java.lang.Object
- org.intermine.model.bio.GeneShadow

All Implemented Interfaces:

Annotatable, BioEntity, Gene, SequenceFeature, org.intermine.model.FastPathObject, org.intermine.model.InterMineFastPathObject, org.intermine.model.InterMineObject, org.intermine.model.ShadowClass
```
public class GeneShadow
extends java.lang.Object
implements Gene, org.intermine.model.ShadowClass
```

Field Summary

Fields
Modifier and Type	Field	Description
`protected java.lang.String`	`briefDescription`
`protected java.util.Set<CDS>`	`CDSs`
`protected java.util.Set<SequenceFeature>`	`childFeatures`
`protected org.intermine.model.InterMineObject`	`chromosome`
`protected org.intermine.model.InterMineObject`	`chromosomeLocation`
`protected java.util.Set<CrossReference>`	`crossReferences`
`protected java.util.Set<DataSet>`	`dataSets`
`protected java.lang.String`	`description`
`protected org.intermine.model.InterMineObject`	`downstreamIntergenicRegion`
`protected java.util.Set<Exon>`	`exons`
`protected java.util.Set<GeneFlankingRegion>`	`flankingRegions`
`protected java.util.Set<Homologue>`	`homologues`
`protected java.lang.Integer`	`id`
`protected java.util.Set<Intron>`	`introns`
`protected java.lang.Integer`	`length`
`protected java.util.Set<Location>`	`locatedFeatures`
`protected java.util.Set<Location>`	`locations`
`protected java.lang.String`	`name`
`protected java.util.Set<OntologyAnnotation>`	`ontologyAnnotations`
`protected org.intermine.model.InterMineObject`	`organism`
`protected java.util.Set<SequenceFeature>`	`overlappingFeatures`
`protected java.lang.String`	`primaryIdentifier`
`protected java.util.Set<Protein>`	`proteins`
`protected java.util.Set<Publication>`	`publications`
`protected java.lang.Double`	`score`
`protected java.lang.String`	`scoreType`
`protected java.lang.String`	`secondaryIdentifier`
`protected org.intermine.model.InterMineObject`	`sequence`
`protected org.intermine.model.InterMineObject`	`sequenceOntologyTerm`
`static java.lang.Class<Gene>`	`shadowOf`
`protected org.intermine.model.InterMineObject`	`strain`
`protected java.lang.String`	`symbol`
`protected java.util.Set<Synonym>`	`synonyms`
`protected org.intermine.model.InterMineObject`	`upstreamIntergenicRegion`
`protected java.util.Set<UTR>`	`UTRs`

Constructor Summary

Constructors
Constructor Description

GeneShadow()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addcDSs(CDS arg)`
`void`	`addChildFeatures(SequenceFeature arg)`
`void`	`addCollectionElement(java.lang.String fieldName, org.intermine.model.InterMineObject element)`
`void`	`addCrossReferences(CrossReference arg)`
`void`	`addDataSets(DataSet arg)`
`void`	`addExons(Exon arg)`
`void`	`addFlankingRegions(GeneFlankingRegion arg)`
`void`	`addHomologues(Homologue arg)`
`void`	`addIntrons(Intron arg)`
`void`	`addLocatedFeatures(Location arg)`
`void`	`addLocations(Location arg)`
`void`	`addOntologyAnnotations(OntologyAnnotation arg)`
`void`	`addOverlappingFeatures(SequenceFeature arg)`
`void`	`addProteins(Protein arg)`
`void`	`addPublications(Publication arg)`
`void`	`addSynonyms(Synonym arg)`
`void`	`adduTRs(UTR arg)`
`boolean`	`equals(java.lang.Object o)`
`java.lang.String`	`getBriefDescription()`
`java.util.Set<CDS>`	`getcDSs()`
`java.util.Set<SequenceFeature>`	`getChildFeatures()`
`Chromosome`	`getChromosome()`
`Location`	`getChromosomeLocation()`
`java.util.Set<CrossReference>`	`getCrossReferences()`
`java.util.Set<DataSet>`	`getDataSets()`
`java.lang.String`	`getDescription()`
`IntergenicRegion`	`getDownstreamIntergenicRegion()`
`java.lang.Class<?>`	`getElementType(java.lang.String fieldName)`
`java.util.Set<Exon>`	`getExons()`
`java.lang.Object`	`getFieldProxy(java.lang.String fieldName)`
`java.lang.Class<?>`	`getFieldType(java.lang.String fieldName)`
`java.lang.Object`	`getFieldValue(java.lang.String fieldName)`
`java.util.Set<GeneFlankingRegion>`	`getFlankingRegions()`
`java.util.Set<Homologue>`	`getHomologues()`
`java.lang.Integer`	`getId()`
`java.util.Set<Intron>`	`getIntrons()`
`java.lang.Integer`	`getLength()`
`java.util.Set<Location>`	`getLocatedFeatures()`
`java.util.Set<Location>`	`getLocations()`
`java.lang.String`	`getName()`
`org.intermine.model.StringConstructor`	`getoBJECT()`
`java.util.Set<OntologyAnnotation>`	`getOntologyAnnotations()`
`Organism`	`getOrganism()`
`java.util.Set<SequenceFeature>`	`getOverlappingFeatures()`
`java.lang.String`	`getPrimaryIdentifier()`
`java.util.Set<Protein>`	`getProteins()`
`java.util.Set<Publication>`	`getPublications()`
`java.lang.Double`	`getScore()`
`java.lang.String`	`getScoreType()`
`java.lang.String`	`getSecondaryIdentifier()`
`Sequence`	`getSequence()`
`SOTerm`	`getSequenceOntologyTerm()`
`Strain`	`getStrain()`
`java.lang.String`	`getSymbol()`
`java.util.Set<Synonym>`	`getSynonyms()`
`IntergenicRegion`	`getUpstreamIntergenicRegion()`
`java.util.Set<UTR>`	`getuTRs()`
`int`	`hashCode()`
`org.intermine.model.InterMineObject`	`proxGetChromosome()`
`org.intermine.model.InterMineObject`	`proxGetChromosomeLocation()`
`org.intermine.model.InterMineObject`	`proxGetDownstreamIntergenicRegion()`
`org.intermine.model.InterMineObject`	`proxGetOrganism()`
`org.intermine.model.InterMineObject`	`proxGetSequence()`
`org.intermine.model.InterMineObject`	`proxGetSequenceOntologyTerm()`
`org.intermine.model.InterMineObject`	`proxGetStrain()`
`org.intermine.model.InterMineObject`	`proxGetUpstreamIntergenicRegion()`
`void`	`proxyChromosome(org.intermine.objectstore.proxy.ProxyReference chromosome)`
`void`	`proxyChromosomeLocation(org.intermine.objectstore.proxy.ProxyReference chromosomeLocation)`
`void`	`proxyDownstreamIntergenicRegion(org.intermine.objectstore.proxy.ProxyReference downstreamIntergenicRegion)`
`void`	`proxyOrganism(org.intermine.objectstore.proxy.ProxyReference organism)`
`void`	`proxySequence(org.intermine.objectstore.proxy.ProxyReference sequence)`
`void`	`proxySequenceOntologyTerm(org.intermine.objectstore.proxy.ProxyReference sequenceOntologyTerm)`
`void`	`proxyStrain(org.intermine.objectstore.proxy.ProxyReference strain)`
`void`	`proxyUpstreamIntergenicRegion(org.intermine.objectstore.proxy.ProxyReference upstreamIntergenicRegion)`
`void`	`setBriefDescription(java.lang.String briefDescription)`
`void`	`setcDSs(java.util.Set<CDS> CDSs)`
`void`	`setChildFeatures(java.util.Set<SequenceFeature> childFeatures)`
`void`	`setChromosome(Chromosome chromosome)`
`void`	`setChromosomeLocation(Location chromosomeLocation)`
`void`	`setCrossReferences(java.util.Set<CrossReference> crossReferences)`
`void`	`setDataSets(java.util.Set<DataSet> dataSets)`
`void`	`setDescription(java.lang.String description)`
`void`	`setDownstreamIntergenicRegion(IntergenicRegion downstreamIntergenicRegion)`
`void`	`setExons(java.util.Set<Exon> exons)`
`void`	`setFieldValue(java.lang.String fieldName, java.lang.Object value)`
`void`	`setFlankingRegions(java.util.Set<GeneFlankingRegion> flankingRegions)`
`void`	`setHomologues(java.util.Set<Homologue> homologues)`
`void`	`setId(java.lang.Integer id)`
`void`	`setIntrons(java.util.Set<Intron> introns)`
`void`	`setLength(java.lang.Integer length)`
`void`	`setLocatedFeatures(java.util.Set<Location> locatedFeatures)`
`void`	`setLocations(java.util.Set<Location> locations)`
`void`	`setName(java.lang.String name)`
`void`	`setoBJECT(java.lang.String[] notXml, org.intermine.objectstore.ObjectStore os)`
`void`	`setoBJECT(java.lang.String notXml, org.intermine.objectstore.ObjectStore os)`
`void`	`setOntologyAnnotations(java.util.Set<OntologyAnnotation> ontologyAnnotations)`
`void`	`setOrganism(Organism organism)`
`void`	`setOverlappingFeatures(java.util.Set<SequenceFeature> overlappingFeatures)`
`void`	`setPrimaryIdentifier(java.lang.String primaryIdentifier)`
`void`	`setProteins(java.util.Set<Protein> proteins)`
`void`	`setPublications(java.util.Set<Publication> publications)`
`void`	`setScore(java.lang.Double score)`
`void`	`setScoreType(java.lang.String scoreType)`
`void`	`setSecondaryIdentifier(java.lang.String secondaryIdentifier)`
`void`	`setSequence(Sequence sequence)`
`void`	`setSequenceOntologyTerm(SOTerm sequenceOntologyTerm)`
`void`	`setStrain(Strain strain)`
`void`	`setSymbol(java.lang.String symbol)`
`void`	`setSynonyms(java.util.Set<Synonym> synonyms)`
`void`	`setUpstreamIntergenicRegion(IntergenicRegion upstreamIntergenicRegion)`
`void`	`setuTRs(java.util.Set<UTR> UTRs)`
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

shadowOf

public static final java.lang.Class<Gene> shadowOf

briefDescription

protected java.lang.String briefDescription

description
```
protected java.lang.String description
```

upstreamIntergenicRegion

protected org.intermine.model.InterMineObject upstreamIntergenicRegion

downstreamIntergenicRegion

protected org.intermine.model.InterMineObject downstreamIntergenicRegion

flankingRegions

protected java.util.Set<GeneFlankingRegion> flankingRegions

introns

protected java.util.Set<Intron> introns

proteins

protected java.util.Set<Protein> proteins

CDSs
```
protected java.util.Set<CDS> CDSs
```

homologues

protected java.util.Set<Homologue> homologues

exons
```
protected java.util.Set<Exon> exons
```

UTRs
```
protected java.util.Set<UTR> UTRs
```

score
```
protected java.lang.Double score
```

scoreType
```
protected java.lang.String scoreType
```

length
```
protected java.lang.Integer length
```

strain

protected org.intermine.model.InterMineObject strain

sequenceOntologyTerm

protected org.intermine.model.InterMineObject sequenceOntologyTerm

chromosomeLocation

protected org.intermine.model.InterMineObject chromosomeLocation

sequence

protected org.intermine.model.InterMineObject sequence

chromosome

protected org.intermine.model.InterMineObject chromosome

overlappingFeatures

protected java.util.Set<SequenceFeature> overlappingFeatures

childFeatures

protected java.util.Set<SequenceFeature> childFeatures

symbol
```
protected java.lang.String symbol
```

name
```
protected java.lang.String name
```

secondaryIdentifier

protected java.lang.String secondaryIdentifier

organism

protected org.intermine.model.InterMineObject organism

locatedFeatures

protected java.util.Set<Location> locatedFeatures

locations

protected java.util.Set<Location> locations

synonyms

protected java.util.Set<Synonym> synonyms

dataSets

protected java.util.Set<DataSet> dataSets

crossReferences

protected java.util.Set<CrossReference> crossReferences

primaryIdentifier

protected java.lang.String primaryIdentifier

ontologyAnnotations

protected java.util.Set<OntologyAnnotation> ontologyAnnotations

publications

protected java.util.Set<Publication> publications

id
```
protected java.lang.Integer id
```

Constructor Detail
- GeneShadow
```
public GeneShadow()
```

Method Detail
- getBriefDescription
```
public java.lang.String getBriefDescription()
```
  Specified by:
  
  getBriefDescription in interface Gene
- setBriefDescription
```
public void setBriefDescription(java.lang.String briefDescription)
```
  Specified by:
  
  setBriefDescription in interface Gene
- getDescription
```
public java.lang.String getDescription()
```
  Specified by:
  
  getDescription in interface Gene
- setDescription
```
public void setDescription(java.lang.String description)
```
  Specified by:
  
  setDescription in interface Gene
- getUpstreamIntergenicRegion
```
public IntergenicRegion getUpstreamIntergenicRegion()
```
  Specified by:
  
  getUpstreamIntergenicRegion in interface Gene
- setUpstreamIntergenicRegion
```
public void setUpstreamIntergenicRegion(IntergenicRegion upstreamIntergenicRegion)
```
  Specified by:
  
  setUpstreamIntergenicRegion in interface Gene
- proxyUpstreamIntergenicRegion
```
public void proxyUpstreamIntergenicRegion(org.intermine.objectstore.proxy.ProxyReference upstreamIntergenicRegion)
```
  Specified by:
  
  proxyUpstreamIntergenicRegion in interface Gene
- proxGetUpstreamIntergenicRegion
```
public org.intermine.model.InterMineObject proxGetUpstreamIntergenicRegion()
```
  Specified by:
  
  proxGetUpstreamIntergenicRegion in interface Gene
- getDownstreamIntergenicRegion
```
public IntergenicRegion getDownstreamIntergenicRegion()
```
  Specified by:
  
  getDownstreamIntergenicRegion in interface Gene
- setDownstreamIntergenicRegion
```
public void setDownstreamIntergenicRegion(IntergenicRegion downstreamIntergenicRegion)
```
  Specified by:
  
  setDownstreamIntergenicRegion in interface Gene
- proxyDownstreamIntergenicRegion
```
public void proxyDownstreamIntergenicRegion(org.intermine.objectstore.proxy.ProxyReference downstreamIntergenicRegion)
```
  Specified by:
  
  proxyDownstreamIntergenicRegion in interface Gene
- proxGetDownstreamIntergenicRegion
```
public org.intermine.model.InterMineObject proxGetDownstreamIntergenicRegion()
```
  Specified by:
  
  proxGetDownstreamIntergenicRegion in interface Gene
- getFlankingRegions
```
public java.util.Set<GeneFlankingRegion> getFlankingRegions()
```
  Specified by:
  
  getFlankingRegions in interface Gene
- setFlankingRegions
```
public void setFlankingRegions(java.util.Set<GeneFlankingRegion> flankingRegions)
```
  Specified by:
  
  setFlankingRegions in interface Gene
- addFlankingRegions
```
public void addFlankingRegions(GeneFlankingRegion arg)
```
  Specified by:
  
  addFlankingRegions in interface Gene
- getIntrons
```
public java.util.Set<Intron> getIntrons()
```
  Specified by:
  
  getIntrons in interface Gene
- setIntrons
```
public void setIntrons(java.util.Set<Intron> introns)
```
  Specified by:
  
  setIntrons in interface Gene
- addIntrons
```
public void addIntrons(Intron arg)
```
  Specified by:
  
  addIntrons in interface Gene
- getProteins
```
public java.util.Set<Protein> getProteins()
```
  Specified by:
  
  getProteins in interface Gene
- setProteins
```
public void setProteins(java.util.Set<Protein> proteins)
```
  Specified by:
  
  setProteins in interface Gene
- addProteins
```
public void addProteins(Protein arg)
```
  Specified by:
  
  addProteins in interface Gene
- getcDSs
```
public java.util.Set<CDS> getcDSs()
```
  Specified by:
  
  getcDSs in interface Gene
- setcDSs
```
public void setcDSs(java.util.Set<CDS> CDSs)
```
  Specified by:
  
  setcDSs in interface Gene
- addcDSs
```
public void addcDSs(CDS arg)
```
  Specified by:
  
  addcDSs in interface Gene
- getHomologues
```
public java.util.Set<Homologue> getHomologues()
```
  Specified by:
  
  getHomologues in interface Gene
- setHomologues
```
public void setHomologues(java.util.Set<Homologue> homologues)
```
  Specified by:
  
  setHomologues in interface Gene
- addHomologues
```
public void addHomologues(Homologue arg)
```
  Specified by:
  
  addHomologues in interface Gene
- getExons
```
public java.util.Set<Exon> getExons()
```
  Specified by:
  
  getExons in interface Gene
- setExons
```
public void setExons(java.util.Set<Exon> exons)
```
  Specified by:
  
  setExons in interface Gene
- addExons
```
public void addExons(Exon arg)
```
  Specified by:
  
  addExons in interface Gene
- getuTRs
```
public java.util.Set<UTR> getuTRs()
```
  Specified by:
  
  getuTRs in interface Gene
- setuTRs
```
public void setuTRs(java.util.Set<UTR> UTRs)
```
  Specified by:
  
  setuTRs in interface Gene
- adduTRs
```
public void adduTRs(UTR arg)
```
  Specified by:
  
  adduTRs in interface Gene
- getScore
```
public java.lang.Double getScore()
```
  Specified by:
  
  getScore in interface SequenceFeature
- setScore
```
public void setScore(java.lang.Double score)
```
  Specified by:
  
  setScore in interface SequenceFeature
- getScoreType
```
public java.lang.String getScoreType()
```
  Specified by:
  
  getScoreType in interface SequenceFeature
- setScoreType
```
public void setScoreType(java.lang.String scoreType)
```
  Specified by:
  
  setScoreType in interface SequenceFeature
- getLength
```
public java.lang.Integer getLength()
```
  Specified by:
  
  getLength in interface SequenceFeature
- setLength
```
public void setLength(java.lang.Integer length)
```
  Specified by:
  
  setLength in interface SequenceFeature
- getStrain
```
public Strain getStrain()
```
  Specified by:
  
  getStrain in interface SequenceFeature
- setStrain
```
public void setStrain(Strain strain)
```
  Specified by:
  
  setStrain in interface SequenceFeature
- proxyStrain
```
public void proxyStrain(org.intermine.objectstore.proxy.ProxyReference strain)
```
  Specified by:
  
  proxyStrain in interface SequenceFeature
- proxGetStrain
```
public org.intermine.model.InterMineObject proxGetStrain()
```
  Specified by:
  
  proxGetStrain in interface SequenceFeature
- getSequenceOntologyTerm
```
public SOTerm getSequenceOntologyTerm()
```
  Specified by:
  
  getSequenceOntologyTerm in interface SequenceFeature
- setSequenceOntologyTerm
```
public void setSequenceOntologyTerm(SOTerm sequenceOntologyTerm)
```
  Specified by:
  
  setSequenceOntologyTerm in interface SequenceFeature
- proxySequenceOntologyTerm
```
public void proxySequenceOntologyTerm(org.intermine.objectstore.proxy.ProxyReference sequenceOntologyTerm)
```
  Specified by:
  
  proxySequenceOntologyTerm in interface SequenceFeature
- proxGetSequenceOntologyTerm
```
public org.intermine.model.InterMineObject proxGetSequenceOntologyTerm()
```
  Specified by:
  
  proxGetSequenceOntologyTerm in interface SequenceFeature
- getChromosomeLocation
```
public Location getChromosomeLocation()
```
  Specified by:
  
  getChromosomeLocation in interface SequenceFeature
- setChromosomeLocation
```
public void setChromosomeLocation(Location chromosomeLocation)
```
  Specified by:
  
  setChromosomeLocation in interface SequenceFeature
- proxyChromosomeLocation
```
public void proxyChromosomeLocation(org.intermine.objectstore.proxy.ProxyReference chromosomeLocation)
```
  Specified by:
  
  proxyChromosomeLocation in interface SequenceFeature
- proxGetChromosomeLocation
```
public org.intermine.model.InterMineObject proxGetChromosomeLocation()
```
  Specified by:
  
  proxGetChromosomeLocation in interface SequenceFeature
- getSequence
```
public Sequence getSequence()
```
  Specified by:
  
  getSequence in interface SequenceFeature
- setSequence
```
public void setSequence(Sequence sequence)
```
  Specified by:
  
  setSequence in interface SequenceFeature
- proxySequence
```
public void proxySequence(org.intermine.objectstore.proxy.ProxyReference sequence)
```
  Specified by:
  
  proxySequence in interface SequenceFeature
- proxGetSequence
```
public org.intermine.model.InterMineObject proxGetSequence()
```
  Specified by:
  
  proxGetSequence in interface SequenceFeature
- getChromosome
```
public Chromosome getChromosome()
```
  Specified by:
  
  getChromosome in interface SequenceFeature
- setChromosome
```
public void setChromosome(Chromosome chromosome)
```
  Specified by:
  
  setChromosome in interface SequenceFeature
- proxyChromosome
```
public void proxyChromosome(org.intermine.objectstore.proxy.ProxyReference chromosome)
```
  Specified by:
  
  proxyChromosome in interface SequenceFeature
- proxGetChromosome
```
public org.intermine.model.InterMineObject proxGetChromosome()
```
  Specified by:
  
  proxGetChromosome in interface SequenceFeature
- getOverlappingFeatures
```
public java.util.Set<SequenceFeature> getOverlappingFeatures()
```
  Specified by:
  
  getOverlappingFeatures in interface SequenceFeature
- setOverlappingFeatures
```
public void setOverlappingFeatures(java.util.Set<SequenceFeature> overlappingFeatures)
```
  Specified by:
  
  setOverlappingFeatures in interface SequenceFeature
- addOverlappingFeatures
```
public void addOverlappingFeatures(SequenceFeature arg)
```
  Specified by:
  
  addOverlappingFeatures in interface SequenceFeature
- getChildFeatures
```
public java.util.Set<SequenceFeature> getChildFeatures()
```
  Specified by:
  
  getChildFeatures in interface SequenceFeature
- setChildFeatures
```
public void setChildFeatures(java.util.Set<SequenceFeature> childFeatures)
```
  Specified by:
  
  setChildFeatures in interface SequenceFeature
- addChildFeatures
```
public void addChildFeatures(SequenceFeature arg)
```
  Specified by:
  
  addChildFeatures in interface SequenceFeature
- getSymbol
```
public java.lang.String getSymbol()
```
  Specified by:
  
  getSymbol in interface BioEntity
- setSymbol
```
public void setSymbol(java.lang.String symbol)
```
  Specified by:
  
  setSymbol in interface BioEntity
- getName
```
public java.lang.String getName()
```
  Specified by:
  
  getName in interface BioEntity
- setName
```
public void setName(java.lang.String name)
```
  Specified by:
  
  setName in interface BioEntity
- getSecondaryIdentifier
```
public java.lang.String getSecondaryIdentifier()
```
  Specified by:
  
  getSecondaryIdentifier in interface BioEntity
- setSecondaryIdentifier
```
public void setSecondaryIdentifier(java.lang.String secondaryIdentifier)
```
  Specified by:
  
  setSecondaryIdentifier in interface BioEntity
- getOrganism
```
public Organism getOrganism()
```
  Specified by:
  
  getOrganism in interface BioEntity
- setOrganism
```
public void setOrganism(Organism organism)
```
  Specified by:
  
  setOrganism in interface BioEntity
- proxyOrganism
```
public void proxyOrganism(org.intermine.objectstore.proxy.ProxyReference organism)
```
  Specified by:
  
  proxyOrganism in interface BioEntity
- proxGetOrganism
```
public org.intermine.model.InterMineObject proxGetOrganism()
```
  Specified by:
  
  proxGetOrganism in interface BioEntity
- getLocatedFeatures
```
public java.util.Set<Location> getLocatedFeatures()
```
  Specified by:
  
  getLocatedFeatures in interface BioEntity
- setLocatedFeatures
```
public void setLocatedFeatures(java.util.Set<Location> locatedFeatures)
```
  Specified by:
  
  setLocatedFeatures in interface BioEntity
- addLocatedFeatures
```
public void addLocatedFeatures(Location arg)
```
  Specified by:
  
  addLocatedFeatures in interface BioEntity
- getLocations
```
public java.util.Set<Location> getLocations()
```
  Specified by:
  
  getLocations in interface BioEntity
- setLocations
```
public void setLocations(java.util.Set<Location> locations)
```
  Specified by:
  
  setLocations in interface BioEntity
- addLocations
```
public void addLocations(Location arg)
```
  Specified by:
  
  addLocations in interface BioEntity
- getSynonyms
```
public java.util.Set<Synonym> getSynonyms()
```
  Specified by:
  
  getSynonyms in interface BioEntity
- setSynonyms
```
public void setSynonyms(java.util.Set<Synonym> synonyms)
```
  Specified by:
  
  setSynonyms in interface BioEntity
- addSynonyms
```
public void addSynonyms(Synonym arg)
```
  Specified by:
  
  addSynonyms in interface BioEntity
- getDataSets
```
public java.util.Set<DataSet> getDataSets()
```
  Specified by:
  
  getDataSets in interface BioEntity
- setDataSets
```
public void setDataSets(java.util.Set<DataSet> dataSets)
```
  Specified by:
  
  setDataSets in interface BioEntity
- addDataSets
```
public void addDataSets(DataSet arg)
```
  Specified by:
  
  addDataSets in interface BioEntity
- getCrossReferences
```
public java.util.Set<CrossReference> getCrossReferences()
```
  Specified by:
  
  getCrossReferences in interface BioEntity
- setCrossReferences
```
public void setCrossReferences(java.util.Set<CrossReference> crossReferences)
```
  Specified by:
  
  setCrossReferences in interface BioEntity
- addCrossReferences
```
public void addCrossReferences(CrossReference arg)
```
  Specified by:
  
  addCrossReferences in interface BioEntity
- getPrimaryIdentifier
```
public java.lang.String getPrimaryIdentifier()
```
  Specified by:
  
  getPrimaryIdentifier in interface Annotatable
- setPrimaryIdentifier
```
public void setPrimaryIdentifier(java.lang.String primaryIdentifier)
```
  Specified by:
  
  setPrimaryIdentifier in interface Annotatable
- getOntologyAnnotations
```
public java.util.Set<OntologyAnnotation> getOntologyAnnotations()
```
  Specified by:
  
  getOntologyAnnotations in interface Annotatable
- setOntologyAnnotations
```
public void setOntologyAnnotations(java.util.Set<OntologyAnnotation> ontologyAnnotations)
```
  Specified by:
  
  setOntologyAnnotations in interface Annotatable
- addOntologyAnnotations
```
public void addOntologyAnnotations(OntologyAnnotation arg)
```
  Specified by:
  
  addOntologyAnnotations in interface Annotatable
- getPublications
```
public java.util.Set<Publication> getPublications()
```
  Specified by:
  
  getPublications in interface Annotatable
- setPublications
```
public void setPublications(java.util.Set<Publication> publications)
```
  Specified by:
  
  setPublications in interface Annotatable
- addPublications
```
public void addPublications(Publication arg)
```
  Specified by:
  
  addPublications in interface Annotatable
- getId
```
public java.lang.Integer getId()
```
  Specified by:
  
  getId in interface org.intermine.model.InterMineFastPathObject
  
  Specified by:
  
  getId in interface org.intermine.model.InterMineObject
- setId
```
public void setId(java.lang.Integer id)
```
  Specified by:
  
  setId in interface org.intermine.model.InterMineFastPathObject
  
  Specified by:
  
  setId in interface org.intermine.model.InterMineObject
- equals
```
public boolean equals(java.lang.Object o)
```
  Overrides:
  
  equals in class java.lang.Object
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class java.lang.Object
- toString
```
public java.lang.String toString()
```
  Overrides:
  
  toString in class java.lang.Object
- getFieldValue
```
public java.lang.Object getFieldValue(java.lang.String fieldName)
                               throws java.lang.IllegalAccessException
```
  Specified by:
  
  getFieldValue in interface org.intermine.model.FastPathObject
  
  Throws:
  
  java.lang.IllegalAccessException
- getFieldProxy
```
public java.lang.Object getFieldProxy(java.lang.String fieldName)
                               throws java.lang.IllegalAccessException
```
  Specified by:
  
  getFieldProxy in interface org.intermine.model.FastPathObject
  
  Throws:
  
  java.lang.IllegalAccessException
- setFieldValue
```
public void setFieldValue(java.lang.String fieldName,
                          java.lang.Object value)
```
  Specified by:
  
  setFieldValue in interface org.intermine.model.FastPathObject
- getFieldType
```
public java.lang.Class<?> getFieldType(java.lang.String fieldName)
```
  Specified by:
  
  getFieldType in interface org.intermine.model.FastPathObject
- getoBJECT
```
public org.intermine.model.StringConstructor getoBJECT()
```
  Specified by:
  
  getoBJECT in interface org.intermine.model.InterMineFastPathObject
  
  Specified by:
  
  getoBJECT in interface org.intermine.model.InterMineObject
- setoBJECT
```
public void setoBJECT(java.lang.String notXml,
                      org.intermine.objectstore.ObjectStore os)
```
  Specified by:
  
  setoBJECT in interface org.intermine.model.InterMineObject
- setoBJECT
```
public void setoBJECT(java.lang.String[] notXml,
                      org.intermine.objectstore.ObjectStore os)
```
  Specified by:
  
  setoBJECT in interface org.intermine.model.InterMineObject
- addCollectionElement
```
public void addCollectionElement(java.lang.String fieldName,
                                 org.intermine.model.InterMineObject element)
```
- getElementType
```
public java.lang.Class<?> getElementType(java.lang.String fieldName)
```
  Specified by:
  
  getElementType in interface org.intermine.model.InterMineFastPathObject
  
  Specified by:
  
  getElementType in interface org.intermine.model.InterMineObject

Class GeneShadow

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

shadowOf

briefDescription

description

upstreamIntergenicRegion

downstreamIntergenicRegion

flankingRegions

introns

proteins

CDSs

homologues

exons

UTRs

score

scoreType

length

strain

sequenceOntologyTerm

chromosomeLocation

sequence

chromosome

overlappingFeatures

childFeatures

symbol

name

secondaryIdentifier

organism

locatedFeatures

locations

synonyms

dataSets

crossReferences

primaryIdentifier

ontologyAnnotations

publications

id

Constructor Detail

GeneShadow

Method Detail

getBriefDescription

setBriefDescription

getDescription

setDescription

getUpstreamIntergenicRegion

setUpstreamIntergenicRegion

proxyUpstreamIntergenicRegion

proxGetUpstreamIntergenicRegion

getDownstreamIntergenicRegion

setDownstreamIntergenicRegion

proxyDownstreamIntergenicRegion

proxGetDownstreamIntergenicRegion

getFlankingRegions

setFlankingRegions

addFlankingRegions

getIntrons

setIntrons

addIntrons

getProteins

setProteins

addProteins

getcDSs

setcDSs

addcDSs

getHomologues

setHomologues

addHomologues

getExons

setExons

addExons

getuTRs

setuTRs

adduTRs

getScore

setScore

getScoreType