Package de.julielab.gene.candidateretrieval

Class GeneRecordHit

java.lang.Object

de.julielab.geneexpbase.candidateretrieval.SynHit

de.julielab.gene.candidateretrieval.GeneRecordHit

All Implemented Interfaces:

Serializable, Cloneable, Comparable<de.julielab.geneexpbase.candidateretrieval.SynHit>

public class GeneRecordHit
extends de.julielab.geneexpbase.candidateretrieval.SynHit

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class de.julielab.geneexpbase.candidateretrieval.SynHit

de.julielab.geneexpbase.candidateretrieval.SynHit.CompareType

Field Summary

Fields inherited from class de.julielab.geneexpbase.candidateretrieval.SynHit

TYPE_GEPRO, TYPE_GROUP

Constructor Summary

Constructors

Constructor	Description
GeneRecordHit(String syn, double score, String id, String source)

Method Summary

Modifier and Type	Method	Description
String[]	getBioThesaurusNames()
String	getChromosome()
Stream<String>	getCommonTokens(de.julielab.geneexpbase.genemodel.GeneMention gm)
String[]	getDescriptions()
String	getEcNumber()
String[]	getFullNames()
Stream<String>	getGeneNames()
String[]	getGeneRifs()
String[]	getGoDescriptors()
String[]	getInteractions()
Map<de.julielab.geneexpbase.genemodel.Specifier,Integer>	getMajoritySpecifiers()
String	getMapLocation()
static Comparator<de.julielab.geneexpbase.candidateretrieval.SynHit>	getNormalizedExactMatchThenLuceneScoreComparator(String geneName, boolean sortByMatchingField)	Returns a comparator that sorts SynHits first according to their equality to the gene name and then by score.This helps to overcome the issue that Lucene's float scores sometimes fail to put an exact equal match to the top of the results.
Set<String>	getNormalizedGeneNameTokenSet()
String[]	getOtherDesignations()
String[]	getSummaries()
String	getSymbol()
String	getSymbolFromNomenclature()
String	getSynonymField()
String[]	getSynonyms()
double	getSynonymSimilarityScore()
String[]	getUniprotNames()
String[]	getXrefs()
void	setBioThesaurusNames(String[] bioThesaurusNames)
void	setChromosome(String chromosome)
void	setDescriptions(String[] descriptions)
void	setEcNumber(String ecNumber)
void	setFullNames(String[] fullNames)
void	setGeneRifs(String[] geneRifs)
void	setGoDescriptors(String[] goDescriptors)
void	setInteractions(String[] interactions)
void	setMapLocation(String mapLocation)
void	setNomenclature(String nomenclature)
void	setOtherDesignations(String[] otherDesignations)
void	setSummaries(String[] summaries)
void	setSymbol(String symbol)
void	setSynonymField(String synonymField)
void	setSynonyms(String[] synonyms)
void	setSynonymSimilarityScore(double synonymTokenJaroScore)
void	setUniprotNames(String[] uniprotNames)
void	setXrefs(String[] xrefs)

Methods inherited from class de.julielab.geneexpbase.candidateretrieval.SynHit

clone, compareTo, equals, getComment, getCompareType, getContextualScore, getEntityType, getGeneIdsOfTaxId, getId, getIds, getIdsSet, getLexicalScore, getLuceneScore, getMappedGeneName, getMappedMention, getNormalizedExactMatchThenLuceneScoreComparator, getOverallScore, getPrioritiesOfIds, getPrioritiesOfIds, getRelevanceScore, getSource, getSpeciesMentionScore, getSpeciesMentionScores, getSynonym, getSynonymPriorities, getSynonymPriority, getTaxId, getTaxIdForGeneId, getTaxIds, getTaxIdsSet, getTaxonomySpecificIds, hashCode, hasTaxId, isAmbiguousInGeneral, isAnchor, isDisambiguated, isExactMatch, isFamilyName, isInterSpeciesAmbiguousInGeneral, isIntraSpeciesAmbiguousInGeneral, isRejectionCandidate, removeAllEntriesButWithPriority, removeEntriesWithPriority, restrictToTaxId, setAnchor, setComment, setCompareType, setContextualScore, setExactMatch, setId, setIds, setLexicalScore, setLuceneScore, setMappedGeneName, setMappedMention, setOverallScore, setRelevanceScore, setSource, setSpeciesMentionScore, setSynonym, setSynonymPriorities, setTaxId, setTaxIds, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

GeneRecordHit

public GeneRecordHit(String syn,
                     double score,
                     String id,
                     String source)

Method Detail

getNormalizedExactMatchThenLuceneScoreComparator

public static Comparator<de.julielab.geneexpbase.candidateretrieval.SynHit> getNormalizedExactMatchThenLuceneScoreComparator(String geneName,
                                                                                                                             boolean sortByMatchingField)

Returns a comparator that sorts SynHits first according to their equality to the gene name and then by score.This helps to overcome the issue that Lucene's float scores sometimes fail to put an exact equal match to the top of the results.

Parameters:

geneName - A gene name to compare to.

sortByMatchingField -

Returns:

A comparator that can be used to sort lists of SynHits.

getCommonTokens

public Stream<String> getCommonTokens(de.julielab.geneexpbase.genemodel.GeneMention gm)

getChromosome

public String getChromosome()

setChromosome

public void setChromosome(String chromosome)

getMapLocation

public String getMapLocation()

setMapLocation

public void setMapLocation(String mapLocation)

getSymbol

public String getSymbol()

setSymbol

public void setSymbol(String symbol)

getSymbolFromNomenclature

public String getSymbolFromNomenclature()

setNomenclature

public void setNomenclature(String nomenclature)

getFullNames

public String[] getFullNames()

setFullNames

public void setFullNames(String[] fullNames)

getSynonyms

public String[] getSynonyms()

setSynonyms

public void setSynonyms(String[] synonyms)

getOtherDesignations

public String[] getOtherDesignations()

setOtherDesignations

public void setOtherDesignations(String[] otherDesignations)

getUniprotNames

public String[] getUniprotNames()

setUniprotNames

public void setUniprotNames(String[] uniprotNames)

getBioThesaurusNames

public String[] getBioThesaurusNames()

setBioThesaurusNames

public void setBioThesaurusNames(String[] bioThesaurusNames)

getXrefs

public String[] getXrefs()

setXrefs

public void setXrefs(String[] xrefs)

getSynonymSimilarityScore

public double getSynonymSimilarityScore()

setSynonymSimilarityScore

public void setSynonymSimilarityScore(double synonymTokenJaroScore)

getSynonymField

public String getSynonymField()

Returns:

The field of the synonym that matched the searched gene name best.

setSynonymField

public void setSynonymField(String synonymField)

Parameters:

synonymField - The field of the synonym that matched the searched gene name best.

getGeneRifs

public String[] getGeneRifs()

setGeneRifs

public void setGeneRifs(String[] geneRifs)

getInteractions

public String[] getInteractions()

setInteractions

public void setInteractions(String[] interactions)

getDescriptions

public String[] getDescriptions()

setDescriptions

public void setDescriptions(String[] descriptions)

getSummaries

public String[] getSummaries()

setSummaries

public void setSummaries(String[] summaries)

getGoDescriptors

public String[] getGoDescriptors()

setGoDescriptors

public void setGoDescriptors(String[] goDescriptors)

getNormalizedGeneNameTokenSet

public Set<String> getNormalizedGeneNameTokenSet()

getGeneNames

public Stream<String> getGeneNames()

getMajoritySpecifiers

public Map<de.julielab.geneexpbase.genemodel.Specifier,Integer> getMajoritySpecifiers()

setEcNumber

public void setEcNumber(String ecNumber)

getEcNumber

public String getEcNumber()