Package psidev.psi.mi.jami.xml.model.extension.xml253

Class XmlPolymer

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.AbstractBaseXmlInteractor

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteractor

psidev.psi.mi.jami.xml.model.extension.xml253.DefaultXmlInteractor

psidev.psi.mi.jami.xml.model.extension.xml253.XmlMolecule

psidev.psi.mi.jami.xml.model.extension.xml253.XmlPolymer

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Interactor, Molecule, Polymer, ExtendedPsiXmlInteractor

public class XmlPolymer
extends XmlMolecule
implements Polymer

Xml implementation of Polymer

Since:

24/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteractor

AbstractXmlInteractor.JAXBAttributeWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.AbstractBaseXmlInteractor

AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.extension.AbstractBaseXmlInteractor

locator

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	createDefaultInteractorType()	createDefaultInteractorType.
String	getSequence()	getSequence.
void	setSequence(String sequence)	Sets the value of the sequence property.
String	toString()	toString

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteractor

initialiseAnnotationWrapper, initialiseNamesContainer, initialiseXrefContainer, setJAXBAttributeWrapper, setJAXBId, setJAXBInteractorType, setJAXBNames, setJAXBOrganism, setJAXBXref

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.AbstractBaseXmlInteractor

getAliases, getAnnotations, getChecksums, getFullName, getId, getIdentifiers, getInteractorType, getNamesContainer, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, getSourceLocator, getXrefs, setFullName, setId, setInteractorType, setJAXBAttributeWrapper, setJAXBInteractorType, setJAXBNames, setJAXBOrganism, setNamesContainer, setOrganism, setShortName, setSourceLocation, setSourceLocator, setXrefContainer, sourceLocation

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, setInteractorType, setOrganism, setShortName

Constructor Detail

XmlPolymer

public XmlPolymer()

Constructor for XmlPolymer.

XmlPolymer

public XmlPolymer(String name,
                  CvTerm type)

Constructor for XmlPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

uniqueId - a Xref object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

type - a CvTerm object.

organism - a Organism object.

uniqueId - a Xref object.

XmlPolymer

public XmlPolymer(String name)

Constructor for XmlPolymer.

Parameters:

name - a String object.

XmlPolymer

public XmlPolymer(String name,
                  String fullName)

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

XmlPolymer

public XmlPolymer(String name,
                  Organism organism)

Constructor for XmlPolymer.

Parameters:

name - a String object.

organism - a Organism object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

XmlPolymer

public XmlPolymer(String name,
                  Xref uniqueId)

Constructor for XmlPolymer.

Parameters:

name - a String object.

uniqueId - a Xref object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

uniqueId - a Xref object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

organism - a Organism object.

uniqueId - a Xref object.

XmlPolymer

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

Constructor for XmlPolymer.

Parameters:

name - a String object.

fullName - a String object.

organism - a Organism object.

uniqueId - a Xref object.

Method Detail

createDefaultInteractorType

protected void createDefaultInteractorType()

createDefaultInteractorType.

Overrides:

createDefaultInteractorType in class AbstractXmlInteractor

getSequence

public String getSequence()

getSequence.

Specified by:

getSequence in interface Polymer

Overrides:

getSequence in class AbstractBaseXmlInteractor

Returns:

a String object.

setSequence

public void setSequence(String sequence)

Sets the value of the sequence property.

Specified by:

setSequence in interface Polymer

Overrides:

setSequence in class AbstractXmlInteractor

Parameters:

sequence - allowed object is String

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class XmlMolecule

Returns:

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