Package psidev.psi.mi.jami.model

Interface Gene

All Superinterfaces:

Interactor, Molecule

All Known Implementing Classes:

DefaultGene, MitabGene, XmlGene, XmlGene, XmlGene

public interface Gene
extends Molecule

Interactor for genetic interactions

Since:

23/11/12

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	GENE	Constant GENE="gene"
static String	GENE_MI	Constant GENE_MI="MI:0250"

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Method Summary

Modifier and Type	Method	Description
String	getEnsembl()	The unique Ensembl accession which identifies the gene.
String	getEnsemblGenome()	The Ensembl genome accession which identifies the gene.
String	getEntrezGeneId()	The Entrez gene id which identifies this gene.
String	getRefseq()	The refseq accession which identifies the gene.
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	setRefseq(String ac)	Sets the refseq accession.

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

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

Field Detail

GENE

static final String GENE

Constant GENE="gene"

See Also:

Constant Field Values

GENE_MI

static final String GENE_MI

Constant GENE_MI="MI:0250"

See Also:

Constant Field Values

Method Detail

getEnsembl

String getEnsembl()

The unique Ensembl accession which identifies the gene. It can be null It is a shortcut which should point to the first ensembl identifier in the collection of identifiers. Ex:ENSG00000172115

Returns:

the ENSEMBL accession

setEnsembl

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

Parameters:

ac - : Ensembl accession

getEnsemblGenome

String getEnsemblGenome()

The Ensembl genome accession which identifies the gene. It can be null. It is a shortcut which should point to the first ensembl genomes identifier in the collection of identifiers. Ex: ENSG00000139618

Returns:

the Ensembl geneome accessiom

setEnsemblGenome

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

Parameters:

ac - : the ensembleGenome ac

getEntrezGeneId

String getEntrezGeneId()

The Entrez gene id which identifies this gene. It can be null It is a shortcut which should point to the first entrez gene identifier in the collection of identifiers. Ex: 54205

Returns:

the Gene id

setEntrezGeneId

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

Parameters:

id - : Entrez gene id

getRefseq

String getRefseq()

The refseq accession which identifies the gene. It can be null It is a shortcut which should point to the first refseq identifier in the collection of identifiers. Ex: NM_001071821.1

Returns:

the Refseq accession

setRefseq

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

Parameters:

ac - : the refseq accession