Uses of Class
de.julielab.jules.ae.genemapping.SynHit

Packages that use SynHit

Package	Description
de.julielab.jules.ae.genemapping
de.julielab.jules.ae.genemapping.disambig
de.julielab.jules.ae.genemapping.genemodel
de.julielab.jules.ae.genemapping.utils

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

Subclasses of SynHit in de.julielab.jules.ae.genemapping

Modifier and Type	Class	Description
static class	MentionMappingResult.RejectionSynHit

Fields in de.julielab.jules.ae.genemapping with type parameters of type SynHit

Modifier and Type	Field	Description
java.util.List<SynHit>	MentionMappingResult.bestCandidate	The best candidate at the current time of the mapping process, defaults to MentionMappingResult.REJECTION.
java.util.List<SynHit>	MentionMappingResult.filteredCandidates	The candidates that have been filtered by some criterion in the attempt to eliminate bad candidates.
java.util.List<SynHit>	MentionMappingResult.originalCandidates	The database candidates found for the name of this gene mention.
static java.util.List<SynHit>	MentionMappingResult.REJECTION
java.util.List<SynHit>	MentionMappingResult.resultEntries
java.util.List<SynHit>	MentionMappingResult.semanticallyOrderedCandidates	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.

Methods in de.julielab.jules.ae.genemapping that return SynHit

Modifier and Type	Method	Description
SynHit	SynHit.clone()

Methods in de.julielab.jules.ae.genemapping that return types with arguments of type SynHit

Modifier and Type	Method	Description
java.util.List<SynHit>	DocumentMappingResult.getAllSynHits()	Returns the SynHits of all mention mapping results.
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>	CandidateRetrieval.getCandidates(java.lang.String originalSearchTerm)
java.util.List<SynHit>	CandidateRetrieval.getCandidates(java.lang.String geneMentionText, java.lang.String organism)
java.util.List<SynHit>	CandidateRetrieval.getCandidates(java.lang.String geneMentionText, java.util.Collection<java.lang.String> organism)
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)
java.util.List<SynHit>	LuceneCandidateRetrieval.getCandidates(java.lang.String originalSearchTerm)
java.util.List<SynHit>	LuceneCandidateRetrieval.getCandidates(java.lang.String geneMentionText, java.lang.String organism)
java.util.List<SynHit>	LuceneCandidateRetrieval.getCandidates(java.lang.String geneMentionText, java.util.Collection<java.lang.String> organism)
java.util.List<SynHit>	CandidateRetrieval.getIndexEntries(java.util.List<java.lang.String> ids)	Retrieves the first index hit for each ID.
java.util.List<SynHit>	LuceneCandidateRetrieval.getIndexEntries(java.util.List<java.lang.String> ids)
java.util.List<SynHit>	GeneMapping.map(java.lang.String searchTerm, org.apache.lucene.search.BooleanQuery contextQuery)	A wrapper to the main mapping function.
java.util.ArrayList<SynHit>	GeneMapping.mapTopN(java.lang.String searchTerm, int topN)	This mapping returns a list of SynHits.

Methods in de.julielab.jules.ae.genemapping with parameters of type SynHit

Modifier and Type	Method	Description
int	SynHit.compareTo(SynHit o)	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

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

Methods in de.julielab.jules.ae.genemapping.disambig that return SynHit

Modifier and Type	Method	Description
SynHit	SemanticContextIndex.doDisambiguation(java.util.List<SynHit> filteredCandidates, org.apache.lucene.search.Query query)	does semantic disambiguation, takes best one
SynHit	SemanticContextIndex.doDisambiguation(java.util.List<SynHit> filteredCandidates, org.apache.lucene.search.Query query, double minContextScore)	does semantic disambiguation, takes best one if its semantic score is above or equals minScore threshold
SynHit	SemanticContextIndex.doSeparateDisambiguation(java.util.ArrayList<SynHit> disambigList, java.lang.String context, double minContextScore)	does semantic disambiguation on each SynHit separately, takes best one if its semantic score is above or equals minScore threshold

Methods in de.julielab.jules.ae.genemapping.disambig with parameters of type SynHit

Modifier and Type	Method	Description
java.util.Map<java.lang.String,java.lang.Float>	ContextItemsIndex.getSynonymRefSeqScoresForTaxIds(SynHit synHit, java.util.Set<java.lang.String> taxonomyIds)

Method parameters in de.julielab.jules.ae.genemapping.disambig with type arguments of type SynHit

Modifier and Type	Method	Description
SynHit	SemanticContextIndex.doDisambiguation(java.util.List<SynHit> filteredCandidates, org.apache.lucene.search.Query query)	does semantic disambiguation, takes best one
SynHit	SemanticContextIndex.doDisambiguation(java.util.List<SynHit> filteredCandidates, org.apache.lucene.search.Query query, double minContextScore)	does semantic disambiguation, takes best one if its semantic score is above or equals minScore threshold
SynHit	SemanticContextIndex.doSeparateDisambiguation(java.util.ArrayList<SynHit> disambigList, java.lang.String context, double minContextScore)	does semantic disambiguation on each SynHit separately, takes best one if its semantic score is above or equals minScore threshold
org.apache.lucene.search.TopDocs	SemanticContextIndex.getContextForSynHits(java.util.List<SynHit> hits, java.util.Map<java.lang.String,SynHit> id2Hit, org.apache.lucene.search.Query query)
org.apache.lucene.search.TopDocs	SemanticContextIndex.getContextForSynHits(java.util.List<SynHit> hits, java.util.Map<java.lang.String,SynHit> id2Hit, org.apache.lucene.search.Query query)
java.util.Map<java.lang.String,java.lang.String>	SemanticContextIndex.retrieveGeneContexts(java.util.List<SynHit> candidates)

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

Methods in de.julielab.jules.ae.genemapping.genemodel that return SynHit

Modifier and Type	Method	Description
SynHit	GeneIdCandidate.getSynonymHit()

Methods in de.julielab.jules.ae.genemapping.genemodel that return types with arguments of type SynHit

Modifier and Type	Method	Description
java.util.List<SynHit>	MeshHeading.getGeneSynonymHits()
java.util.List<SynHit>	GeneSet.getSetId()	The set ID represent the gene ID that all elements in the set belong to

Methods in de.julielab.jules.ae.genemapping.genemodel with parameters of type SynHit

Modifier and Type	Method	Description
void	GeneIdCandidate.setSynonymHit(SynHit synonymHit)

Method parameters in de.julielab.jules.ae.genemapping.genemodel with type arguments of type SynHit

Modifier and Type	Method	Description
void	MeshHeading.setGeneSynonymHits(java.util.List<SynHit> geneSynonymHits)
void	GeneSet.setSetId(java.util.List<SynHit> setId)

Constructors in de.julielab.jules.ae.genemapping.genemodel with parameters of type SynHit

Constructor	Description
GeneIdCandidate(java.lang.String geneId, java.lang.String taxId, java.lang.Number synonymPriority, SynHit synonymHit, GeneMention geneMention)

Constructor parameters in de.julielab.jules.ae.genemapping.genemodel with type arguments of type SynHit

Constructor	Description
GeneSet(java.util.HashSet<GeneMention> genes, java.util.List<SynHit> setId)

Uses of SynHit in de.julielab.jules.ae.genemapping.utils

Method parameters in de.julielab.jules.ae.genemapping.utils with type arguments of type SynHit

Modifier and Type	Method	Description
static java.lang.String	SynHitUtils.showHitIDs(java.util.ArrayList<SynHit> filteredHits)
static java.lang.String	SynHitUtils.showHitIDs(java.util.HashMap<java.lang.String,SynHit> filteredHits)
static void	SynHitUtils.showHits(java.util.ArrayList<SynHit> hitList)
static void	SynHitUtils.showHits(java.util.HashMap<java.lang.String,SynHit> hitList)	shows all hits in an arraylist of SynHits objects