Uses of Class de.julielab.jules.ae.genemapping.genemodel.GeneMention (Gene Mapping 1.0.1 API)

Packages that use GeneMention
Package	Description
de.julielab.jules.ae.genemapping
de.julielab.jules.ae.genemapping.disambig
de.julielab.jules.ae.genemapping.genemodel
de.julielab.jules.ae.genemapping.mappingcores

Uses of GeneMention in de.julielab.jules.ae.genemapping

Fields in de.julielab.jules.ae.genemapping declared as GeneMention
Modifier and Type	Field	Description
`GeneMention`	MentionMappingResult.`mappedMention`

Methods in de.julielab.jules.ae.genemapping with parameters of type GeneMention
Modifier and Type	Method	Description
`java.util.List<SynHit>`	CandidateRetrieval.`getCandidates(GeneMention geneMention)`
`java.util.List<SynHit>`	CandidateRetrieval.`getCandidates(GeneMention geneMention, java.lang.String organism)`
`java.util.List<SynHit>`	CandidateRetrieval.`getCandidates(GeneMention geneMention, java.util.Collection<java.lang.String> organisms)`
`java.util.List<SynHit>`	LuceneCandidateRetrieval.`getCandidates(GeneMention geneMention)`
`java.util.List<SynHit>`	LuceneCandidateRetrieval.`getCandidates(GeneMention geneMention, java.lang.String organism)`
`java.util.List<SynHit>`	LuceneCandidateRetrieval.`getCandidates(GeneMention geneMention, java.util.Collection<java.lang.String> organisms)`
`MentionMappingResult`	GeneMapping.`map(GeneMention searchTerm, org.apache.lucene.search.BooleanQuery contextQuery, java.lang.String documentContext)`	Actual mapping method.

Uses of GeneMention in de.julielab.jules.ae.genemapping.disambig

Methods in de.julielab.jules.ae.genemapping.disambig that return GeneMention
Modifier and Type	Method	Description
`GeneMention`	MentionDisambiguationData.`getMention()`
`GeneMention`	WeepingTreeMentionDisambiguationData.`getMention()`

Constructors in de.julielab.jules.ae.genemapping.disambig with parameters of type GeneMention
Constructor	Description
`WeepingTreeMentionDisambiguationData(GeneMention gm, java.util.Set<java.lang.String> taxonomyIds)`

Uses of GeneMention in de.julielab.jules.ae.genemapping.genemodel

Methods in de.julielab.jules.ae.genemapping.genemodel that return GeneMention
Modifier and Type	Method	Description
`GeneMention`	GeneIdCandidate.`getGeneMention()`
`GeneMention`	GeneMention.`getParent()`	A parent GeneMention is a GeneMention that has been split into sub-mentions, most commonly due to conjunctions or enumerations within a GeneMention.

Methods in de.julielab.jules.ae.genemapping.genemodel that return types with arguments of type GeneMention
Modifier and Type	Method	Description
`java.util.List<GeneMention>`	GeneDocument.`getAllGenes()`	Returns the raw gene mentions in this document, without any filtering, unification, aggregation or whatsoever and possibly from multiple taggers.
`de.julielab.java.utilities.spanutils.OffsetMap<java.util.List<GeneMention>>`	GeneDocument.`getGeneMap()`
`java.util.stream.Stream<GeneMention>`	GeneDocument.`getGeneMentionsAtOffsets(org.apache.commons.lang3.Range<java.lang.Integer> offsets)`
`java.util.stream.Stream<GeneMention>`	GeneDocument.`getGenes()`	Returns those genes that have been selected from the original set of all genes.
`java.lang.Iterable<GeneMention>`	GeneDocument.`getGenesIterable()`
`java.util.Iterator<GeneMention>`	GeneDocument.`getGenesIterator()`
`java.util.stream.Stream<GeneMention>`	GeneDocument.`getGenesWithText(java.lang.String text)`
`java.util.stream.Stream<GeneMention>`	GeneDocument.`getOverlappingGenes(org.apache.commons.lang3.Range<java.lang.Integer> range)`	Returns genes overlapping with the given range.
`java.util.stream.Stream<GeneMention>`	GeneDocument.`getOverlappingGoldGenes(org.apache.commons.lang3.Range<java.lang.Integer> range)`

Methods in de.julielab.jules.ae.genemapping.genemodel with parameters of type GeneMention
Modifier and Type	Method	Description
`void`	GeneDocument.`addGene(GeneMention gene)`
`void`	GeneDocument.`putGoldGene(GeneMention gm)`
`void`	GeneDocument.`removeGene(GeneMention gm)`
`void`	GeneDocument.`selectGene(GeneMention gm)`	Adds the given GeneMention to the set of currently selected genes but not to the allGenes set.
`void`	GeneIdCandidate.`setGeneMention(GeneMention geneMention)`
`void`	GeneDocument.`setGenes(GeneMention... genes)`
`void`	GeneMention.`setParent(GeneMention parent)`
`com.google.common.collect.Multimap<java.lang.String,GeneSpeciesOccurrence>`	GeneDocument.`setSpeciesHints(GeneMention gm)`	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.

Method parameters in de.julielab.jules.ae.genemapping.genemodel with type arguments of type GeneMention
Modifier and Type	Method	Description
`void`	GeneDocument.`setGenes(java.util.Collection<GeneMention> genes)`
`void`	GeneDocument.`setGenes(java.util.stream.Stream<GeneMention> genes)`
`void`	GeneDocument.`unifyGenesPrioritizeTagger(java.util.NavigableSet<GeneMention> sortedGenes, GeneMention.GeneTagger tagger)`

Constructors in de.julielab.jules.ae.genemapping.genemodel with parameters of type GeneMention
Constructor	Description
`GeneIdCandidate(java.lang.String geneId, java.lang.String taxId, java.lang.Number synonymPriority, SynHit synonymHit, GeneMention geneMention)`
`GeneMention(GeneMention gm)`	Makes a copy of the given GeneMention but NOT from its MentionMappingResult.

Constructor parameters in de.julielab.jules.ae.genemapping.genemodel with type arguments of type GeneMention
Constructor	Description
`GeneSet(java.util.HashSet<GeneMention> genes, java.util.List<SynHit> setId)`

Uses of GeneMention in de.julielab.jules.ae.genemapping.mappingcores

Methods in de.julielab.jules.ae.genemapping.mappingcores with parameters of type GeneMention
Modifier and Type	Method	Description
`MentionMappingResult`	MappingCore.`map(GeneMention geneMention)`
`MentionMappingResult`	WeepingTreeMappingCore.`map(GeneMention geneMention)`