Package psidev.psi.mi.jami.tab.extension

Class MitabGene

java.lang.Object

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

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

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

psidev.psi.mi.jami.tab.extension.MitabGene

All Implemented Interfaces:

FileSourceContext, Gene, Interactor, Molecule

public class MitabGene
extends DefaultGene
implements FileSourceContext

Mitab extension for Gene. It contains FileSourceContext

Since:

11/06/13

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
MitabGene(String name)	Constructor for MitabGene.
MitabGene(String name, String fullName)	Constructor for MitabGene.
MitabGene(String name, String fullName, String ensembl)	Constructor for MitabGene.
MitabGene(String name, String fullName, Organism organism)	Constructor for MitabGene.
MitabGene(String name, String fullName, Organism organism, String ensembl)	Constructor for MitabGene.
MitabGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabGene.
MitabGene(String name, String fullName, Xref uniqueId)	Constructor for MitabGene.
MitabGene(String name, Organism organism)	Constructor for MitabGene.
MitabGene(String name, Organism organism, String ensembl)	Constructor for MitabGene.
MitabGene(String name, Organism organism, Xref uniqueId)	Constructor for MitabGene.
MitabGene(String name, Xref uniqueId)	Constructor for MitabGene.

Method Summary

Modifier and Type	Method	Description
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

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

clearPropertiesLinkedToIdentifiers, getEnsembl, getEnsemblGenome, getEntrezGeneId, getPreferredIdentifier, getRefseq, initialiseIdentifiers, processAddedIdentifierEvent, processRemovedIdentifierEvent, setEnsembl, setEnsemblGenome, setEntrezGeneId, setInteractorType, setRefseq

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

MitabGene

public MitabGene(String name)

Constructor for MitabGene.

Parameters:

name - a String object.

MitabGene

public MitabGene(String name,
                 String fullName)

Constructor for MitabGene.

Parameters:

name - a String object.

fullName - a String object.

MitabGene

public MitabGene(String name,
                 Organism organism)

Constructor for MitabGene.

Parameters:

name - a String object.

organism - a Organism object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

MitabGene

public MitabGene(String name,
                 Xref uniqueId)

Constructor for MitabGene.

Parameters:

name - a String object.

uniqueId - a Xref object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

fullName - a String object.

ensembl - a String object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

organism - a Organism object.

ensembl - a String object.

MitabGene

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

Constructor for MitabGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

ensembl - a String object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultGene

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties