Package psidev.psi.mi.jami.model.impl

Class DefaultGene

java.lang.Object

psidev.psi.mi.jami.model.impl.DefaultInteractor

psidev.psi.mi.jami.model.impl.DefaultMolecule

psidev.psi.mi.jami.model.impl.DefaultGene

All Implemented Interfaces:

Gene, Interactor, Molecule

Direct Known Subclasses:

MitabGene, XmlGene, XmlGene, XmlGene

public class DefaultGene
extends DefaultMolecule
implements Gene

Default implementation for gene Notes: The equals and hashcode methods have NOT been overridden because the Gene object is a complex object. To compare Gene objects, you can use some comparators provided by default: - DefaultGeneComparator - UnambiguousGeneComparator - DefaultExactGeneComparator - UnambiguousExactGeneComparator - GeneComparator

Since:

24/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.Gene

GENE, GENE_MI

Fields inherited from interface psidev.psi.mi.jami.model.Interactor

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Constructor Summary

Constructors

Constructor	Description
DefaultGene(String name)	Constructor for DefaultGene.
DefaultGene(String name, String fullName)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, String ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Organism organism)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, Organism organism)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, Organism organism, String ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, Xref uniqueId)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Organism organism)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Organism organism, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, Organism organism)	Constructor for DefaultGene.
DefaultGene(String name, Organism organism, String ensembl)	Constructor for DefaultGene.
DefaultGene(String name, Organism organism, Xref uniqueId)	Constructor for DefaultGene.
DefaultGene(String name, Xref uniqueId)	Constructor for DefaultGene.

Method Summary

Modifier and Type	Method	Description
protected void	clearPropertiesLinkedToIdentifiers()
String	getEnsembl()	Getter for the field ensembl.
String	getEnsemblGenome()	Getter for the field ensemblGenome.
String	getEntrezGeneId()	Getter for the field entrezGeneId.
Xref	getPreferredIdentifier()	getPreferredIdentifier
String	getRefseq()	Getter for the field refseq.
protected void	initialiseIdentifiers()	initialiseIdentifiers
protected void	processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
void	setEnsembl(String ac)	Sets the Ensembl accession for this gene.
void	setEnsemblGenome(String ac)	Sets the Ensembl genomes identifier It will remove the old ensembl genomes identifier from the collection of identifiers and replace it with the new ensembl genomes identifier.
void	setEntrezGeneId(String id)	Sets the Entrez gene id.
void	setInteractorType(CvTerm type)	Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)
void	setRefseq(String ac)	Sets the refseq accession.
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.DefaultInteractor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredName, getShortName, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumsWith, initialiseIdentifiersWith, initialiseXrefs, initialiseXrefsWith, setFullName, setOrganism, setShortName

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface psidev.psi.mi.jami.model.Interactor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

Constructor Detail

DefaultGene

public DefaultGene(String name)

Constructor for DefaultGene.

Parameters:

name - a String object.

DefaultGene

public DefaultGene(String name,
                   String fullName)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

DefaultGene

public DefaultGene(String name,
                   Organism organism)

Constructor for DefaultGene.

Parameters:

name - a String object.

organism - a Organism object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   Organism organism)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

DefaultGene

public DefaultGene(String name,
                   Xref uniqueId)

Constructor for DefaultGene.

Parameters:

name - a String object.

uniqueId - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   Xref uniqueId)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

DefaultGene

public DefaultGene(String name,
                   Organism organism,
                   Xref uniqueId)

Constructor for DefaultGene.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   Organism organism,
                   Xref uniqueId)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   String ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

ensembl - a String object.

DefaultGene

public DefaultGene(String name,
                   CvTerm type,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

type - a CvTerm object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   CvTerm type,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   CvTerm type,
                   Organism organism,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   CvTerm type,
                   Organism organism,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   CvTerm type,
                   Xref uniqueId,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   CvTerm type,
                   Xref uniqueId,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   CvTerm type,
                   Organism organism,
                   Xref uniqueId,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   CvTerm type,
                   Organism organism,
                   Xref uniqueId,
                   Xref ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

ensembl - a Xref object.

DefaultGene

public DefaultGene(String name,
                   Organism organism,
                   String ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

organism - a Organism object.

ensembl - a String object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   Organism organism,
                   String ensembl)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

ensembl - a String object.

DefaultGene

public DefaultGene(String name,
                   CvTerm type)

Constructor for DefaultGene.

Parameters:

name - a String object.

type - a CvTerm object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   CvTerm type)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

DefaultGene

public DefaultGene(String name,
                   CvTerm type,
                   Organism organism)

Constructor for DefaultGene.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

DefaultGene

public DefaultGene(String name,
                   String fullName,
                   CvTerm type,
                   Organism organism)

Constructor for DefaultGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

Method Detail

initialiseIdentifiers

protected void initialiseIdentifiers()

initialiseIdentifiers

Overrides:

initialiseIdentifiers in class DefaultInteractor

getPreferredIdentifier

public Xref getPreferredIdentifier()

getPreferredIdentifier

Return the first ensembl identifier if provided, otherwise the first ensemblGenomes if provided, otherwise the first entrez/gene id if provided, otherwise the first refseq id if provided otherwise the first identifier in the list of identifiers

Specified by:

getPreferredIdentifier in interface Interactor

Overrides:

getPreferredIdentifier in class DefaultInteractor

Returns:

the first identifier in the list of identifiers or null if the list is empty

getEnsembl

public String getEnsembl()

Getter for the field ensembl.

Specified by:

getEnsembl in interface Gene

Returns:

a String object.

setEnsembl

public void setEnsembl(String ac)

Sets the Ensembl accession for this gene. It will remove the old ensembl identifier from the collection of identifiers and replace it with the new ensembl identifier. If the new ensembl identifier is null, all the existing ensembl identifiers will be removed from the collection of identifiers

Specified by:

setEnsembl in interface Gene

Parameters:

ac - : Ensembl accession

getEnsemblGenome

public String getEnsemblGenome()

Getter for the field ensemblGenome.

Specified by:

getEnsemblGenome in interface Gene

Returns:

a String object.

setEnsemblGenome

public void setEnsemblGenome(String ac)

Sets the Ensembl genomes identifier It will remove the old ensembl genomes identifier from the collection of identifiers and replace it with the new ensembl genomes identifier. If the new ensembl genomes identifier is null, all the existing ensembl genomes identifiers will be removed from the collection of identifiers

Specified by:

setEnsemblGenome in interface Gene

Parameters:

ac - : the ensembleGenome ac

getEntrezGeneId

public String getEntrezGeneId()

Getter for the field entrezGeneId.

Specified by:

getEntrezGeneId in interface Gene

Returns:

a String object.

setEntrezGeneId

public void setEntrezGeneId(String id)

Sets the Entrez gene id. It will remove the old entrez/gene identifier from the collection of identifiers and replace it with the new entrez/gene identifier. If the new entrez/gene identifier is null, all the existing entrez/gene identifiers will be removed from the collection of identifiers

Specified by:

setEntrezGeneId in interface Gene

Parameters:

id - : Entrez gene id

getRefseq

public String getRefseq()

Getter for the field refseq.

Specified by:

getRefseq in interface Gene

Returns:

a String object.

setRefseq

public void setRefseq(String ac)

Sets the refseq accession. It will remove the old refseq identifier from the collection of identifiers and replace it with the new refseq identifier. If the new refseq identifier is null, all the existing refseq identifiers will be removed from the collection of identifiers

Specified by:

setRefseq in interface Gene

Parameters:

ac - : the refseq accession

processAddedIdentifierEvent

protected void processAddedIdentifierEvent(Xref added)

processAddedIdentifierEvent

Parameters:

added - a Xref object.

processRemovedIdentifierEvent

protected void processRemovedIdentifierEvent(Xref removed)

processRemovedIdentifierEvent

Parameters:

removed - a Xref object.

clearPropertiesLinkedToIdentifiers

protected void clearPropertiesLinkedToIdentifiers()

clearPropertiesLinkedToIdentifiers

setInteractorType

public void setInteractorType(CvTerm type)

Description copied from class: DefaultInteractor

Sets the molecule type for this interactor If the given type is null, this method automatically sets the interactor type to 'unknown participant' (MI:0329)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultInteractor

Parameters:

type - : molecule type

toString

public String toString()

Overrides:

toString in class DefaultInteractor