Index (Gene Mapping 1.0.1 API)

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

A

accept(File, String) - Method in class de.julielab.jules.ae.genemapping.utils.ExtensionFileFilter
acceptHighestScoringTaxForBestMappingCandidate() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention: Sets the currently highest-scoring taxonomy ID to the current bestcandidate of the mentionMappingResult, which also causes the bestcandidate to set the corresponding gene/protein ID as its ID.
Acronym - Class in de.julielab.jules.ae.genemapping.genemodel
Acronym() - Constructor for class de.julielab.jules.ae.genemapping.genemodel.Acronym
Acronym(String, int, int, AcronymLongform) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.Acronym
AcronymLongform - Class in de.julielab.jules.ae.genemapping.genemodel
AcronymLongform() - Constructor for class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
AcronymLongform(String, int, int) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
addGene(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
addMeshHit(MeshHeading) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
addPair(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor: simple pair add rule: terms must not be the same and must have at least one token in common.
addPair(String, String, double, int) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor: overlap must be at least overlapRatio in both terms and both terms must not be longer than a maximal synonym length
addPairSpecialRules(String, String, double, int) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor: as addPair but pair is only allowed if - difference is not only a number or a single character - overlap is not only a number or a single character
addTaggingModifier(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
addTaxonomyId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
adjustFailureTransitionsSize(int) - Method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized
adjustOutputTableSize(int) - Method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized
adjustTransitionsTableSize(int) - Method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized
agglomerateByAcronyms() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Merges those gene sets that are connected via acronym resolution or, for gene mentions that are not covered by any acronym, merges by name.
agglomerateByNames() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
AhoCorasickLongestMatchCallback - Class in de.julielab.jules.ae.genemapping: To be used with an instance of AhoCorasickOptimized.
AhoCorasickLongestMatchCallback() - Constructor for class de.julielab.jules.ae.genemapping.AhoCorasickLongestMatchCallback
AhoCorasickOptimized - Class in com.lahodiuk.ahocorasick: TAKEN FROM: https://github.com/lagodiuk/aho-corasick-optimized/blob/master/src/main/java/com/lahodiuk/ahocorasick/AhoCorasickOptimized.java Implementation of the Aho-Corasick string matching algorithm, described in the paper "Efficient String Matching: An Aid to Bibliographic Search", written by Alfred V.
AhoCorasickOptimized(String...) - Constructor for class com.lahodiuk.ahocorasick.AhoCorasickOptimized
AhoCorasickOptimized(List<String>) - Constructor for class com.lahodiuk.ahocorasick.AhoCorasickOptimized
AhoCorasickOptimized.MatchCallback - Interface in com.lahodiuk.ahocorasick
AhoCorasickOptimized.Util - Class in com.lahodiuk.ahocorasick
allowGeneMentionsByRegularExpression(GeneMention.GeneTagger, Pattern...) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Adds gene mentions to the selected set of gene mentions based on a tagger (optional) and regular expressions matched on the mention string.
ambiguityDegree - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult
AMINO_ACIDS - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
ANYWHERE - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
appendAutomatonTransitionGraphviz(AhoCorasickOptimized, StringBuilder, int, int) - Static method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized.Util
APPROX - de.julielab.jules.ae.genemapping.MentionMappingResult.MatchType
APPROX_SCORER_TYPE - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
available() - Method in class de.julielab.jules.ae.genemapping.utils.ReaderInputStream

B

BANNER - de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger
bestCandidate - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult: The best candidate at the current time of the mapping process, defaults to MentionMappingResult.REJECTION.
BioThesaurusIproClassMerger - Class in de.julielab.jules.ae.genemapping.utils.dict
buildGeneNameTrie() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Builds an instance of AhoCorasickOptimized from the currently selected genes.

C

CandidateCacheKey - Class in de.julielab.jules.ae.genemapping
CandidateCacheKey(GeneName) - Constructor for class de.julielab.jules.ae.genemapping.CandidateCacheKey: Gets gene candidates based only on the name making no restrictions on species.
CandidateCacheKey(GeneName, String) - Constructor for class de.julielab.jules.ae.genemapping.CandidateCacheKey: Gets gene candidates accordingi to geneName but restricted to species with taxonomy ID taxId.
CandidateFilter - Class in de.julielab.jules.ae.genemapping
CandidateFilter() - Constructor for class de.julielab.jules.ae.genemapping.CandidateFilter
candidateLog - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
CandidateRetrieval - Interface in de.julielab.jules.ae.genemapping
candidateRetrievalTime - Variable in class de.julielab.jules.ae.genemapping.DocumentMappingResult
clear() - Method in class de.julielab.jules.ae.genemapping.AhoCorasickLongestMatchCallback
clone() - Method in class de.julielab.jules.ae.genemapping.SynHit
close() - Method in class de.julielab.jules.ae.genemapping.utils.ReaderInputStream
Column - Class in de.julielab.jules.ae.genemapping.utils.dict
com.lahodiuk.ahocorasick - package com.lahodiuk.ahocorasick
compareStrings(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor: TODO: comment!
compareTo(MentionMappingResult) - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult: The comparison is delegated to the order of the resultEntry SynHits.
compareTo(SynHit) - Method in class de.julielab.jules.ae.genemapping.SynHit: the comparator for two SynHits: order by score as set by setCompareType method TODO: find rule how to order if several SynHits have same score currently, random number is chosen
COMPONENT_ID - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator
COMPOUND - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence: For GNAT species assigner
COMPOUND_PRECEED - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
COMPOUND_SUCCEED - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
confidence - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult
CONTEXT_INDEX - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
CONTEXT_ITEMS_INDEX - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
CONTEXT_WINDOW_SIZE - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator
ContextGenerator - Class in de.julielab.jules.ae.genemapping.index
ContextGenerator(String, String) - Constructor for class de.julielab.jules.ae.genemapping.index.ContextGenerator: constructor which creates semantic context index in the specified directory on the disk file paths are hard-coded due to size issues
ContextIndexFieldNames - Class in de.julielab.jules.ae.genemapping.index
ContextIndexFieldNames() - Constructor for class de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
ContextItemsCacheKey - Class in de.julielab.jules.ae.genemapping
ContextItemsCacheKey(String, String) - Constructor for class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
ContextItemsIndex - Class in de.julielab.jules.ae.genemapping.disambig
ContextItemsIndex(GeneMappingConfiguration) - Constructor for class de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex
ContextUtils - Class in de.julielab.jules.ae.genemapping.utils
ContextUtils() - Constructor for class de.julielab.jules.ae.genemapping.utils.ContextUtils
createGeneDocument(JCas, Map<String, Matcher>, Function<EntityMention, Pair<String, BooleanQuery>>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocumentFactory: Creates a document by setting all required information from the jCas.

D

de.julielab.jules.ae.genemapping - package de.julielab.jules.ae.genemapping
de.julielab.jules.ae.genemapping.disambig - package de.julielab.jules.ae.genemapping.disambig
de.julielab.jules.ae.genemapping.genemodel - package de.julielab.jules.ae.genemapping.genemodel
de.julielab.jules.ae.genemapping.index - package de.julielab.jules.ae.genemapping.index
de.julielab.jules.ae.genemapping.mappingcores - package de.julielab.jules.ae.genemapping.mappingcores
de.julielab.jules.ae.genemapping.scoring - package de.julielab.jules.ae.genemapping.scoring
de.julielab.jules.ae.genemapping.utils - package de.julielab.jules.ae.genemapping.utils
de.julielab.jules.ae.genemapping.utils.dict - package de.julielab.jules.ae.genemapping.utils.dict
de.julielab.jules.ae.genemapping.utils.norm - package de.julielab.jules.ae.genemapping.utils.norm
DEFAULT - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
DEFAULT_SPECIES - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
disambiguateDocument(DocumentDisambiguationData) - Method in interface de.julielab.jules.ae.genemapping.disambig.SemanticDisambiguation
disambiguateDocument(DocumentDisambiguationData) - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDisambiguation
disambiguateMention(MentionDisambiguationData) - Method in interface de.julielab.jules.ae.genemapping.disambig.SemanticDisambiguation
disambiguateMention(MentionDisambiguationData) - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDisambiguation
disambiguationTime - Variable in class de.julielab.jules.ae.genemapping.DocumentMappingResult
docId - Variable in class de.julielab.jules.ae.genemapping.DocumentMappingResult
DocumentDisambiguationData - Interface in de.julielab.jules.ae.genemapping.disambig
DocumentMappingResult - Class in de.julielab.jules.ae.genemapping: This class is thought to be used as an overall result when all gene mentions of a document are mapped in a single process.
DocumentMappingResult() - Constructor for class de.julielab.jules.ae.genemapping.DocumentMappingResult
doDisambiguation(List<SynHit>, Query) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex: does semantic disambiguation, takes best one
doDisambiguation(List<SynHit>, Query, double) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex: does semantic disambiguation, takes best one if its semantic score is above or equals minScore threshold
DOMAIN_FAMILIES - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
DOMAINMOTIF - de.julielab.jules.ae.genemapping.genemodel.GeneMention.SpecificType
doSeparateDisambiguation(ArrayList<SynHit>, String, double) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex: does semantic disambiguation on each SynHit separately, takes best one if its semantic score is above or equals minScore threshold

E

ecNumberRegExp - Static variable in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
ENTITY_MAPPING_TYPES - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator
equals(Object) - Method in class de.julielab.jules.ae.genemapping.CandidateCacheKey
equals(Object) - Method in class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
equals(Object) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
equals(Object) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
equals(Object) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
equals(Object) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
eval(Classifier, InstanceList) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML
EXACT - de.julielab.jules.ae.genemapping.MentionMappingResult.MatchType
EXACT_SCORER_TYPE - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
expendGreek(String) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter: Looks for single letters that could be interpreted as the short form of a greek character such as a -> alpha, b -> beta und returns a string with expanded greek letters.
explainScore(StringWrapper, StringWrapper) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
ExtensionFileFilter - Class in de.julielab.jules.ae.genemapping.utils
ExtensionFileFilter(String) - Constructor for class de.julielab.jules.ae.genemapping.utils.ExtensionFileFilter

F

FAMILYNAME - de.julielab.jules.ae.genemapping.genemodel.GeneMention.SpecificType
FIELD_GENERIF - Static variable in class de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
FIELD_INTERACTION - Static variable in class de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
FIELD_SUMMARY - Static variable in class de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
FILTERED - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames: A boolean-numerical (0 or 1) value to indicate whether the value was recognized as being unspecific or otherwise non-helpful.
filteredCandidates - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult: The candidates that have been filtered by some criterion in the attempt to eliminate bad candidates.
filterOut(String, String) - Method in class de.julielab.jules.ae.genemapping.CandidateFilter: method to filtered out some hits by some rules rule 1: if overlap is only constituted by numbers
FIRST - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence

G

GAZETTEER - de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger
GENE - de.julielab.jules.ae.genemapping.genemodel.GeneMention.SpecificType
GeneCandidateRetrievalException - Exception in de.julielab.jules.ae.genemapping.utils
GeneCandidateRetrievalException() - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneCandidateRetrievalException
GeneCandidateRetrievalException(String) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneCandidateRetrievalException
GeneCandidateRetrievalException(String, Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneCandidateRetrievalException
GeneCandidateRetrievalException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneCandidateRetrievalException
GeneCandidateRetrievalException(Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneCandidateRetrievalException
GeneDocument - Class in de.julielab.jules.ae.genemapping.genemodel
GeneDocument() - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
GeneDocument(GeneDocument) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Copies the template document.
GeneDocument(String) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
GeneDocumentFactory - Class in de.julielab.jules.ae.genemapping.genemodel
GeneIdCandidate - Class in de.julielab.jules.ae.genemapping.genemodel
GeneIdCandidate(String, String, Number, SynHit, GeneMention) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
geneIdCandidates - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult: This field is set towards the end of the mapping/disambiguation process.
GeneMapperRuntimeException - Exception in de.julielab.jules.ae.genemapping.utils
GeneMapperRuntimeException() - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(String) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(String, Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMapperRuntimeException
GeneMapperRuntimeException(Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMapperRuntimeException
GeneMapping - Class in de.julielab.jules.ae.genemapping
GeneMapping(GeneMappingConfiguration) - Constructor for class de.julielab.jules.ae.genemapping.GeneMapping
GeneMapping(File) - Constructor for class de.julielab.jules.ae.genemapping.GeneMapping: Main constructor for the GeneMapper reading especially properties information.
GeneMappingAnnotator - Class in de.julielab.jules.ae.genemapping
GeneMappingAnnotator() - Constructor for class de.julielab.jules.ae.genemapping.GeneMappingAnnotator
GeneMappingConfiguration - Class in de.julielab.jules.ae.genemapping
GeneMappingConfiguration() - Constructor for class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
GeneMappingConfiguration(File) - Constructor for class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
GeneMappingException - Exception in de.julielab.jules.ae.genemapping.utils
GeneMappingException() - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMappingException
GeneMappingException(String) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMappingException
GeneMappingException(String, Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMappingException
GeneMappingException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMappingException
GeneMappingException(Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.utils.GeneMappingException
GeneMention - Class in de.julielab.jules.ae.genemapping.genemodel: A basic "gene mention" that most of all contains the text of the mention.
GeneMention() - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneMention
GeneMention(GeneMention) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneMention: Makes a copy of the given GeneMention but NOT from its MentionMappingResult.
GeneMention(String) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneMention
GeneMention(String, int, int) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneMention
GeneMention(String, TermNormalizer) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneMention
GeneMention.GeneTagger - Enum in de.julielab.jules.ae.genemapping.genemodel
GeneMention.SpecificType - Enum in de.julielab.jules.ae.genemapping.genemodel
geneName - Variable in class de.julielab.jules.ae.genemapping.CandidateCacheKey
GeneName - Class in de.julielab.jules.ae.genemapping.genemodel
GeneName(String, TermNormalizer) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneName
generateGraphvizAutomatonRepresentation(boolean) - Method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized
generateGraphvizAutomatonRepresentation(AhoCorasickOptimized, boolean) - Static method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized.Util
generateVariants(String) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer
GeneSet - Class in de.julielab.jules.ae.genemapping.genemodel
GeneSet() - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneSet
GeneSet(HashSet<GeneMention>, List<SynHit>) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneSet
GeneSets - Class in de.julielab.jules.ae.genemapping.genemodel
GeneSets() - Constructor for class de.julielab.jules.ae.genemapping.genemodel.GeneSets
GeneSpeciesOccurrence - Enum in de.julielab.jules.ae.genemapping.genemodel: Descending order of reliability according to Hakenberg et al.
getAcronym() - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
getAcronymLongformAndOffsets(Acronym) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getAcronymLongforms() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getAcronyms() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getAllGenes() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Returns the raw gene mentions in this document, without any filtering, unification, aggregation or whatsoever and possibly from multiple taggers.
getAllSynHits() - Method in class de.julielab.jules.ae.genemapping.DocumentMappingResult: Returns the SynHits of all mention mapping results.
getAnnotations(JCas, Annotation, Class<T>) - Static method in class de.julielab.jules.ae.genemapping.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.jules.ae.genemapping.genemodel.Acronym
getBegin() - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
getBegin() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getCandidateRetrieval() - Method in interface de.julielab.jules.ae.genemapping.mappingcores.MappingCore
getCandidateRetrieval() - Method in class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore
getCandidateRetrievalTime() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult
getCandidates(GeneMention) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getCandidates(GeneMention) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getCandidates(GeneMention, String) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getCandidates(GeneMention, String) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getCandidates(GeneMention, Collection<String>) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getCandidates(GeneMention, Collection<String>) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getCandidates(String) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getCandidates(String) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getCandidates(String, String) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getCandidates(String, String) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getCandidates(String, Collection<String>) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getCandidates(String, Collection<String>) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getChunks() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getColumn() - Method in class de.julielab.jules.ae.genemapping.utils.dict.Column
getCommonWords(String[], String[]) - Static method in class de.julielab.jules.ae.genemapping.utils.Utils: returns a TreeSet of the common tokens of two strings (white space tokenization is done)
getCompareType() - Method in class de.julielab.jules.ae.genemapping.SynHit
getConfiguration() - Method in class de.julielab.jules.ae.genemapping.GeneMapping
getContainingAnnotation(JCas, Annotation, Class<T>) - Static method in class de.julielab.jules.ae.genemapping.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.
getContentTokens(String[]) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter
getContext(String) - Method in class de.julielab.jules.ae.genemapping.index.ContextGenerator: Builds the semantic context for a given Gene ID
getContextForSynHits(List<SynHit>, Map<String, SynHit>, Query) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
getContextItems(ContextItemsCacheKey) - Method in class de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex
getContextItems(String, String) - Method in class de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex
getContextItemsSearcher() - Method in class de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex
getContextQuery() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getCoveredText(int, int) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getCoveredText(Span) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getCoveredText(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getDefaultSpecies() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getDifferentWords(String[], String[]) - Static method in class de.julielab.jules.ae.genemapping.utils.Utils
getDisambiguationTime() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult
getDocId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getDocument() - Method in interface de.julielab.jules.ae.genemapping.disambig.DocumentDisambiguationData
getDocument() - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDocumentDisambiguationData
getDocumentContext() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getDocumentText() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getDocumentTitle() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getEnd() - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
getEnd() - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
getEnd() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getFeatureVector() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getFeatureVector() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
getFilter() - Method in class de.julielab.jules.ae.genemapping.utils.dict.Column
getGeneDocument() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getGeneId() - Method in class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
getGeneId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
getGeneIdsOfTaxId(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
getGeneMap() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getGeneMention() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
getGeneMentionsAtOffsets(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getGeneName() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getGeneNameDictionary() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getGenes() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Returns those genes that have been selected from the original set of all genes.
getGeneSets() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: On first call, creates a trivial GeneSets object where each gene is in its own set.
getGenesIterable() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getGenesIterator() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getGenesWithText(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getGeneSynonymHits() - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
getGoldTaxonomyId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getHeading() - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
getId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention: The gene ID of this gene mention.
getId() - Method in class de.julielab.jules.ae.genemapping.SynHit
getIds() - Method in class de.julielab.jules.ae.genemapping.SynHit
getIndexEntries(List<String>) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval: Retrieves the first index hit for each ID.
getIndexEntries(List<String>) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getIndexField() - Method in class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
getInstance() - Static method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocumentFactory
getInstance() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
getLastPosTag(Range<Integer>, Set<String>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getLongestMatches() - Method in class de.julielab.jules.ae.genemapping.AhoCorasickLongestMatchCallback
getLongform() - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
getMappedGeneName() - Method in class de.julielab.jules.ae.genemapping.SynHit
getMappedMention() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
getMappedMention() - Method in class de.julielab.jules.ae.genemapping.SynHit: The potentially normalized and/or transformed original entity text mention for which this candidate has been retrieved.
getMappingCore() - Method in class de.julielab.jules.ae.genemapping.GeneMapping
getMatchStyle() - Method in class de.julielab.jules.ae.genemapping.utils.dict.Column
getMaxLenDiffScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.SimpleScorer
getMention() - Method in interface de.julielab.jules.ae.genemapping.disambig.MentionDisambiguationData
getMention() - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeMentionDisambiguationData
getMentionIndexSearcher() - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getMentionMappingResult() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getMentionScore() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
getMentionScore() - Method in class de.julielab.jules.ae.genemapping.SynHit
getMeshCandidates() - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
getMeshHeadings() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getMeshHits() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
getNearestNextSpeciesMention(Range<Integer>, String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getNearestPreviousSpeciesMention(Range<Integer>, String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getNormalizedText() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getNormalizedText() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
getNormalizedTextVariant() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getNormalizedTextVariant() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
getNormalizer() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getNormalizer() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
getNormalizer() - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getNumberOfCommonTokens(String, String) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter
getNumbers(String[]) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter
getOffsets() - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
getOffsets() - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
getOffsets() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getOriginalMappedObject() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention: The original UIMA annotation that is mapped.
getovappingSentence(Span) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getovappingSentence(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getOverallScore() - Method in class de.julielab.jules.ae.genemapping.SynHit
getOverlappingAcronymLongforms(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getOverlappingAcronyms(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Returns acronyms (not full forms!) overlapping with the given range.
getOverlappingChunks(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Returns chunks overlapping with the given range.
getOverlappingChunks(Range<Integer>, String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Returns chunks of the given type overlapping with the given range.
getOverlappingGenes(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Returns genes overlapping with the given range.
getOverlappingGoldGenes(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getOverlappingPosTags(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getOverlapRatio(String, String) - Static method in class de.julielab.jules.ae.genemapping.utils.Utils: gets the token overlap ratio between two strings whitespace split to get tokens ratio returned is minimum of overlap ratios of both strings
getParent() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention: A parent GeneMention is a GeneMention that has been split into sub-mentions, most commonly due to conjunctions or enumerations within a GeneMention.
getPosTags() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getPosTags() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getPrioritiesOfIds(String[]) - Method in class de.julielab.jules.ae.genemapping.SynHit
getPrioritiesOfIds(Stream<String>) - Method in class de.julielab.jules.ae.genemapping.SynHit
getPriorityNames(String, int) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getPriorityNames(List<String>, int) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getReducedNameForExactMatch() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getRepresentationText() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet: Returns the text of any gene mention in this set or null, if the set is empty.
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.JaroWinklerScorer
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.LevenshteinScorer
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.LuceneScorer
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorer: get the score for an unlabeled pair
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.Scorer
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.SimpleScorer: get the score for an unlabeled pair
getScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarityScorer
getScorer() - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getScorerInfo() - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getScorerType() - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.JaroWinklerScorer
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.LevenshteinScorer
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.LuceneScorer
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorer
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.Scorer
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.SimpleScorer
getScorerType() - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarityScorer
getSemanticDisambiguation() - Method in interface de.julielab.jules.ae.genemapping.mappingcores.MappingCore
getSemanticDisambiguation() - Method in class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore
getSemanticIndex() - Method in interface de.julielab.jules.ae.genemapping.disambig.SemanticDisambiguation
getSemanticIndex() - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDisambiguation
getSemanticIndexSearcher() - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
getSemanticScore() - Method in class de.julielab.jules.ae.genemapping.SynHit
getSentences() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getSetId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet: The set ID represent the gene ID that all elements in the set belong to
getSingleSymbols(String[]) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter: Single characters, numbers, greek characters.
getSource() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
getSource() - Method in class de.julielab.jules.ae.genemapping.SynHit
getSpecies() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getSpeciesMentionScore(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
getSpeciesMentionScores() - Method in class de.julielab.jules.ae.genemapping.SynHit
getSpecificType() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getSpecificType() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
getSpecificTypeConfidence() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getSpecificTypeConfidence() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
getSpellingChecker() - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getStemmingStream(String) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils
getSynonym() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
getSynonym() - Method in class de.julielab.jules.ae.genemapping.SynHit
getSynonymHit() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
getSynonymPriorities() - Method in class de.julielab.jules.ae.genemapping.SynHit
getSynonymPriority() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
getSynonymPriority() - Method in class de.julielab.jules.ae.genemapping.SynHit
getSynonymRefSeqScoresForTaxIds(SynHit, Set<String>) - Method in class de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex
getSynonyms(String) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
getSynonyms(String) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
getTag() - Method in class de.julielab.jules.ae.genemapping.genemodel.PosTag
getTagger() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaggingModifiers() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
getTaxId() - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesMention
getTaxId() - Method in class de.julielab.jules.ae.genemapping.SynHit: Returns this single accepted taxonomy ID for this synonym (depends on the document context and may be differ for different textual occurrences of this synonym) or null if not set.
getTaxIds() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
getTaxIds() - Method in class de.julielab.jules.ae.genemapping.SynHit
getTaxonomyCandidates() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxonomyId() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxonomyIds() - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDocumentDisambiguationData
getTaxonomyIds() - Method in class de.julielab.jules.ae.genemapping.disambig.WeepingTreeMentionDisambiguationData
getTaxonomyIds() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxonomyIds() - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
getTaxonomyReliability() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxonomyScore(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxonomyScores() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getTaxonomySpecificIds() - Method in class de.julielab.jules.ae.genemapping.SynHit
getTermNormalizer() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
getTermNormalizer() - Method in interface de.julielab.jules.ae.genemapping.mappingcores.MappingCore
getTermNormalizer() - Method in class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore
getText() - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
getText() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
getText() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
getText() - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesMention
getTextCandidates() - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
getTitleCandidates() - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
getTokenTranspositions(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
getTransposition(StringWrapper, StringWrapper) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
GOLD - de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger
GREEK - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
GREEK_REGEX - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
greekAbbrMap - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter

H

hasContradictingGreek(String, String) - Method in class de.julielab.jules.ae.genemapping.CandidateFilter
hashCode() - Method in class de.julielab.jules.ae.genemapping.CandidateCacheKey
hashCode() - Method in class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
hashCode() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
hashCode() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
hashCode() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
hashCode() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
hasTaxId(String) - Method in class de.julielab.jules.ae.genemapping.SynHit

I

ID_FIELD - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames
ID_FIELD_LEGACY - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames
info() - Method in class de.julielab.jules.ae.genemapping.scoring.JaroWinklerScorer
info() - Method in class de.julielab.jules.ae.genemapping.scoring.LevenshteinScorer
info() - Method in class de.julielab.jules.ae.genemapping.scoring.LuceneScorer
info() - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorer
info() - Method in class de.julielab.jules.ae.genemapping.scoring.Scorer
info() - Method in class de.julielab.jules.ae.genemapping.scoring.SimpleScorer
info() - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarityScorer
initialize(GeneMapping) - Static method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocumentFactory
initialize(UimaContext) - Method in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator: initiaziation of GeneMapper: load the index, get some parameters
initPreModifiers() - Method in class de.julielab.jules.ae.genemapping.CandidateFilter
initUnspecifieds() - Method in class de.julielab.jules.ae.genemapping.CandidateFilter
IOUtils - Class in de.julielab.jules.ae.genemapping.utils
IOUtils() - Constructor for class de.julielab.jules.ae.genemapping.utils.IOUtils
isAmbiguousInGeneral() - Method in class de.julielab.jules.ae.genemapping.SynHit: Returns true if there is more than one gene ID associated with this synonym.
isDisambiguated() - Method in class de.julielab.jules.ae.genemapping.SynHit: Returns true if a single gene or protein ID of this synonym has been determined.
isEntryPrefix(String) - Method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized: Added by Erik Faessler, 2017-11-11: This method does not find dictionary entries in the given string but just checks if the given string is a strict prefix of at least one dictionary entry.
isExactMatch() - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult.RejectionSynHit
isExactMatch() - Method in class de.julielab.jules.ae.genemapping.SynHit
isInterSpeciesAmbiguousInGeneral() - Method in class de.julielab.jules.ae.genemapping.SynHit: Returns true if there are at least two distinct taxonomy IDs associated with this synonym.
isIntraSpeciesAmbiguousInGeneral() - Method in class de.julielab.jules.ae.genemapping.SynHit: Returns true if at least one taxonomy ID associated with this synonym appears multiple times.
isNonDescriptive(String) - Method in class de.julielab.jules.ae.genemapping.CandidateFilter
isNonDescriptive(String) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer
isNumberCompatible(String, String) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter
isPerfectMatch(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.Scorer: checks wether we have a perfect match TODO Seems to have an awful performance footprint.
isPlural() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
isUnspecified(String) - Method in class de.julielab.jules.ae.genemapping.CandidateFilter

J

JAROWINKLER_SCORER - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
JAROWINKLER_SCORER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
JaroWinklerScorer - Class in de.julielab.jules.ae.genemapping.scoring
JaroWinklerScorer() - Constructor for class de.julielab.jules.ae.genemapping.scoring.JaroWinklerScorer
JNET - de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger

L

LAT_NUM - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
LAT_NUM_REGEX - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
LEGACY_INDEX_SUPPORT - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
LEVENSHTEIN_SCORER - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
LEVENSHTEIN_SCORER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
LevenshteinScorer - Class in de.julielab.jules.ae.genemapping.scoring
LevenshteinScorer() - Constructor for class de.julielab.jules.ae.genemapping.scoring.LevenshteinScorer
lociRegExp - Static variable in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
LOGGER_NAME_CANDIDATES - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
LOOKUP_CONTEXT_FIELD - Static variable in class de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
LOOKUP_ID_FIELD - Static variable in class de.julielab.jules.ae.genemapping.index.ContextIndexFieldNames
LOOKUP_SYN_FIELD - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames: The index field name for the normalized gene / protein name.
LUCENE_SCORER - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
LUCENE_SCORER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
LuceneCandidateRetrieval - Class in de.julielab.jules.ae.genemapping
LuceneCandidateRetrieval(GeneMappingConfiguration) - Constructor for class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
LuceneCandidateRetrieval(IndexSearcher, Scorer) - Constructor for class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval: Deprecated.
LuceneScorer - Class in de.julielab.jules.ae.genemapping.scoring
LuceneScorer() - Constructor for class de.julielab.jules.ae.genemapping.scoring.LuceneScorer

M

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.CandidateFilter
main(String[]) - Static method in class de.julielab.jules.ae.genemapping.scoring.JaroWinklerScorer
main(String[]) - Static method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorer
main(String[]) - Static method in class de.julielab.jules.ae.genemapping.scoring.SimpleScorer
main(String[]) - Static method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
main(String[]) - Static method in class de.julielab.jules.ae.genemapping.utils.dict.BioThesaurusIproClassMerger
main(String[]) - Static method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer: run the term normalizer on a file to be normalized (biothesaurus?)
makeBigrams(String) - Static method in class de.julielab.jules.ae.genemapping.utils.Utils
makeConjunctiveQuery(String, String) - Static method in class de.julielab.jules.ae.genemapping.QueryGenerator
makeContext(JCas, int, EntityMention) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils
makeContextQuery(String) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
makeContextQuery(String) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils: builds the Lucene context query a given text
makeContextQuery(JCas) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils: makes the context query.
makeContextQuery(JCas, int, EntityMention) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils: makes the context query.
makeContextTokens(String) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils
makeContextTypes(String) - Static method in class de.julielab.jules.ae.genemapping.utils.ContextUtils
makeDisjunctionMaxQuery(CandidateCacheKey, SpellChecker) - Static method in class de.julielab.jules.ae.genemapping.QueryGenerator
makeDisjunctiveQuery(String) - Static method in class de.julielab.jules.ae.genemapping.QueryGenerator
makeDisjunctiveQuery(String, String) - Static method in class de.julielab.jules.ae.genemapping.QueryGenerator
makeInstances(ArrayList<String[]>) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML
makeInstances(ArrayList<String[]>, Pipe) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML
makeQuery(String[], Query) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
makeQuery(String, BooleanQuery) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
makeSeparateQuery(String, String) - Method in class de.julielab.jules.ae.genemapping.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.
makeUnderScoreBigrams(String) - Static method in class de.julielab.jules.ae.genemapping.utils.Utils
map(GeneDocument) - Method in class de.julielab.jules.ae.genemapping.GeneMapping
map(GeneDocument) - Method in interface de.julielab.jules.ae.genemapping.mappingcores.MappingCore
map(GeneDocument) - Method in class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore
map(GeneMention) - Method in interface de.julielab.jules.ae.genemapping.mappingcores.MappingCore
map(GeneMention) - Method in class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore
map(GeneMention, BooleanQuery, String) - Method in class de.julielab.jules.ae.genemapping.GeneMapping: Actual mapping method.
map(String, BooleanQuery) - Method in class de.julielab.jules.ae.genemapping.GeneMapping: A wrapper to the main mapping function.
map(String, BooleanQuery, String) - Method in class de.julielab.jules.ae.genemapping.GeneMapping: Convenience method mostly used for tests.
mapGeneIdToTaxId(String) - Method in interface de.julielab.jules.ae.genemapping.CandidateRetrieval
mapGeneIdToTaxId(String) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
mappedMention - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult
MAPPER_CONFIG_FILE - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator
MAPPING_CORE - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping: Deprecated.
MAPPING_CORE - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
MappingCore - Interface in de.julielab.jules.ae.genemapping.mappingcores
mapTopN(String, int) - Method in class de.julielab.jules.ae.genemapping.GeneMapping: This mapping returns a list of SynHits.
match(String, AhoCorasickOptimized.MatchCallback) - Method in class com.lahodiuk.ahocorasick.AhoCorasickOptimized
matcherNonDesc - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
matcherUnspecifieds - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
matchType - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult
MAXENT_SCORER - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
MAXENT_SCORER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
MAXENT_SCORER_MODEL - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval: default model for MaxEntScorer
MaxEntScorer - Class in de.julielab.jules.ae.genemapping.scoring
MaxEntScorer(File) - Constructor for class de.julielab.jules.ae.genemapping.scoring.MaxEntScorer
MaxEntScorer(InputStream) - Constructor for class de.julielab.jules.ae.genemapping.scoring.MaxEntScorer
MaxEntScorerFeaturePipe - Class in de.julielab.jules.ae.genemapping.scoring
MaxEntScorerFeaturePipe() - Constructor for class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerFeaturePipe
MaxEntScorerML - Class in de.julielab.jules.ae.genemapping.scoring
MaxEntScorerML() - Constructor for class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML
MaxEntScorerPairExtractor - Class in de.julielab.jules.ae.genemapping.scoring
MaxEntScorerPairExtractor() - Constructor for class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor
MENTION_INDEX - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
MentionDisambiguationData - Interface in de.julielab.jules.ae.genemapping.disambig
MentionMappingResult - Class in de.julielab.jules.ae.genemapping
MentionMappingResult() - Constructor for class de.julielab.jules.ae.genemapping.MentionMappingResult
MentionMappingResult.MatchType - Enum in de.julielab.jules.ae.genemapping
MentionMappingResult.RejectionSynHit - Class in de.julielab.jules.ae.genemapping
mentionResults - Variable in class de.julielab.jules.ae.genemapping.DocumentMappingResult
MESH - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
MeshHeading - Class in de.julielab.jules.ae.genemapping.genemodel
MeshHeading(String) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
MODIFIER - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter

N

NAME_PRIO_DELIMITER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
NOID - Static variable in class de.julielab.jules.ae.genemapping.genemodel.GeneMention: Constant meaning that no ID is given for a GeneMention.
NON_DESC - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
NON_DESCRIPTIVE - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
normalize(String) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer: normalize a single synonym
normalizeFile(File, File) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer: normalize all synonyms in a file (biothesaurus) where the first column is the synonym and the second column is id.

O

onMatch(int, int, String) - Method in interface com.lahodiuk.ahocorasick.AhoCorasickOptimized.MatchCallback
onMatch(int, int, String) - Method in class de.julielab.jules.ae.genemapping.AhoCorasickLongestMatchCallback
ORIGINAL_NAME - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames: The index field name for the original, unnormalized (however, lower-cased) gene / protein name.
originalCandidates - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult: The database candidates found for the name of this gene mention.

P

patternDomainFamilies - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
patternNonDesc - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
patternPreMods - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
patternUnspecifieds - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
PERFECT_SCORE - Static variable in class de.julielab.jules.ae.genemapping.scoring.Scorer
PHRASE - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
pipe(Instance) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerFeaturePipe: the main function of a pipe used to acutally build the features
PosTag - Class in de.julielab.jules.ae.genemapping.genemodel
PosTag(String, Range<Integer>) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.PosTag
predict(Instance, Classifier) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML: return the probability of the true class
PREMODS - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
prepare(String) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
PREVIOUS_SENTENCE - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
PRIORITY - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames: A numerical priority where 1 is the highest priority.
process(JCas) - Method in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator: The process method.
putGoldGene(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument

Q

QueryGenerator - Class in de.julielab.jules.ae.genemapping
QueryGenerator() - Constructor for class de.julielab.jules.ae.genemapping.QueryGenerator

R

RANDOM - de.julielab.jules.ae.genemapping.SynHit.CompareType
read() - Method in class de.julielab.jules.ae.genemapping.utils.ReaderInputStream
read(byte[], int, int) - Method in class de.julielab.jules.ae.genemapping.utils.ReaderInputStream
ReaderInputStream - Class in de.julielab.jules.ae.genemapping.utils: This class convert Reader to InputStream.
ReaderInputStream(Reader) - Constructor for class de.julielab.jules.ae.genemapping.utils.ReaderInputStream: Creates new input stream from the given reader.
ReaderInputStream(Reader, String) - Constructor for class de.julielab.jules.ae.genemapping.utils.ReaderInputStream: Creates new input stream from the given reader and encoding.
readFile2ArrayList(File) - Static method in class de.julielab.jules.ae.genemapping.utils.IOUtils
readFile2String(File) - Static method in class de.julielab.jules.ae.genemapping.utils.IOUtils
REJECTION - Static variable in class de.julielab.jules.ae.genemapping.MentionMappingResult
removeDomainFamilies(String) - Static method in class de.julielab.jules.ae.genemapping.GeneMapping
removeGene(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
removeGenesWithoutCandidates() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
removeModifiers(String) - Static method in class de.julielab.jules.ae.genemapping.GeneMapping
removeNondescriptives(String) - Static method in class de.julielab.jules.ae.genemapping.GeneMapping
removeNonDescriptives(String) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer
removePremodifiers(String) - Static method in class de.julielab.jules.ae.genemapping.GeneMapping
removeSpeciesMention(MultiPatternSearcher) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Removes all prefixes belonging to a species, e.g.
removeUnspecifieds(String) - Static method in class de.julielab.jules.ae.genemapping.GeneMapping
restrictToTaxId(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
resultEntries - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult
retrieveGeneContexts(List<SynHit>) - Method in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex

S

score(StringWrapper, StringWrapper) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
SCORE - de.julielab.jules.ae.genemapping.SynHit.CompareType
Scorer - Class in de.julielab.jules.ae.genemapping.scoring
Scorer() - Constructor for class de.julielab.jules.ae.genemapping.scoring.Scorer
searcher - Variable in class de.julielab.jules.ae.genemapping.disambig.ContextItemsIndex
searcher - Variable in class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
selectAllGenes() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Builds the internal gene offset map with all available genes, overlapping or not.
selectGene(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Adds the given GeneMention to the set of currently selected genes but not to the allGenes set.
selectGeneMentionsByTagger(GeneMention.GeneTagger...) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Builds the internal gene offset map and only keeps gene mentions found by the given taggers.
semanticallyOrderedCandidates - Variable in class de.julielab.jules.ae.genemapping.MentionMappingResult: This list contains the same elements as MentionMappingResult.filteredCandidates but sorted for semantic score, after the respective external algorithm in a disambiguation class has set this field.
SemanticContextIndex - Class in de.julielab.jules.ae.genemapping.disambig
SemanticContextIndex(File) - Constructor for class de.julielab.jules.ae.genemapping.disambig.SemanticContextIndex
SemanticDisambiguation - Interface in de.julielab.jules.ae.genemapping.disambig: Implementing classes of this interface are used at the very end of the gene mapping process.
SemanticIndex - Interface in de.julielab.jules.ae.genemapping.disambig: A common interface for all kinds of indices for gene mention disambiguation.
SEMSCORE - de.julielab.jules.ae.genemapping.SynHit.CompareType
SENTENCE - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
setAcronym(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
setAcronyms(OffsetMap<Acronym>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setAcronyms(Acronym...) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setAcronyms(Collection<Acronym>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setAcronyms(Stream<Acronym>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setCandidateRetrievalTime(long) - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult
setChunks(OffsetMap<String>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setCompareType(SynHit.CompareType) - Method in class de.julielab.jules.ae.genemapping.SynHit
setContextQuery(Query) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setDefaultSpecies(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setDisambiguationTime(long) - Method in class de.julielab.jules.ae.genemapping.MentionMappingResult
setDocId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setDocumentContext(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setDocumentText(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setDocumentTitle(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setFeatureVector(FeatureVector) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setFeatureVector(FeatureVector) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
setGeneDocument(GeneDocument) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setGeneId(String) - Method in class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
setGeneId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
setGeneMention(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
setGenes(GeneMention...) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setGenes(Collection<GeneMention>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setGenes(Stream<GeneMention>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setGeneSynonymHits(List<SynHit>) - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
setGoldTaxonomyId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setHeading(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
setId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setId(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
setIds(List<String>) - Method in class de.julielab.jules.ae.genemapping.SynHit
setIndexField(String) - Method in class de.julielab.jules.ae.genemapping.ContextItemsCacheKey
setInstance(Instance) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
setLongform(AcronymLongform) - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
setMappedGeneName(GeneName) - Method in class de.julielab.jules.ae.genemapping.SynHit
setMappedMention(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
setMappingCore(MappingCore) - Method in class de.julielab.jules.ae.genemapping.GeneMapping
setMentionMappingResult(MentionMappingResult) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setMentionScore(double) - Method in class de.julielab.jules.ae.genemapping.SynHit
setMeshCandidates(Set<String>) - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
setMeshHeadings(Collection<MeshHeading>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setMeshHits(List<MeshHeading>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
setNormalizer(TermNormalizer) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setNormalizer(TermNormalizer) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
setNormalizer(TermNormalizer) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
setOffsets(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
setOffsets(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
setOffsets(Range<Integer>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setOriginalMappedObject(Object) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setOverallScore(double) - Method in class de.julielab.jules.ae.genemapping.SynHit
setParent(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setPlural(boolean) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
setPosTags(Collection<PosTag>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setPosTags(List<PosTag>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setPosTags(Stream<PosTag>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setReducedNameForExactMatch(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setScorerType(int) - Method in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
setSemanticScore(double) - Method in class de.julielab.jules.ae.genemapping.SynHit
setSentences(OffsetSet) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setSetId(List<SynHit>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
setSource(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
setSpecies(SpeciesCandidates) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setSpeciesHints(GeneMention) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: This will try to map genes to species using a multi-stage procedure as detailed in "Inter-species normalization of gene mentions with GNAT" by Hakenberg et al.
setSpeciesMentionScore(String, double) - Method in class de.julielab.jules.ae.genemapping.SynHit
setSpeciesMeshHeadings(Collection<MeshHeading>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setSpecificType(GeneMention.SpecificType) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setSpecificType(GeneMention.SpecificType) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
setSpecificTypeConfidence(double) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setSpecificTypeConfidence(double) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneSet
setSynonym(String) - Method in class de.julielab.jules.ae.genemapping.SynHit
setSynonymHit(SynHit) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
setSynonymPriorities(List<Number>) - Method in class de.julielab.jules.ae.genemapping.SynHit
setSynonymPriority(Number) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
setTag(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.PosTag
setTagger(GeneMention.GeneTagger) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setTaxId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
setTaxId(String) - Method in class de.julielab.jules.ae.genemapping.SynHit: Accepts the passed taxonomy ID as assigned to this synonym.
setTaxIds(List<String>) - Method in class de.julielab.jules.ae.genemapping.SynHit
setTaxonomyCandidates(Multimap<String, GeneSpeciesOccurrence>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setTaxonomyId(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setTaxonomyIds(List<String>) - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
setTaxonomyReliability(GeneSpeciesOccurrence) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setTaxonomyScore(String, double) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setTaxonomyScores(Map<String, Double>) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setTermNormalizer(TermNormalizer) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
setText(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
setText(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
setText(String) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneName
setTextCandidates(OffsetMap<SpeciesMention>) - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
setTitleCandidates(OffsetMap<SpeciesMention>) - Method in class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
showHitIDs(ArrayList<SynHit>) - Static method in class de.julielab.jules.ae.genemapping.utils.SynHitUtils
showHitIDs(HashMap<String, SynHit>) - Static method in class de.julielab.jules.ae.genemapping.utils.SynHitUtils
showHits(ArrayList<SynHit>) - Static method in class de.julielab.jules.ae.genemapping.utils.SynHitUtils
showHits(HashMap<String, SynHit>) - Static method in class de.julielab.jules.ae.genemapping.utils.SynHitUtils: shows all hits in an arraylist of SynHits objects
showPairs(ArrayList<String[]>) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor
SIMPLE_SCORER - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
SIMPLE_SCORER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
SimpleScorer - Class in de.julielab.jules.ae.genemapping.scoring
SimpleScorer() - Constructor for class de.julielab.jules.ae.genemapping.scoring.SimpleScorer
SOURCE_DEFINITION - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
SPECIES_PREFIX - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
SpeciesCandidates - Class in de.julielab.jules.ae.genemapping.genemodel
SpeciesCandidates(int, int, Set<String>, OffsetMap<SpeciesMention>) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates: If the textCandidates include species mentions for the title, this constructor will automatically derive the title species IDs.
SpeciesCandidates(OffsetMap<SpeciesMention>, Set<String>, OffsetMap<SpeciesMention>) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.SpeciesCandidates
SpeciesMention - Class in de.julielab.jules.ae.genemapping.genemodel
SpeciesMention(String, String) - Constructor for class de.julielab.jules.ae.genemapping.genemodel.SpeciesMention
SPELLING_INDEX - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
splitAwayRomanNumbers(List<String>) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer
STEMMED_NORMALIZED_NAME - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames: The index field name for the normalized and then token-wise stemmed gene / protein name.
stemNameTokens(String) - Method in class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer: Splits the input term at white spaces, stems the resulting tokens and joins the stemmed tokens with white spaces again.
STOPWORDS - Static variable in class de.julielab.jules.ae.genemapping.utils.ContextUtils
storePairs(ArrayList<String[]>, File) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerPairExtractor
SUB_GREEK - Static variable in class de.julielab.jules.ae.genemapping.CandidateFilter
SynHit - Class in de.julielab.jules.ae.genemapping
SynHit(String, double, String, String) - Constructor for class de.julielab.jules.ae.genemapping.SynHit
SynHit(String, double, List<String>, String, List<String>) - Constructor for class de.julielab.jules.ae.genemapping.SynHit
SynHit.CompareType - Enum in de.julielab.jules.ae.genemapping
SynHitUtils - Class in de.julielab.jules.ae.genemapping.utils
SynHitUtils() - Constructor for class de.julielab.jules.ae.genemapping.utils.SynHitUtils
SYNONYM_INDEX - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingConfiguration
SynonymIndexFieldNames - Class in de.julielab.jules.ae.genemapping.index
SynonymIndexFieldNames() - Constructor for class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames

T

TAX_ID_FIELD - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames
TAX_IDS - Static variable in class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore: Configuration parameter.
taxId - Variable in class de.julielab.jules.ae.genemapping.CandidateCacheKey
TermNormalizer - Class in de.julielab.jules.ae.genemapping.utils.norm
TermNormalizer() - Constructor for class de.julielab.jules.ae.genemapping.utils.norm.TermNormalizer
TFIDF - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping: Deprecated.
TFIDF - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
TITLE - de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence
TOKEN_CONTEXT - Static variable in class de.julielab.jules.ae.genemapping.GeneMappingAnnotator
TOKEN_JAROWINKLER_SCORER - Static variable in class de.julielab.jules.ae.genemapping.GeneMapping
TOKEN_JAROWINKLER_SCORER - Static variable in class de.julielab.jules.ae.genemapping.LuceneCandidateRetrieval
TokenJaroSimilarity - Class in de.julielab.jules.ae.genemapping.scoring: Jaro distance metric.
TokenJaroSimilarity() - Constructor for class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
TokenJaroSimilarityScorer - Class in de.julielab.jules.ae.genemapping.scoring
TokenJaroSimilarityScorer() - Constructor for class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarityScorer
tokenScore(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
toString() - Method in class de.julielab.jules.ae.genemapping.CandidateCacheKey
toString() - Method in class de.julielab.jules.ae.genemapping.genemodel.Acronym
toString() - Method in class de.julielab.jules.ae.genemapping.genemodel.AcronymLongform
toString() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneIdCandidate
toString() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneMention
toString() - Method in class de.julielab.jules.ae.genemapping.genemodel.MeshHeading
toString() - Method in class de.julielab.jules.ae.genemapping.genemodel.PosTag
toString() - Method in class de.julielab.jules.ae.genemapping.scoring.Scorer
toString() - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity
toString() - Method in class de.julielab.jules.ae.genemapping.SynHit
train(InstanceList) - Method in class de.julielab.jules.ae.genemapping.scoring.MaxEntScorerML: train the classifier
transpositions(String, String) - Method in class de.julielab.jules.ae.genemapping.scoring.TokenJaroSimilarity

U

UIMAUtils - Class in de.julielab.jules.ae.genemapping.utils: copied from Ph.
UIMAUtils() - Constructor for class de.julielab.jules.ae.genemapping.utils.UIMAUtils
unifyAcronymsLongerFirst() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
unifyAllGenesLongerFirst() - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Unifies all genes with the longer-span-first strategy.
unifyAllGenesLongerFirst(GeneMention.GeneTagger...) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
unifyGeneMentionsAtEqualOffsets(GeneMention.GeneTagger...) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument: Creates the internal gene map without allowing exact duplicate ranges where begin and end are equal but still allows overlapping.
unifyGenesPrioritizeTagger(NavigableSet<GeneMention>, GeneMention.GeneTagger) - Method in class de.julielab.jules.ae.genemapping.genemodel.GeneDocument
UNSPECIFIEDS - Variable in class de.julielab.jules.ae.genemapping.CandidateFilter
Util() - Constructor for class com.lahodiuk.ahocorasick.AhoCorasickOptimized.Util
Utils - Class in de.julielab.jules.ae.genemapping.utils
Utils() - Constructor for class de.julielab.jules.ae.genemapping.utils.Utils

V

valueOf(String) - Static method in enum de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.julielab.jules.ae.genemapping.genemodel.GeneMention.SpecificType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.julielab.jules.ae.genemapping.MentionMappingResult.MatchType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.julielab.jules.ae.genemapping.SynHit.CompareType: Returns the enum constant of this type with the specified name.
values() - Static method in enum de.julielab.jules.ae.genemapping.genemodel.GeneMention.GeneTagger: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.julielab.jules.ae.genemapping.genemodel.GeneMention.SpecificType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.julielab.jules.ae.genemapping.genemodel.GeneSpeciesOccurrence: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.julielab.jules.ae.genemapping.MentionMappingResult.MatchType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.julielab.jules.ae.genemapping.SynHit.CompareType: Returns an array containing the constants of this enum type, in the order they are declared.
VARIANT_NAME - Static variable in class de.julielab.jules.ae.genemapping.index.SynonymIndexFieldNames: The index field name for the normalized variant of the original gene / protein name.

W

WeepingTreeDisambiguation - Class in de.julielab.jules.ae.genemapping.disambig: Some simple disambiguation steps for ambiguous synonyms, nothing majorly fancy.
WeepingTreeDisambiguation(GeneMappingConfiguration) - Constructor for class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDisambiguation
WeepingTreeDocumentDisambiguationData - Class in de.julielab.jules.ae.genemapping.disambig
WeepingTreeDocumentDisambiguationData(GeneDocument, Set<String>) - Constructor for class de.julielab.jules.ae.genemapping.disambig.WeepingTreeDocumentDisambiguationData
WeepingTreeMappingCore - Class in de.julielab.jules.ae.genemapping.mappingcores: A rather relaxed mapping that doesn't try hard to disambiguate and does not filter out gene families or domains.
WeepingTreeMappingCore(GeneMappingConfiguration) - Constructor for class de.julielab.jules.ae.genemapping.mappingcores.WeepingTreeMappingCore
WeepingTreeMentionDisambiguationData - Class in de.julielab.jules.ae.genemapping.disambig
WeepingTreeMentionDisambiguationData(GeneMention, Set<String>) - Constructor for class de.julielab.jules.ae.genemapping.disambig.WeepingTreeMentionDisambiguationData

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