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

Class XmlNucleicAcid

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.DefaultNucleicAcid

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

All Implemented Interfaces:

FileSourceContext, Interactor, Molecule, NucleicAcid, Polymer, ExtendedPsiXmlInteractor

public class XmlNucleicAcid
extends DefaultNucleicAcid
implements ExtendedPsiXmlInteractor, FileSourceContext

Xml implementation of Nucleic acid

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.NucleicAcid

NULCEIC_ACID, NULCEIC_ACID_MI

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

POLYMER, POLYMER_MI

Constructor Summary

Constructors

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

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 interactor type of this NucleicAcid.
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.DefaultNucleicAcid

clearPropertiesLinkedToIdentifiers, getDdbjEmblGenbank, getPreferredIdentifier, getRefseq, initialiseIdentifiers, processAddedIdentifiersEvent, processRemovedIdentifierEvent, setDdbjEmblGenbank, setRefseq

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, 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

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

getSequence, setSequence

Constructor Detail

XmlNucleicAcid

public XmlNucleicAcid(String name,
                      CvTerm type)

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlNucleicAcid

public XmlNucleicAcid(String name)

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

XmlNucleicAcid

public XmlNucleicAcid(String name,
                      String fullName)

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

XmlNucleicAcid

public XmlNucleicAcid(String name,
                      Organism organism)

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

organism - a Organism object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

XmlNucleicAcid

public XmlNucleicAcid(String name,
                      Xref uniqueId)

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

uniqueId - a Xref object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlNucleicAcid

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

Constructor for XmlNucleicAcid.

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 interactor type of this NucleicAcid. If the interactor type is null, it will set the interactor type to nucleic acid (MI:0318)

Specified by:

setInteractorType in interface Interactor

Overrides:

setInteractorType in class DefaultNucleicAcid

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 DefaultNucleicAcid

Returns:

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