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

Class XmlParticipant

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlEntity<F>

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlParticipant<Interaction,Feature>

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

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Entity<Feature>, NamedParticipant<Interaction,Feature>, Participant<Interaction,Feature>, ExtendedPsiXmlEntity<Feature>

public class XmlParticipant
extends AbstractXmlParticipant<Interaction,Feature>

Xml implementation of a simple participant

Since:

08/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	XmlParticipant.JAXBFeatureWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlParticipant

AbstractXmlParticipant.JAXBAttributeWrapper, AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>

Field Summary

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

ACCEPTOR_ROLE, ACCEPTOR_ROLE_MI, BAIT_ROLE, BAIT_ROLE_MI, DONOR_ROLE, DONOR_ROLE_MI, ELECTRON_ACCEPTOR_ROLE, ELECTRON_ACCEPTOR_ROLE_MI, ELECTRON_DONOR_ROLE, ELECTRON_DONOR_ROLE_MI, ENZYME_REGULATOR_ROLE, ENZYME_REGULATOR_ROLE_MI, ENZYME_ROLE, ENZYME_ROLE_MI, ENZYME_TARGET_ROLE, ENZYME_TARGET_ROLE_MI, FLUORESCENCE_ACCEPTOR_ROLE, FLUORESCENCE_ACCEPTOR_ROLE_MI, FLUORESCENCE_DONOR_ROLE, FLUORESCENCE_DONOR_ROLE_MI, INHIBITED, INHIBITED_MI, INHIBITOR, INHIBITOR_MI, NEUTRAL, NEUTRAL_MI, PHOSPHATE_ACCEPTOR_ROLE, PHOSPHATE_ACCEPTOR_ROLE_MI, PHOSPHATE_DONOR_ROLE, PHOSPHATE_DONOR_ROLE_MI, PHOTON_ACCEPTOR_ROLE, PHOTON_ACCEPTOR_ROLE_MI, PHOTON_DONOR_ROLE, PHOTON_DONOR_ROLE_MI, PREDETERMINED, PREDETERMINED_MI, PREY, PREY_MI, PUTATIVE_SELF_ROLE, PUTATIVE_SELF_ROLE_MI, SELF_ROLE, SELF_ROLE_MI, SUPPRESSED_GENE_ROLE, SUPPRESSED_GENE_ROLE_MI, SUPPRESSOR_GENE_ROLE, SUPPRESSOR_GENE_ROLE_MI, UNSPECIFIED_ROLE, UNSPECIFIED_ROLE_MI

Constructor Summary

Constructors

Constructor	Description
XmlParticipant()	Constructor for XmlParticipant.
XmlParticipant(Interactor interactor)	Constructor for XmlParticipant.
XmlParticipant(Interactor interactor, CvTerm bioRole)	Constructor for XmlParticipant.
XmlParticipant(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)	Constructor for XmlParticipant.
XmlParticipant(Interactor interactor, Stoichiometry stoichiometry)	Constructor for XmlParticipant.

Method Summary

Modifier and Type	Method	Description
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
protected void	initialiseFeatureWrapper()	initialiseFeatureWrapper.
void	setJAXBAttributeWrapper(AbstractXmlParticipant.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBBiologicalRole(XmlCvTerm bioRole)	Sets the value of the biologicalRole property.
void	setJAXBFeatureWrapper(XmlParticipant.JAXBFeatureWrapper jaxbFeatureWrapper)	setJAXBFeatureWrapper.
void	setJAXBId(int value)	setJAXBId.
void	setJAXBInteractionRef(Integer value)	Sets the value of the interactionRef property.
void	setJAXBInteractor(DefaultXmlInteractor interactor)	setJAXBInteractor.
void	setJAXBInteractorRef(Integer value)	Sets the value of the interactorRef property.
void	setJAXBNames(NamesContainer value)	Sets the value of the namesContainer property.
void	setJAXBStoichiometry(XmlStoichiometry stoichiometry)	setJAXBStoichiometry.
void	setJAXBStoichiometryRange(XmlStoichiometryRange stoichiometry)	setJAXBStoichiometryRange.
void	setJAXBXref(XrefContainer value)	Sets the value of the xrefContainer property.

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlParticipant

getAliases, getAnnotations, getBiologicalEffect, getBiologicalRole, getFullName, getInteraction, getParticipantPool, getShortName, getStoichiometry, getXrefs, initialiseAnnotationWrapper, initialiseStoichiometry, setBiologicalEffect, setBiologicalRole, setFullName, setInteraction, setInteractionAndAddParticipant, setJAXBInteractorCandidates, setShortName, setStoichiometry, setStoichiometry

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlEntity

addAllFeatures, addFeature, getCausalRelationships, getChangeListener, getFeatures, getId, getInteractor, getParticipantLocator, initialiseUnspecifiedInteractor, processAddedFeature, removeAllFeatures, removeFeature, setChangeListener, setFeatureWrapper, setId, setInteractor, setSourceLocator, sourceLocation, toString

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.Entity

addAllFeatures, addFeature, getCausalRelationships, getChangeListener, getFeatures, getInteractor, removeAllFeatures, removeFeature, setChangeListener, setInteractor

Methods inherited from interface psidev.psi.mi.jami.xml.model.extension.ExtendedPsiXmlEntity

getId, setId

Methods inherited from interface psidev.psi.mi.jami.datasource.FileSourceContext

setSourceLocator, toString

Methods inherited from interface com.sun.xml.bind.Locatable

sourceLocation

Constructor Detail

XmlParticipant

public XmlParticipant()

Constructor for XmlParticipant.

XmlParticipant

public XmlParticipant(Interactor interactor)

Constructor for XmlParticipant.

Parameters:

interactor - a Interactor object.

XmlParticipant

public XmlParticipant(Interactor interactor,
                      Stoichiometry stoichiometry)

Constructor for XmlParticipant.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

XmlParticipant

public XmlParticipant(Interactor interactor,
                      CvTerm bioRole)

Constructor for XmlParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

XmlParticipant

public XmlParticipant(Interactor interactor,
                      CvTerm bioRole,
                      Stoichiometry stoichiometry)

Constructor for XmlParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

Method Detail

setJAXBNames

public void setJAXBNames(NamesContainer value)

Sets the value of the namesContainer property.

Overrides:

setJAXBNames in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

value - allowed object is NamesContainer

setJAXBXref

public void setJAXBXref(XrefContainer value)

Sets the value of the xrefContainer property.

Overrides:

setJAXBXref in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

value - allowed object is XrefContainer

setJAXBInteractor

public void setJAXBInteractor(DefaultXmlInteractor interactor)

setJAXBInteractor.

Overrides:

setJAXBInteractor in class AbstractXmlEntity<Feature>

Parameters:

interactor - a DefaultXmlInteractor object.

setJAXBInteractionRef

public void setJAXBInteractionRef(Integer value)

Sets the value of the interactionRef property.

Overrides:

setJAXBInteractionRef in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

value - allowed object is Integer

setJAXBInteractorRef

public void setJAXBInteractorRef(Integer value)

Sets the value of the interactorRef property.

Overrides:

setJAXBInteractorRef in class AbstractXmlEntity<Feature>

Parameters:

value - allowed object is Integer

setJAXBBiologicalRole

public void setJAXBBiologicalRole(XmlCvTerm bioRole)

Sets the value of the biologicalRole property.

Overrides:

setJAXBBiologicalRole in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

bioRole - allowed object is XmlCvTerm

setJAXBId

public void setJAXBId(int value)

setJAXBId.

Parameters:

value - a int.

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlParticipant.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Overrides:

setJAXBAttributeWrapper in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

jaxbAttributeWrapper - a AbstractXmlParticipant.JAXBAttributeWrapper object.

setJAXBFeatureWrapper

public void setJAXBFeatureWrapper(XmlParticipant.JAXBFeatureWrapper jaxbFeatureWrapper)

setJAXBFeatureWrapper.

Parameters:

jaxbFeatureWrapper - a XmlParticipant.JAXBFeatureWrapper object.

setJAXBStoichiometry

public void setJAXBStoichiometry(XmlStoichiometry stoichiometry)

setJAXBStoichiometry.

Overrides:

setJAXBStoichiometry in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

stoichiometry - a XmlStoichiometry object.

setJAXBStoichiometryRange

public void setJAXBStoichiometryRange(XmlStoichiometryRange stoichiometry)

setJAXBStoichiometryRange.

Overrides:

setJAXBStoichiometryRange in class AbstractXmlParticipant<Interaction,Feature>

Parameters:

stoichiometry - a XmlStoichiometryRange object.

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Overrides:

getSourceLocator in class AbstractXmlEntity<Feature>

Returns:

a FileSourceLocator object.

initialiseFeatureWrapper

protected void initialiseFeatureWrapper()

initialiseFeatureWrapper.

Overrides:

initialiseFeatureWrapper in class AbstractXmlEntity<Feature>