Package org.intermine.model.bio

Class ProteinShadow

java.lang.Object

org.intermine.model.bio.ProteinShadow

All Implemented Interfaces:

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

public class ProteinShadow
extends java.lang.Object
implements Protein, org.intermine.model.ShadowClass

Field Summary

Fields

Modifier and Type	Field	Description
protected java.util.Set<CDS>	CDSs
protected java.util.Set<CrossReference>	crossReferences
protected java.util.Set<DataSet>	dataSets
protected java.util.Set<Gene>	genes
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	md5checksum
protected java.lang.Double	molecularWeight
protected java.lang.String	name
protected java.util.Set<OntologyAnnotation>	ontologyAnnotations
protected org.intermine.model.InterMineObject	organism
protected java.lang.String	primaryAccession
protected java.lang.String	primaryIdentifier
protected java.util.Set<Publication>	publications
protected java.lang.String	secondaryIdentifier
protected org.intermine.model.InterMineObject	sequence
static java.lang.Class<Protein>	shadowOf
protected java.lang.String	symbol
protected java.util.Set<Synonym>	synonyms
protected java.util.Set<Transcript>	transcripts

Constructor Summary

Constructors

Constructor	Description
ProteinShadow()

Method Summary

Modifier and Type	Method	Description
void	addcDSs(CDS arg)
void	addCollectionElement(java.lang.String fieldName, org.intermine.model.InterMineObject element)
void	addCrossReferences(CrossReference arg)
void	addDataSets(DataSet arg)
void	addGenes(Gene arg)
void	addLocatedFeatures(Location arg)
void	addLocations(Location arg)
void	addOntologyAnnotations(OntologyAnnotation arg)
void	addPublications(Publication arg)
void	addSynonyms(Synonym arg)
void	addTranscripts(Transcript arg)
boolean	equals(java.lang.Object o)
java.util.Set<CDS>	getcDSs()
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)
java.util.Set<Gene>	getGenes()
java.lang.Integer	getId()
java.lang.Integer	getLength()
java.util.Set<Location>	getLocatedFeatures()
java.util.Set<Location>	getLocations()
java.lang.String	getMd5checksum()
java.lang.Double	getMolecularWeight()
java.lang.String	getName()
org.intermine.model.StringConstructor	getoBJECT()
java.util.Set<OntologyAnnotation>	getOntologyAnnotations()
Organism	getOrganism()
java.lang.String	getPrimaryAccession()
java.lang.String	getPrimaryIdentifier()
java.util.Set<Publication>	getPublications()
java.lang.String	getSecondaryIdentifier()
Sequence	getSequence()
java.lang.String	getSymbol()
java.util.Set<Synonym>	getSynonyms()
java.util.Set<Transcript>	getTranscripts()
int	hashCode()
org.intermine.model.InterMineObject	proxGetOrganism()
org.intermine.model.InterMineObject	proxGetSequence()
void	proxyOrganism(org.intermine.objectstore.proxy.ProxyReference organism)
void	proxySequence(org.intermine.objectstore.proxy.ProxyReference sequence)
void	setcDSs(java.util.Set<CDS> CDSs)
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	setGenes(java.util.Set<Gene> genes)
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	setMd5checksum(java.lang.String md5checksum)
void	setMolecularWeight(java.lang.Double molecularWeight)
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	setPrimaryAccession(java.lang.String primaryAccession)
void	setPrimaryIdentifier(java.lang.String primaryIdentifier)
void	setPublications(java.util.Set<Publication> publications)
void	setSecondaryIdentifier(java.lang.String secondaryIdentifier)
void	setSequence(Sequence sequence)
void	setSymbol(java.lang.String symbol)
void	setSynonyms(java.util.Set<Synonym> synonyms)
void	setTranscripts(java.util.Set<Transcript> transcripts)
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<Protein> shadowOf

md5checksum

protected java.lang.String md5checksum

primaryAccession

protected java.lang.String primaryAccession

molecularWeight

protected java.lang.Double molecularWeight

length

protected java.lang.Integer length

sequence

protected org.intermine.model.InterMineObject sequence

CDSs

protected java.util.Set<CDS> CDSs

genes

protected java.util.Set<Gene> genes

transcripts

protected java.util.Set<Transcript> transcripts

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

ProteinShadow

public ProteinShadow()

Method Detail

getMd5checksum

public java.lang.String getMd5checksum()

Specified by:

getMd5checksum in interface Protein

setMd5checksum

public void setMd5checksum(java.lang.String md5checksum)

Specified by:

setMd5checksum in interface Protein

getPrimaryAccession

public java.lang.String getPrimaryAccession()

Specified by:

getPrimaryAccession in interface Protein

setPrimaryAccession

public void setPrimaryAccession(java.lang.String primaryAccession)

Specified by:

setPrimaryAccession in interface Protein

getMolecularWeight

public java.lang.Double getMolecularWeight()

Specified by:

getMolecularWeight in interface Protein

setMolecularWeight

public void setMolecularWeight(java.lang.Double molecularWeight)

Specified by:

setMolecularWeight in interface Protein

getLength

public java.lang.Integer getLength()

Specified by:

getLength in interface Protein

setLength

public void setLength(java.lang.Integer length)

Specified by:

setLength in interface Protein

getSequence

public Sequence getSequence()

Specified by:

getSequence in interface Protein

setSequence

public void setSequence(Sequence sequence)

Specified by:

setSequence in interface Protein

proxySequence

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

Specified by:

proxySequence in interface Protein

proxGetSequence

public org.intermine.model.InterMineObject proxGetSequence()

Specified by:

proxGetSequence in interface Protein

getcDSs

public java.util.Set<CDS> getcDSs()

Specified by:

getcDSs in interface Protein

setcDSs

public void setcDSs(java.util.Set<CDS> CDSs)

Specified by:

setcDSs in interface Protein

addcDSs

public void addcDSs(CDS arg)

Specified by:

addcDSs in interface Protein

getGenes

public java.util.Set<Gene> getGenes()

Specified by:

getGenes in interface Protein

setGenes

public void setGenes(java.util.Set<Gene> genes)

Specified by:

setGenes in interface Protein

addGenes

public void addGenes(Gene arg)

Specified by:

addGenes in interface Protein

getTranscripts

public java.util.Set<Transcript> getTranscripts()

Specified by:

getTranscripts in interface Protein

setTranscripts

public void setTranscripts(java.util.Set<Transcript> transcripts)

Specified by:

setTranscripts in interface Protein

addTranscripts

public void addTranscripts(Transcript arg)

Specified by:

addTranscripts in interface Protein

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