Package org.intermine.model.bio

Interface SequenceFeature

All Superinterfaces:

Annotatable, BioEntity, org.intermine.model.FastPathObject, org.intermine.model.InterMineFastPathObject, org.intermine.model.InterMineObject

All Known Subinterfaces:

CDS, Chromosome, Exon, Gene, GeneFlankingRegion, IntergenicRegion, Intron, SyntenicRegion, Transcript, UTR

All Known Implementing Classes:

CDSShadow, ChromosomeShadow, ExonShadow, GeneFlankingRegionShadow, GeneShadow, IntergenicRegionShadow, IntronShadow, SequenceFeatureShadow, SyntenicRegionShadow, TranscriptShadow, UTRShadow

public interface SequenceFeature
extends BioEntity

Method Summary

Modifier and Type	Method	Description
void	addChildFeatures(SequenceFeature arg)
void	addOverlappingFeatures(SequenceFeature arg)
java.util.Set<SequenceFeature>	getChildFeatures()
Chromosome	getChromosome()
Location	getChromosomeLocation()
java.lang.Integer	getLength()
java.util.Set<SequenceFeature>	getOverlappingFeatures()
java.lang.Double	getScore()
java.lang.String	getScoreType()
Sequence	getSequence()
SOTerm	getSequenceOntologyTerm()
Strain	getStrain()
org.intermine.model.InterMineObject	proxGetChromosome()
org.intermine.model.InterMineObject	proxGetChromosomeLocation()
org.intermine.model.InterMineObject	proxGetSequence()
org.intermine.model.InterMineObject	proxGetSequenceOntologyTerm()
org.intermine.model.InterMineObject	proxGetStrain()
void	proxyChromosome(org.intermine.objectstore.proxy.ProxyReference chromosome)
void	proxyChromosomeLocation(org.intermine.objectstore.proxy.ProxyReference chromosomeLocation)
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	setChildFeatures(java.util.Set<SequenceFeature> childFeatures)
void	setChromosome(Chromosome chromosome)
void	setChromosomeLocation(Location chromosomeLocation)
void	setLength(java.lang.Integer length)
void	setOverlappingFeatures(java.util.Set<SequenceFeature> overlappingFeatures)
void	setScore(java.lang.Double score)
void	setScoreType(java.lang.String scoreType)
void	setSequence(Sequence sequence)
void	setSequenceOntologyTerm(SOTerm sequenceOntologyTerm)
void	setStrain(Strain strain)

Methods inherited from interface org.intermine.model.bio.Annotatable

addOntologyAnnotations, addPublications, getOntologyAnnotations, getPrimaryIdentifier, getPublications, setOntologyAnnotations, setPrimaryIdentifier, setPublications

Methods inherited from interface org.intermine.model.bio.BioEntity

addCrossReferences, addDataSets, addLocatedFeatures, addLocations, addSynonyms, getCrossReferences, getDataSets, getLocatedFeatures, getLocations, getName, getOrganism, getSecondaryIdentifier, getSymbol, getSynonyms, proxGetOrganism, proxyOrganism, setCrossReferences, setDataSets, setLocatedFeatures, setLocations, setName, setOrganism, setSecondaryIdentifier, setSymbol, setSynonyms

Methods inherited from interface org.intermine.model.FastPathObject

getFieldProxy, getFieldType, getFieldValue, setFieldValue

Methods inherited from interface org.intermine.model.InterMineObject

getElementType, getId, getoBJECT, setId, setoBJECT, setoBJECT

Method Detail

getScore

java.lang.Double getScore()

setScore

void setScore(java.lang.Double score)

getScoreType

java.lang.String getScoreType()

setScoreType

void setScoreType(java.lang.String scoreType)

getLength

java.lang.Integer getLength()

setLength

void setLength(java.lang.Integer length)

getStrain

Strain getStrain()

setStrain

void setStrain(Strain strain)

proxyStrain

void proxyStrain(org.intermine.objectstore.proxy.ProxyReference strain)

proxGetStrain

org.intermine.model.InterMineObject proxGetStrain()

getSequenceOntologyTerm

SOTerm getSequenceOntologyTerm()

setSequenceOntologyTerm

void setSequenceOntologyTerm(SOTerm sequenceOntologyTerm)

proxySequenceOntologyTerm

void proxySequenceOntologyTerm(org.intermine.objectstore.proxy.ProxyReference sequenceOntologyTerm)

proxGetSequenceOntologyTerm

org.intermine.model.InterMineObject proxGetSequenceOntologyTerm()

getChromosomeLocation

Location getChromosomeLocation()

setChromosomeLocation

void setChromosomeLocation(Location chromosomeLocation)

proxyChromosomeLocation

void proxyChromosomeLocation(org.intermine.objectstore.proxy.ProxyReference chromosomeLocation)

proxGetChromosomeLocation

org.intermine.model.InterMineObject proxGetChromosomeLocation()

getSequence

Sequence getSequence()

setSequence

void setSequence(Sequence sequence)

proxySequence

void proxySequence(org.intermine.objectstore.proxy.ProxyReference sequence)

proxGetSequence

org.intermine.model.InterMineObject proxGetSequence()

getChromosome

Chromosome getChromosome()

setChromosome

void setChromosome(Chromosome chromosome)

proxyChromosome

void proxyChromosome(org.intermine.objectstore.proxy.ProxyReference chromosome)

proxGetChromosome

org.intermine.model.InterMineObject proxGetChromosome()

getOverlappingFeatures

java.util.Set<SequenceFeature> getOverlappingFeatures()

setOverlappingFeatures

void setOverlappingFeatures(java.util.Set<SequenceFeature> overlappingFeatures)

addOverlappingFeatures

void addOverlappingFeatures(SequenceFeature arg)

getChildFeatures

java.util.Set<SequenceFeature> getChildFeatures()

setChildFeatures

void setChildFeatures(java.util.Set<SequenceFeature> childFeatures)

addChildFeatures

void addChildFeatures(SequenceFeature arg)