationRoute
process(JCas) - Method in class de.julielab.genemapper.uima.EGSummaryStructureAnnotator
process(JCas) - Method in class de.julielab.genemapper.uima.EmbeddingsWithTokensConnectionAnnotator
process(JCas) - Method in class de.julielab.genemapper.uima.ExtendedProteinsMerger
process(JCas) - Method in class de.julielab.genemapper.uima.GeneMapperAnnotator: The process method.
process(JCas) - Method in class de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter
process(JCas) - Method in class de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter
process(JCas) - Method in class de.julielab.genemapper.uima.GeneToProteinConverter
process(JCas) - Method in class de.julielab.genemapper.uima.ProteinConsistencyTagger
process(JCas) - Method in class de.julielab.genemapper.uima.ProteinFamilyRulesApplier
process(JCas) - Method in class de.julielab.genemapper.uima.ProteinToGeneConverter
process(JCas) - Method in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
process(JCas) - Method in class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
ProteinConsistencyTagger - Class in de.julielab.genemapper.uima
ProteinConsistencyTagger() - Constructor for class de.julielab.genemapper.uima.ProteinConsistencyTagger
ProteinFamilyRulesApplier - Class in de.julielab.genemapper.uima
ProteinFamilyRulesApplier() - Constructor for class de.julielab.genemapper.uima.ProteinFamilyRulesApplier
ProteinModifier - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
ProteinModifier() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier: Never called.
ProteinModifier(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier: Internal - constructor used by generator
ProteinModifier(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier
ProteinModifier(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier
ProteinModifier_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
ProteinModifier_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier_Type: initialize variables to correspond with Cas Type and Features
ProteinSymbols - Class in de.julielab.genemapper.filtering.families: Taken from GNormPlus code: Wei, C.
ProteinSymbols() - Constructor for class de.julielab.genemapper.filtering.families.ProteinSymbols
ProteinToGeneConverter - Class in de.julielab.genemapper.uima
ProteinToGeneConverter() - Constructor for class de.julielab.genemapper.uima.ProteinToGeneConverter
ProtEnum - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
ProtEnum() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum: Never called.
ProtEnum(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum: Internal - constructor used by generator
ProtEnum(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum
ProtEnum(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum
ProtEnum_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyResolution: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
ProtEnum_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum_Type: initialize variables to correspond with Cas Type and Features

Q

QuercusCandidateSetter - Class in de.julielab.genemapper.mappingcores
QuercusCandidateSetter(NameCentricRetrieval, CandidateRetrieval) - Constructor for class de.julielab.genemapper.mappingcores.QuercusCandidateSetter
QuercusDisambiguation - Class in de.julielab.genemapper.mappingcores
QuercusDisambiguation(CandidateRetrieval, OfficialSymbolPromotionDisambiguationStep, BioThesaurusFilterDisambiguationStep, TestDisambiguationStep, UnderspecifiedNameDisambiguationStep, GeneRecordQueryDisambiguationStep, SemanticIndexDisambiguationStep, AnchorDisambiguationStep) - Constructor for class de.julielab.genemapper.mappingcores.QuercusDisambiguation
QuercusDisambiguationStep - Interface in de.julielab.genemapper.mappingcores.quercus
QuercusMappingCore - Class in de.julielab.genemapper.mappingcores
QuercusMappingCore(GeneCompositeNameResolver, QuercusCandidateSetter, QuercusDisambiguation, GeneSpeciesAssigner, SpeciesAssignmentFilter) - Constructor for class de.julielab.genemapper.mappingcores.QuercusMappingCore

R

rankCandidates(GeneMention, AtomicInteger, Parameters) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
RANKING_SCORE - Static variable in class de.julielab.genemapper.RejectionConstants
read() - Method in class de.julielab.genemapper.utils.ReaderInputStream
read(byte[], int, int) - Method in class de.julielab.genemapper.utils.ReaderInputStream
ReaderInputStream - Class in de.julielab.genemapper.utils: This class convert Reader to InputStream.
ReaderInputStream(Reader) - Constructor for class de.julielab.genemapper.utils.ReaderInputStream: Creates new input stream from the given reader.
ReaderInputStream(Reader, String) - Constructor for class de.julielab.genemapper.utils.ReaderInputStream: Creates new input stream from the given reader and encoding.
readFile2ArrayList(File) - Static method in class de.julielab.genemapper.utils.IOUtils
readFile2String(File) - Static method in class de.julielab.genemapper.utils.IOUtils
recordStats - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
reduceToFirstCharacters(String[], int) - Static method in class de.julielab.genemapper.filtering.StringHelper: Goes through an array of strings and reduces every element to its first suffixLength characters.
RefCounter - Class in de.julielab.genemapper.utils.dict
RegExPipe - Class in de.julielab.genemapper.filtering
RegExPipe(String, Pattern) - Constructor for class de.julielab.genemapper.filtering.RegExPipe
rejectFamilyInNp(GeneDocument, Parameters) - Static method in class de.julielab.genemapper.disambig.DypsisCandidateRejector
rejectFamilyMentions(GeneDocument, Parameters) - Static method in class de.julielab.genemapper.disambig.DypsisCandidateRejector
RejectionConstants - Class in de.julielab.genemapper
RejectionConstants() - Constructor for class de.julielab.genemapper.RejectionConstants
rejectLowScoreResults(GeneDocument, Parameters) - Static method in class de.julielab.genemapper.disambig.DypsisCandidateRejector
REMOVE_EXISTING_RESOURCE_ENTRIES - Static variable in class de.julielab.genemapper.uima.GeneMapperAnnotator
removeGenesWithVerbs(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector: Call AFTER selecting genes.
removeSpeciesMention(MultiPatternSearcher, GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector: Removes all prefixes belonging to a species, e.g.
removeSpeciesMention(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector
removeSpeciesPrefixesFromGenes(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector
removeStrings(String[], String[]) - Static method in class de.julielab.genemapper.filtering.StringHelper: Removes all tokens in strings that are also in unwantedStrings.
removeStringsIgnoreCase(String[], String[]) - Static method in class de.julielab.genemapper.filtering.StringHelper: Removes all tokens in strings that are also in unwantedStrings.
renderCorrectGeneSetMention(GeneMention, String) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderCorrectIdGeneMention(GeneMention) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderCorrectRejection(GeneMention) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderIncorrectRejection(GeneMention) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderMissedRejection(GeneMention) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderNoCorrectCandidateIdGeneMention(GeneMention) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderNoCorrectMentionGeneSet(GeneMention, String) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderWrongGeneSetMention(GeneMention, String) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderWrongIdGeneMention(GeneMention) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
renderWrongIdGeneMention(GeneMention, CandidateRetrieval, QueryGenerator) - Static method in class de.julielab.genemapper.evaluation.GeneIdCorrectnessRenderer
resolve(GeneMention, boolean...) - Method in class de.julielab.genemapper.composites.GeneCompositeNameResolver
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.CompositePatternResolver
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.EmbeddedAcronymPatternResolver
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.EnumerationResolver
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.NumberElipseEnumerationPatternResolver
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.PatternResolutionChain
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.SlashDashAlternativePatternResolver
resolve(String, Pair<List<CompositeToken>, String>) - Method in class de.julielab.genemapper.composites.TwoPartedRangePatternResolver
ResolvedCompositeGeneName - Class in de.julielab.genemapper.composites: This class represents a re-assembled gene name from a formerly tokenized and possibly rearranged composite gene name to identify multiple gene names denoted by one composite expression.
ResolvedCompositeGeneName(Class<? extends CompositePatternResolver>) - Constructor for class de.julielab.genemapper.composites.ResolvedCompositeGeneName
ResolvedCompositeGeneName(List<CompositeToken>, Class<? extends CompositePatternResolver>) - Constructor for class de.julielab.genemapper.composites.ResolvedCompositeGeneName
retainAll(Set<SynHit>) - Method in class de.julielab.genemapper.SynHitSet
retrieveGeneContexts(List<SynHit>) - Method in class de.julielab.genemapper.disambig.SemanticContextIndex
rightWordBoundary - Static variable in class de.julielab.genemapper.filtering.UnspecificNameFilter: characters that appear on the right side of a proper word: white space, comma, bracket ends, ..
Roman - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Roman() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman: Never called.
Roman(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman: Internal - constructor used by generator
Roman(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman
Roman(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman
Roman_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Roman_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman_Type: initialize variables to correspond with Cas Type and Features
RRFSynHitListFusion - Class in de.julielab.genemapper.disambig
RRFSynHitListFusion() - Constructor for class de.julielab.genemapper.disambig.RRFSynHitListFusion
RuleBasedFamilyAssigner - Class in de.julielab.genemapper.filtering.families
RuleBasedFamilyAssigner(CandidateRetrieval) - Constructor for class de.julielab.genemapper.filtering.families.RuleBasedFamilyAssigner

S

save(File, Parameters) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
saveCandidateSetter(File, Parameters) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
saveModel(File, Parameters) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
saveParameter(File) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
searchCandidatesForFamilyNames(GeneMention) - Method in class de.julielab.genemapper.filtering.families.FamilyMatchPipe: Iterates through all the candidates that belong to the assigned species of the given gene mention.
searcher - Variable in class de.julielab.genemapper.disambig.ContextItemRecordsIndex: Deprecated.
searcher - Variable in class de.julielab.genemapper.disambig.ContextItemsIndex
searcher - Variable in class de.julielab.genemapper.disambig.SemanticContextIndex
searcher - Static variable in class de.julielab.genemapper.utils.SpeciesMultiPatternSearcher
searchWikipedia(String) - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaIndexReader
selectLongerGazetteerMatchesOverFlair(GeneDocument) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector: Call BEFORE selecting genes.
SemanticContextIndex - Class in de.julielab.genemapper.disambig
SemanticContextIndex(File) - Constructor for class de.julielab.genemapper.disambig.SemanticContextIndex
SemanticIndex - Interface in de.julielab.genemapper.disambig: A common interface for all kinds of indices for gene mention disambiguation.
SemanticIndexDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus
SemanticIndexDisambiguationStep(Configuration) - Constructor for class de.julielab.genemapper.mappingcores.quercus.SemanticIndexDisambiguationStep
setCandidates(GeneDocument) - Method in class de.julielab.genemapper.mappingcores.QuercusCandidateSetter
setCandidates(GeneDocument, Parameters, Stats) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
setCandidates(GeneMention, AtomicInteger, Parameters, Stats) - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
setCandidatesToGoldMentions(GeneDocument) - Method in class de.julielab.genemapper.mappingcores.QuercusCandidateSetter: Set candidates to the gold mentions; the only purpose is to determine whether there exists an exact database match for it or not.
setClassifier(Classifier) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
setCounter(int) - Method in class de.julielab.genemapper.utils.dict.RefCounter
setDisambiguationClassifier(Classifier) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
setDisambiguationRanker(RankLibRanker) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
setDocument(GeneDocument) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
setFamilyNameFeatures(GeneDocument) - Static method in class de.julielab.genemapper.filtering.families.GeneMentionFamilyFeatureSetter
SetFeatureVectorToGeneSetPipe - Class in de.julielab.genemapper.filtering.families
SetFeatureVectorToGeneSetPipe() - Constructor for class de.julielab.genemapper.filtering.families.SetFeatureVectorToGeneSetPipe
setFn(int) - Method in class de.julielab.genemapper.evaluation.tools.DocResult
setFp(int) - Method in class de.julielab.genemapper.evaluation.tools.DocResult
setGeneDocument(GeneDocument) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
setGeneId(int, String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family_Type
setGeneId(int, String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
setGeneId(int, String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym_Type
setGeneId(int, String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
setGeneId(String) - Method in class de.julielab.genemapper.ContextItemsCacheKey
setGeneId(String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family: setter for geneId - sets geneId
setGeneId(String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym: setter for geneId - sets geneId
setGeneId(String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym: setter for geneId - sets geneId
setGeneId(String) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym: setter for geneId - sets geneId
setGeneSetContext2ContextItemsScores(GeneDocument, Set<String>, Parameters) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker: Obtains scores by assembling the token context of the gene set where each gene ID occurs in an matching this to the context items via a Lucene disjunction query.
setGoldRelevanceScores(GeneMention, MentionMappingResult) - Static method in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker
setIndexField(String) - Method in class de.julielab.genemapper.ContextItemsCacheKey
SetInstanceSourceToGeneSetPipe - Class in de.julielab.genemapper.filtering.families
SetInstanceSourceToGeneSetPipe() - Constructor for class de.julielab.genemapper.filtering.families.SetInstanceSourceToGeneSetPipe
setK(String[]) - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator: Sets the evaluation points in number of errors.
setListresult(TAPEvaluator.TapResultRecord) - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultList
setLongform(int, int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
setLongform(int, int) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
setLongform(Family) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym: setter for longform - sets longform
setLongform(Family) - Method in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym: setter for longform - sets longform
setMappingCore(MappingCore) - Method in class de.julielab.genemapper.GeneMapper
setMaxAgglomerationCandidates(int) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
setNameLevelUnificationStrategies(Set<DypsisMappingCore.NameLevelUnificationStrategy>) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
setOmitCandidateSetting(boolean) - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
setPlural(boolean) - Method in class de.julielab.genemapper.composites.CompositeToken
setRanker(RankLibRanker) - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
setRightWs(boolean) - Method in class de.julielab.genemapper.composites.CompositeToken
setStats(Stats) - Method in class de.julielab.genemapper.disambig.DypsisDocumentDisambiguationData
setTag(char) - Method in class de.julielab.genemapper.composites.CompositeToken
setTp(int) - Method in class de.julielab.genemapper.evaluation.tools.DocResult
showHitIDs(ArrayList<SynHit>) - Static method in class de.julielab.genemapper.utils.SynHitUtils
showHitIDs(HashMap<String, SynHit>) - Static method in class de.julielab.genemapper.utils.SynHitUtils
showHits(ArrayList<SynHit>) - Static method in class de.julielab.genemapper.utils.SynHitUtils
showHits(HashMap<String, SynHit>) - Static method in class de.julielab.genemapper.utils.SynHitUtils: shows all hits in an arraylist of SynHits objects
shutdown() - Method in class de.julielab.genemapper.classification.TransformerClassifier
shutdown() - Method in class de.julielab.genemapper.composites.FlairCompositeMentionTagger
shutdown() - Method in class de.julielab.genemapper.composites.GeneCompositeNameResolver
shutdown() - Method in class de.julielab.genemapper.disambig.DypsisContextRanker
shutdown() - Method in class de.julielab.genemapper.mappingcores.DypsisCandidateSetter
shutdown() - Method in class de.julielab.genemapper.mappingcores.DypsisMappingCore
shutdown() - Method in interface de.julielab.genemapper.mappingcores.MappingCore: Indicates that the mapping process has finished and all held resources should be freed.
shutdown() - Method in class de.julielab.genemapper.mappingcores.QuercusMappingCore
SlashDashAlternativePatternResolver - Class in de.julielab.genemapper.composites
SlashDashAlternativePatternResolver() - Constructor for class de.julielab.genemapper.composites.SlashDashAlternativePatternResolver
SmacRunRepeater - Class in de.julielab.genemapper.apps: This class was created for debugging purposes.
SmacRunRepeater() - Constructor for class de.julielab.genemapper.apps.SmacRunRepeater
SpeciesMultiPatternSearcher - Class in de.julielab.genemapper.utils
SpeciesMultiPatternSearcher() - Constructor for class de.julielab.genemapper.utils.SpeciesMultiPatternSearcher
SpecifiedMoleculeType - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
SpecifiedMoleculeType() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType: Never called.
SpecifiedMoleculeType(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType: Internal - constructor used by generator
SpecifiedMoleculeType(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType
SpecifiedMoleculeType(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType
SpecifiedMoleculeType_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
SpecifiedMoleculeType_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType_Type: initialize variables to correspond with Cas Type and Features
Specifier - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Specifier() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier: Never called.
Specifier(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier: Internal - constructor used by generator
Specifier(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier
Specifier(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier
Specifier_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Specifier_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier_Type: initialize variables to correspond with Cas Type and Features
SpecifierDetectionPipe - Class in de.julielab.genemapper.filtering.families
SpecifierDetectionPipe() - Constructor for class de.julielab.genemapper.filtering.families.SpecifierDetectionPipe
SPELLING_INDEX - Static variable in class de.julielab.genemapper.Configuration
splitAndSort(String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Splits a string into tokens at whitespaces and sorts them alphabetically.
splitDashGenes(GeneDocument, CandidateRetrieval) - Static method in class de.julielab.genemapper.mappingcores.DypsisGeneSelector: Call AFTER selecting genes.
Stats - Class in de.julielab.genemapper.evaluation.tools
Stats() - Constructor for class de.julielab.genemapper.evaluation.tools.Stats
STOPWORD_SET - Static variable in class de.julielab.genemapper.utils.ContextUtils
stopWords - Static variable in class de.julielab.genemapper.filtering.StringHelper: stop words
STOPWORDS - Static variable in class de.julielab.genemapper.utils.ContextUtils
StringHelper - Class in de.julielab.genemapper.filtering: This class offers some methods useful when working with (arrays of) strings.
stringLengthComparatorAscending - Static variable in class de.julielab.genemapper.filtering.StringHelper: A comparator that sorts strings by length, in ascending order (shorest first).
stringLengthComparatorDescending - Static variable in class de.julielab.genemapper.filtering.StringHelper: A comparator that sorts strings by length, in descending order (longest first).
SymbolPrefixPipe - Class in de.julielab.genemapper.filtering.families: This pipe adds a feature indicated whether the given gene name is a prefix of the official symbol of the gene candidate that was retrieved for the gene name.
SymbolPrefixPipe(String, Configuration) - Constructor for class de.julielab.genemapper.filtering.families.SymbolPrefixPipe
SynHitListFusion - Interface in de.julielab.genemapper.disambig
SynHitSet - Class in de.julielab.genemapper
SynHitSet() - Constructor for class de.julielab.genemapper.SynHitSet
SynHitSet(Collection<SynHit>) - Constructor for class de.julielab.genemapper.SynHitSet
SynHitUtils - Class in de.julielab.genemapper.utils
SynHitUtils() - Constructor for class de.julielab.genemapper.utils.SynHitUtils
Synonym - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
Synonym() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym: Never called.
Synonym(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym: Internal - constructor used by generator
Synonym(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym
Synonym(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym
SYNONYM_INDEX - Static variable in class de.julielab.genemapper.Configuration
Synonym_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
Synonym_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym_Type: initialize variables to correspond with Cas Type and Features
SynonymStopword - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
SynonymStopword() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword: Never called.
SynonymStopword(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword: Internal - constructor used by generator
SynonymStopword(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword
SynonymStopword(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword
SynonymStopword_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
SynonymStopword_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword_Type: initialize variables to correspond with Cas Type and Features

T

tagGeneMention(String, Range<Integer>, GeneDocument) - Method in class de.julielab.genemapper.composites.FlairCompositeMentionTagger
tagGeneMention(List<String>, Range<Integer>, GeneDocument) - Method in class de.julielab.genemapper.composites.FlairCompositeMentionTagger
TAP_EXEC - Static variable in class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TAP_EXEC_WORKING_DIR - Static variable in class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TAPEvaluator - Class in de.julielab.genemapper.evaluation.tools
TAPEvaluator() - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TAPEvaluator(File) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TAPEvaluator(File, File) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TAPEvaluator.TapInputLine - Class in de.julielab.genemapper.evaluation.tools
TAPEvaluator.TapInputList - Class in de.julielab.genemapper.evaluation.tools
TAPEvaluator.TapResult - Class in de.julielab.genemapper.evaluation.tools
TAPEvaluator.TapResultList - Class in de.julielab.genemapper.evaluation.tools
TAPEvaluator.TapResultRecord - Class in de.julielab.genemapper.evaluation.tools
tapInputDir - Variable in class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TapInputLine(int, double) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputLine
TapInputList(String) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputList
TapResult(String[]) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResult
TapResultList(String) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultList
TapResultRecord(String, int, double, double) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
TapResultRecord(String, String, double) - Constructor for class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapResultRecord
tapStatsDir - Variable in class de.julielab.genemapper.evaluation.tools.TAPEvaluator
TaxIdIntegratedTextWriter - Class in de.julielab.genemapper.uima
TaxIdIntegratedTextWriter() - Constructor for class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
TaxIdSentenceLabelWriter - Class in de.julielab.genemapper.uima
TaxIdSentenceLabelWriter() - Constructor for class de.julielab.genemapper.uima.TaxIdSentenceLabelWriter
TEST_MODE - Static variable in class de.julielab.genemapper.GeneMapper
TestDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus
TestDisambiguationStep() - Constructor for class de.julielab.genemapper.mappingcores.quercus.TestDisambiguationStep
textHasPlural(String, String) - Static method in class de.julielab.genemapper.filtering.UnspecificNameFilter
ThesaurusCleaner - Class in de.julielab.genemapper.utils.dict
ThesaurusCleaner() - Constructor for class de.julielab.genemapper.utils.dict.ThesaurusCleaner
THRESHOLD - Static variable in class de.julielab.genemapper.RejectionConstants
timerLog - Static variable in class de.julielab.genemapper.mappingcores.DypsisMappingCore
TITLE - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
TITLEISINPLURAL - Static variable in class de.julielab.genemapper.index.WikipediaIndexFields
toDetailedString() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
TOKEN_CONTEXT - Static variable in class de.julielab.genemapper.uima.GeneMapperAnnotator
tokenize(String) - Method in class de.julielab.genemapper.composites.CompositeMentionTokenizer
tokenizeToLowerCase(String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Splits a given text into tokens, all transformed into lower case.
TokenPrefixPipe - Class in de.julielab.genemapper.filtering
TokenPrefixPipe(String, int) - Constructor for class de.julielab.genemapper.filtering.TokenPrefixPipe
toSingularForm(String) - Static method in class de.julielab.genemapper.filtering.StringHelper: Checks a word, assertedNoun for a plural form.
toSingularForms(String[]) - Static method in class de.julielab.genemapper.filtering.StringHelper: Checks an array of words for plural forms.
toString() - Method in class de.julielab.genemapper.composites.CompositeToken
toString() - Method in class de.julielab.genemapper.composites.ResolvedCompositeGeneName
toString() - Method in class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
toString() - Method in class de.julielab.genemapper.evaluation.tools.DocResult
toString() - Method in class de.julielab.genemapper.utils.dict.RefCounter
toTapInputLine() - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator.TapInputLine
train(Stream<GeneDocument>) - Method in class de.julielab.genemapper.filtering.MLGeneFilter: The genes of al documents must have already have been selected.
TransformerClassifier - Class in de.julielab.genemapper.classification
TransformerClassifier(CacheService, String, Configuration) - Constructor for class de.julielab.genemapper.classification.TransformerClassifier
TransformerDisambiguationDataUtils - Class in de.julielab.genemapper.classification
TransformerDisambiguationDataUtils() - Constructor for class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
TwoPartedRangePatternResolver - Class in de.julielab.genemapper.composites: For composites like AKR1C1-AKR1C4.
TwoPartedRangePatternResolver() - Constructor for class de.julielab.genemapper.composites.TwoPartedRangePatternResolver
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of
type - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.EgSummaryEntity
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Family
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyAcronym
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyCue
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.FamilyStopword
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.GeneId
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Line
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.Synonym
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.SynonymStopword
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Det
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Domain
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.DomainCue
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Family
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyAcronym
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyCue
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.FamilyIndicator
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.NonFamilyIndicator
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.Of
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.FamilyResolution.ProtEnum
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.Be
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGeneCue
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer.NonGenePhrase
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration.OrganismEnumeration
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ClosedParenthesis
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Dash
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ExtendedProtein
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Greek
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.JJ
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.MoleculeType
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Plural
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.ProteinModifier
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Roman
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.SpecifiedMoleculeType
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.Specifier
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.A
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Be
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Det
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Entity
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.EntityChunk
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.FamilyCue
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.Of
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle_Type
typeIndexID - Static variable in class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle
TypeWord - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
TypeWord() - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord: Never called.
TypeWord(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord: Internal - constructor used by generator
TypeWord(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord
TypeWord(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord
TypeWord_Type - Class in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion: Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
TypeWord_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion.TypeWord_Type: initialize variables to correspond with Cas Type and Features

U

UIMAUtils - Class in de.julielab.genemapper.utils: copied from Ph.
UIMAUtils() - Constructor for class de.julielab.genemapper.utils.UIMAUtils
UnderspecifiedNameDisambiguationStep - Class in de.julielab.genemapper.mappingcores.quercus
UnderspecifiedNameDisambiguationStep(NameCentricRetrieval) - Constructor for class de.julielab.genemapper.mappingcores.quercus.UnderspecifiedNameDisambiguationStep
UNIT_TEST_WIKIPEDIA_TITLES_ACCUMULATION_SET - Static variable in class de.julielab.genemapper.disambig.wikipedia.WikipediaIndexReader
UnspecificNameFilter - Class in de.julielab.genemapper.filtering: Also known as the CrazyRegExFilter.
UnspecificNameFilter() - Constructor for class de.julielab.genemapper.filtering.UnspecificNameFilter
UnspecifiedDeterminer - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
UnspecifiedDeterminer() - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer: Never called.
UnspecifiedDeterminer(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer: Internal - constructor used by generator
UnspecifiedDeterminer(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer
UnspecifiedDeterminer(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer
UnspecifiedDeterminer_Type - Class in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction: Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
UnspecifiedDeterminer_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction.UnspecifiedDeterminer_Type: initialize variables to correspond with Cas Type and Features
UnspecifiedPipe - Class in de.julielab.genemapper.filtering.families
UnspecifiedPipe(String) - Constructor for class de.julielab.genemapper.filtering.families.UnspecifiedPipe
UnspecTitle - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022 XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
UnspecTitle() - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle: Never called.
UnspecTitle(int, TOP_Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle: Internal - constructor used by generator
UnspecTitle(JCas) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle
UnspecTitle(JCas, int, int) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle
UnspecTitle_Type - Class in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing: Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
UnspecTitle_Type(JCas, Type) - Constructor for class de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing.UnspecTitle_Type: initialize variables to correspond with Cas Type and Features
USE_GOLD_TAX_FOR_CANDIDATE_RETRIEVAL - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
USE_LUCENE_CANDIDATES_CACHE - Static variable in class de.julielab.genemapper.Configuration
USE_ORIGINAL_QUERY_NAMES - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils

V

VALUE_ADDITIONAL_SEARCH - Static variable in class de.julielab.genemapper.Configuration
VALUE_ALL - Static variable in class de.julielab.genemapper.Configuration
VALUE_BALANCED_SCORES - Static variable in class de.julielab.genemapper.Configuration: Boolean toggle.
VALUE_CNF_RELEVANCE_SIGNAL - Static variable in class de.julielab.genemapper.Configuration
VALUE_CONTEXT_SCORES - Static variable in class de.julielab.genemapper.Configuration
VALUE_DISJUNCTION - Static variable in class de.julielab.genemapper.Configuration
VALUE_DISMAX - Static variable in class de.julielab.genemapper.Configuration
VALUE_GENE_MENTIONS - Static variable in class de.julielab.genemapper.Configuration
VALUE_GENE_RECORDS - Static variable in class de.julielab.genemapper.Configuration
VALUE_GENESETS - Static variable in class de.julielab.genemapper.Configuration
VALUE_LINEAR_COMBINATION - Static variable in class de.julielab.genemapper.Configuration
VALUE_MAJORITY_VOTE - Static variable in class de.julielab.genemapper.Configuration
VALUE_MAX - Static variable in class de.julielab.genemapper.Configuration
VALUE_MAX_BALANCED_SCORE - Static variable in class de.julielab.genemapper.Configuration
VALUE_MAX_BALANCED_SCORE_SUM - Static variable in class de.julielab.genemapper.Configuration
VALUE_MEAN_SCORE - Static variable in class de.julielab.genemapper.Configuration: Gene set rejection homogenization method that calculates the mean score of the gene mentions in the set and compares this against the rejection threshold.
VALUE_NAME_CENTRIC - Static variable in class de.julielab.genemapper.Configuration
VALUE_NO_GS_HOMOGENIZATION - Static variable in class de.julielab.genemapper.Configuration
VALUE_NONE - Static variable in class de.julielab.genemapper.Configuration
VALUE_RANK_FUSION - Static variable in class de.julielab.genemapper.Configuration: Method to combine lexical and semantic ranking.
VALUE_SEMANTIC_CONTEXT - Static variable in class de.julielab.genemapper.Configuration: The disambiguation strategy employed by Li, L., Liu, S., Li, L., Fan, W., Huang, D., & Zhou, H.
VALUE_SUM - Static variable in class de.julielab.genemapper.Configuration
valueOf(String) - Static method in enum de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy: Returns the enum constant of this type with the specified name.
values() - Static method in enum de.julielab.genemapper.mappingcores.DypsisMappingCore.NameLevelUnificationStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
VERSION - Static variable in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils

W

WIKIPEDIA_INDEX - Static variable in class de.julielab.genemapper.Configuration
WikipediaCategoryManager - Class in de.julielab.genemapper
WikipediaCategoryManager(String, boolean) - Constructor for class de.julielab.genemapper.WikipediaCategoryManager
WikipediaClassLookupDevelopment - Class in de.julielab.genemapper.evaluation
WikipediaClassLookupDevelopment() - Constructor for class de.julielab.genemapper.evaluation.WikipediaClassLookupDevelopment
WikipediaEntity - Class in de.julielab.genemapper.disambig.wikipedia
WikipediaEntity(float, String, String, double, List<String>, List<String>, boolean, boolean) - Constructor for class de.julielab.genemapper.disambig.wikipedia.WikipediaEntity
WikipediaEntityClassDecisionBear - Class in de.julielab.genemapper.disambig.wikipedia: (()__(() / \ ( / \ \ \ o o / (_()_)__/ \ / _,==.____ \ ( |--| ) /\_.|__|'-.__/\_ / ( / \ \ \ ( / ) '._____) / (((____.--(((____/mrf
WikipediaEntityClassDecisionBear(WikipediaIndexReader, TermNormalizer) - Constructor for class de.julielab.genemapper.disambig.wikipedia.WikipediaEntityClassDecisionBear
WikipediaIndexFields - Class in de.julielab.genemapper.index
WikipediaIndexFields() - Constructor for class de.julielab.genemapper.index.WikipediaIndexFields
WikipediaIndexReader - Class in de.julielab.genemapper.disambig.wikipedia
WikipediaIndexReader(String, TermNormalizer) - Constructor for class de.julielab.genemapper.disambig.wikipedia.WikipediaIndexReader
WikipediaModule - Class in de.julielab.genemapper.ioc
WikipediaModule() - Constructor for class de.julielab.genemapper.ioc.WikipediaModule
WordClassPipe - Class in de.julielab.genemapper.filtering
WordClassPipe(String, boolean) - Constructor for class de.julielab.genemapper.filtering.WordClassPipe
WordEmbeddingPipe - Class in de.julielab.genemapper.filtering.families
WordEmbeddingPipe() - Constructor for class de.julielab.genemapper.filtering.families.WordEmbeddingPipe
writeData(GeneMapper, File, Stream<GeneDocument>) - Static method in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
writeData(BufferedWriter, GeneMapper, GeneDocument) - Static method in class de.julielab.genemapper.classification.TransformerDisambiguationDataUtils
writeModel(File) - Method in class de.julielab.genemapper.filtering.MLGeneFilter
writeTapInputFile(File, String, Multimap<String, String>, Multimap<String, GeneMention>, Function<SynHit, Double>) - Method in class de.julielab.genemapper.evaluation.tools.TAPEvaluator: Writes TAP input list data created by TAPEvaluator.makeTapInputLists(String, Multimap, Multimap, Function) to tapInputFile.
writeUntokenizedText(JCas, String, StringBuilder) - Method in class de.julielab.genemapper.uima.TaxIdIntegratedTextWriter
wrong - Static variable in class de.julielab.genemapper.mappingcores.DypsisCandidateRanker

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