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

Class XmlProtein

java.lang.Object

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

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

psidev.psi.mi.jami.model.impl.DefaultPolymer

psidev.psi.mi.jami.model.impl.DefaultProtein

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

All Implemented Interfaces:

FileSourceContext, Interactor, Molecule, Polymer, Protein, ExtendedPsiXmlInteractor

public class XmlProtein
extends DefaultProtein
implements ExtendedPsiXmlInteractor, FileSourceContext

Xml implementation of protein

Since:

24/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

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

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

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

POLYMER, POLYMER_MI

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

PEPTIDE, PEPTIDE_MI, PROTEIN, PROTEIN_MI

Constructor Summary

Constructors

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

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.DefaultProtein

clearPropertiesLinkedToAliases, clearPropertiesLinkedToChecksums, clearPropertiesLinkedToIdentifiers, getGeneName, getPreferredIdentifier, getPreferredName, getRefseq, getRogid, getUniprotkb, initialiseAliases, initialiseChecksums, initialiseIdentifiers, processAddedAliasEvent, processAddedChecksumEvent, processAddedIdentifierEvent, processRemovedAliasEvent, processRemovedChecksumEvent, processRemovedIdentifierEvent, setGeneName, setRefseq, setRogid, setUniprotkb

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

getSequence, setSequence

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

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getShortName, getXrefs, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, 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

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

getSequence, setSequence

Constructor Detail

XmlProtein

public XmlProtein(String name,
                  CvTerm type)

Constructor for XmlProtein.

Parameters:

name - a String object.

type - a CvTerm object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlProtein

public XmlProtein(String name,
                  CvTerm type,
                  Xref uniqueId)

Constructor for XmlProtein.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlProtein

public XmlProtein(String name,
                  String fullName,
                  CvTerm type,
                  Xref uniqueId)

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlProtein

public XmlProtein(String name)

Constructor for XmlProtein.

Parameters:

name - a String object.

XmlProtein

public XmlProtein(String name,
                  String fullName)

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

XmlProtein

public XmlProtein(String name,
                  Organism organism)

Constructor for XmlProtein.

Parameters:

name - a String object.

organism - a Organism object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

XmlProtein

public XmlProtein(String name,
                  Xref uniqueId)

Constructor for XmlProtein.

Parameters:

name - a String object.

uniqueId - a Xref object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlProtein

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

Constructor for XmlProtein.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - 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) Sets the interactor type of this polymer. If the given interactorType is null, it sets the interactorType to 'biopolymer'(MI:0383) Sets the interactor type of this protein. If the given interactorType is null, it will set the interactor type to 'protein' (MI:0326)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultProtein

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 DefaultProtein

Returns:

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