Package psidev.psi.mi.jami.xml.model.extension.xml300

Class XmlGene

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.xml.model.extension.xml300.XmlGene

All Implemented Interfaces:

FileSourceContext, Gene, Interactor, Molecule, ExtendedPsiXmlInteractor

public class XmlGene
extends DefaultGene
implements ExtendedPsiXmlInteractor, FileSourceContext

Xml implementation of a Gene

Since:

24/07/13

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

Method Summary

Modifier and Type	Method	Description
int	getId()	Gets the value of the id property.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setId(int value)	setId.
void	setInteractorType(CvTerm interactorType)	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	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
void	setSourceLocator(PsiXmlLocator sourceLocator)	Setter for the field sourceLocator.
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, 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, getPreferredIdentifier, getPreferredName, getShortName, getXrefs, setFullName, setOrganism, setShortName

Constructor Detail

XmlGene

public XmlGene(String name)

Constructor for XmlGene.

Parameters:

name - a String object.

XmlGene

public XmlGene(String name,
               String fullName)

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

XmlGene

public XmlGene(String name,
               Organism organism)

Constructor for XmlGene.

Parameters:

name - a String object.

organism - a Organism object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

XmlGene

public XmlGene(String name,
               Xref uniqueId)

Constructor for XmlGene.

Parameters:

name - a String object.

uniqueId - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

type - a CvTerm object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

ensembl - a Xref object.

XmlGene

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

Constructor for XmlGene.

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.

Method Detail

setInteractorType

public void setInteractorType(CvTerm interactorType)

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 DefaultGene

Parameters:

interactorType - : molecule type

getId

public int getId()

Gets the value of the id property.

Specified by:

getId in interface ExtendedPsiXmlInteractor

Returns:

a int.

setId

public void setId(int value)

setId.

Sets the value of the id property.

Specified by:

setId in interface ExtendedPsiXmlInteractor

Parameters:

value - a int.

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

setSourceLocator

public void setSourceLocator(PsiXmlLocator sourceLocator)

Setter for the field sourceLocator.

Parameters:

sourceLocator - a PsiXmlLocator object.

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