Package org.intermine.model.bio

Class CDSShadow

java.lang.Object

org.intermine.model.bio.CDSShadow

All Implemented Interfaces:

Annotatable, BioEntity, CDS, SequenceFeature, org.intermine.model.FastPathObject, org.intermine.model.InterMineFastPathObject, org.intermine.model.InterMineObject, org.intermine.model.ShadowClass

public class CDSShadow
extends java.lang.Object
implements CDS, org.intermine.model.ShadowClass

Field Summary

Fields

Modifier and Type	Field	Description
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 org.intermine.model.InterMineObject	gene
protected java.lang.Integer	id
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 org.intermine.model.InterMineObject	protein
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<CDS>	shadowOf
protected org.intermine.model.InterMineObject	strain
protected java.lang.String	symbol
protected java.util.Set<Synonym>	synonyms

Constructor Summary

Constructors

Constructor	Description
CDSShadow()

Method Summary

Modifier and Type	Method	Description
void	addChildFeatures(SequenceFeature arg)
void	addCollectionElement(java.lang.String fieldName, org.intermine.model.InterMineObject element)
void	addCrossReferences(CrossReference arg)
void	addDataSets(DataSet arg)
void	addLocatedFeatures(Location arg)
void	addLocations(Location arg)
void	addOntologyAnnotations(OntologyAnnotation arg)
void	addOverlappingFeatures(SequenceFeature arg)
void	addPublications(Publication arg)
void	addSynonyms(Synonym arg)
boolean	equals(java.lang.Object o)
java.util.Set<SequenceFeature>	getChildFeatures()
Chromosome	getChromosome()
Location	getChromosomeLocation()
java.util.Set<CrossReference>	getCrossReferences()
java.util.Set<DataSet>	getDataSets()
java.lang.Class<?>	getElementType(java.lang.String fieldName)
java.lang.Object	getFieldProxy(java.lang.String fieldName)
java.lang.Class<?>	getFieldType(java.lang.String fieldName)
java.lang.Object	getFieldValue(java.lang.String fieldName)
Gene	getGene()
java.lang.Integer	getId()
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()
Protein	getProtein()
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()
int	hashCode()
org.intermine.model.InterMineObject	proxGetChromosome()
org.intermine.model.InterMineObject	proxGetChromosomeLocation()
org.intermine.model.InterMineObject	proxGetGene()
org.intermine.model.InterMineObject	proxGetOrganism()
org.intermine.model.InterMineObject	proxGetProtein()
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	proxyGene(org.intermine.objectstore.proxy.ProxyReference gene)
void	proxyOrganism(org.intermine.objectstore.proxy.ProxyReference organism)
void	proxyProtein(org.intermine.objectstore.proxy.ProxyReference protein)
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	setCrossReferences(java.util.Set<CrossReference> crossReferences)
void	setDataSets(java.util.Set<DataSet> dataSets)
void	setFieldValue(java.lang.String fieldName, java.lang.Object value)
void	setGene(Gene gene)
void	setId(java.lang.Integer id)
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	setProtein(Protein protein)
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)
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<CDS> shadowOf

gene

protected org.intermine.model.InterMineObject gene

protein

protected org.intermine.model.InterMineObject protein

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

CDSShadow

public CDSShadow()

Method Detail

getGene

public Gene getGene()

Specified by:

getGene in interface CDS

setGene

public void setGene(Gene gene)

Specified by:

setGene in interface CDS

proxyGene

public void proxyGene(org.intermine.objectstore.proxy.ProxyReference gene)

Specified by:

proxyGene in interface CDS

proxGetGene

public org.intermine.model.InterMineObject proxGetGene()

Specified by:

proxGetGene in interface CDS

getProtein

public Protein getProtein()

Specified by:

getProtein in interface CDS

setProtein

public void setProtein(Protein protein)

Specified by:

setProtein in interface CDS

proxyProtein

public void proxyProtein(org.intermine.objectstore.proxy.ProxyReference protein)

Specified by:

proxyProtein in interface CDS

proxGetProtein

public org.intermine.model.InterMineObject proxGetProtein()

Specified by:

proxGetProtein in interface CDS

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