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

Class XmlParticipantEvidence

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlEntity<F>

psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

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

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Entity<FeatureEvidence>, ExperimentalEntity, NamedParticipant<InteractionEvidence,FeatureEvidence>, Participant<InteractionEvidence,FeatureEvidence>, ParticipantEvidence, ExtendedPsiXmlEntity<FeatureEvidence>, ExtendedPsiXmlParticipant<InteractionEvidence,FeatureEvidence>, ExtendedPsiXmlParticipantEvidence

public class XmlParticipantEvidence
extends AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>
implements ExtendedPsiXmlParticipantEvidence

Xml implementation of ParticipantEvidence

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	XmlParticipantEvidence.JAXBConfidenceWrapper
static class	XmlParticipantEvidence.JAXBExperimentalInteractorWrapper
static class	XmlParticipantEvidence.JAXBExperimentalPreparationWrapper
static class	XmlParticipantEvidence.JAXBExperimentalRoleWrapper
static class	XmlParticipantEvidence.JAXBFeatureWrapper
static class	XmlParticipantEvidence.JAXBHostOrganismWrapper
static class	XmlParticipantEvidence.JAXBInteractorCandidatesWrapper
static class	XmlParticipantEvidence.JAXBParameterWrapper
static class	XmlParticipantEvidence.JAXBParticipantIdentificationWrapper

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml253.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
XmlParticipantEvidence()	Constructor for XmlParticipantEvidence.
XmlParticipantEvidence(Interactor interactor)	Constructor for XmlParticipantEvidence.
XmlParticipantEvidence(Interactor interactor, CvTerm bioRole)	Constructor for XmlParticipantEvidence.
XmlParticipantEvidence(Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry)	Constructor for XmlParticipantEvidence.
XmlParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry)	Constructor for XmlParticipantEvidence.

Method Summary

Modifier and Type	Method	Description
Collection<Confidence>	getConfidences()	getConfidences.
List<AbstractExperimentalInteractor>	getExperimentalInteractors()	getExperimentalInteractors.
Collection<CvTerm>	getExperimentalPreparations()	getExperimentalPreparations.
CvTerm	getExperimentalRole()	getExperimentalRole.
List<CvTerm>	getExperimentalRoles()	getExperimentalRoles.
Organism	getExpressedInOrganism()	getExpressedInOrganism.
List<Organism>	getHostOrganisms()	getHostOrganisms.
Collection<CvTerm>	getIdentificationMethods()	getIdentificationMethods.
protected ExtendedPsiXmlInteractionEvidence	getOriginalInteraction()	Getter for the field originalInteraction.
Collection<Parameter>	getParameters()	getParameters.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
protected void	initialiseConfidenceWrapper()	initialiseConfidenceWrapper.
protected void	initialiseExperimentalInteractorWrapper()	initialiseExperimentalInteractorWrapper.
protected void	initialiseExperimentalPreparationWrapper()	initialiseExperimentalPreparationWrapper.
protected void	initialiseExperimentalRoleWrapper()	initialiseExperimentalRoleWrapper.
protected void	initialiseFeatureWrapper()	initialiseFeatureWrapper.
protected void	initialiseHostOrganismWrapper()	initialiseHostOrganismWrapper.
protected void	initialiseIdentificationMethodWrapper()	initialiseIdentificationMethodWrapper.
protected void	initialiseParameterWrapper()	initialiseParameterWrapper.
void	processAddedFeature(FeatureEvidence feature)	processAddedFeature.
void	setExperimentalInteractorWrapper(XmlParticipantEvidence.JAXBExperimentalInteractorWrapper wrapper)	setExperimentalInteractorWrapper.
void	setExperimentalRole(CvTerm expRole)	Sets the experimental role.
void	setExpressedInOrganism(Organism organism)	Sets the expressed in organism
void	setFeatureWrapper(XmlParticipantEvidence.JAXBFeatureWrapper jaxbFeatureWrapper)	setFeatureWrapper.
void	setJAXBAttributeWrapper(AbstractXmlParticipant.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBBiologicalRole(XmlCvTerm bioRole)	Sets the value of the biologicalRole property.
void	setJAXBConfidenceWrapper(XmlParticipantEvidence.JAXBConfidenceWrapper wrapper)	setJAXBConfidenceWrapper.
void	setJAXBExperimentalPreparationWrapper(XmlParticipantEvidence.JAXBExperimentalPreparationWrapper wrapper)	setJAXBExperimentalPreparationWrapper.
void	setJAXBExperimentalRoleWrapper(XmlParticipantEvidence.JAXBExperimentalRoleWrapper wrapper)	setJAXBExperimentalRoleWrapper.
void	setJAXBHostOrganismWrapper(XmlParticipantEvidence.JAXBHostOrganismWrapper wrapper)	setJAXBHostOrganismWrapper.
void	setJAXBId(int value)	setJAXBId.
void	setJAXBInteractionRef(Integer value)	Sets the value of the interactionRef property.
void	setJAXBInteractor(DefaultXmlInteractor interactor)	setJAXBInteractor.
void	setJAXBInteractorCandidates(XmlParticipantEvidence.JAXBInteractorCandidatesWrapper pool)	setJAXBInteractorCandidates.
void	setJAXBInteractorRef(Integer value)	Sets the value of the interactorRef property.
void	setJAXBNames(NamesContainer value)	Sets the value of the namesContainer property.
void	setJAXBParameterWrapper(XmlParticipantEvidence.JAXBParameterWrapper wrapper)	setJAXBParameterWrapper.
void	setJAXBParticipantIdentificationMethodWrapper(XmlParticipantEvidence.JAXBParticipantIdentificationWrapper wrapper)	setJAXBParticipantIdentificationMethodWrapper.
void	setJAXBStoichiometry(XmlStoichiometry stoichiometry)	setJAXBStoichiometry.
void	setJAXBStoichiometryRange(XmlStoichiometryRange stoichiometry)	setJAXBStoichiometryRange.
void	setJAXBXref(XrefContainer value)	Sets the value of the xrefContainer property.
protected void	setOriginalXmlInteraction(ExtendedPsiXmlInteractionEvidence i)	setOriginalXmlInteraction.

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

addAllFeatures, addFeature, getCausalRelationships, getChangeListener, getFeatures, getId, getInteractor, getParticipantLocator, initialiseUnspecifiedInteractor, 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, getStoichiometry, removeAllFeatures, removeFeature, setChangeListener, setInteractor, setStoichiometry, setStoichiometry

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

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

getFullName, getShortName, setFullName, setShortName

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

getAliases, getAnnotations, getBiologicalEffect, getBiologicalRole, getInteraction, getXrefs, setBiologicalEffect, setBiologicalRole, setInteraction, setInteractionAndAddParticipant

Constructor Detail

XmlParticipantEvidence

public XmlParticipantEvidence()

Constructor for XmlParticipantEvidence.

XmlParticipantEvidence

public XmlParticipantEvidence(Interactor interactor)

Constructor for XmlParticipantEvidence.

Parameters:

interactor - a Interactor object.

XmlParticipantEvidence

public XmlParticipantEvidence(Interactor interactor,
                              CvTerm bioRole)

Constructor for XmlParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

XmlParticipantEvidence

public XmlParticipantEvidence(Interactor interactor,
                              Stoichiometry stoichiometry)

Constructor for XmlParticipantEvidence.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

XmlParticipantEvidence

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

Constructor for XmlParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

Method Detail

initialiseExperimentalPreparationWrapper

protected void initialiseExperimentalPreparationWrapper()

initialiseExperimentalPreparationWrapper.

initialiseExperimentalRoleWrapper

protected void initialiseExperimentalRoleWrapper()

initialiseExperimentalRoleWrapper.

initialiseConfidenceWrapper

protected void initialiseConfidenceWrapper()

initialiseConfidenceWrapper.

initialiseParameterWrapper

protected void initialiseParameterWrapper()

initialiseParameterWrapper.

initialiseIdentificationMethodWrapper

protected void initialiseIdentificationMethodWrapper()

initialiseIdentificationMethodWrapper.

initialiseHostOrganismWrapper

protected void initialiseHostOrganismWrapper()

initialiseHostOrganismWrapper.

initialiseExperimentalInteractorWrapper

protected void initialiseExperimentalInteractorWrapper()

initialiseExperimentalInteractorWrapper.

getExperimentalRole

public CvTerm getExperimentalRole()

getExperimentalRole.

Specified by:

getExperimentalRole in interface ParticipantEvidence

Returns:

a CvTerm object.

setExperimentalRole

public void setExperimentalRole(CvTerm expRole)

Sets the experimental role. If expRole is null, it should create a unspecified role (MI:0499)

Specified by:

setExperimentalRole in interface ParticipantEvidence

Parameters:

expRole - : experimental role

getIdentificationMethods

public Collection<CvTerm> getIdentificationMethods()

getIdentificationMethods.

Specified by:

getIdentificationMethods in interface ParticipantEvidence

Returns:

a Collection object.

getExperimentalPreparations

public Collection<CvTerm> getExperimentalPreparations()

getExperimentalPreparations.

Specified by:

getExperimentalPreparations in interface ParticipantEvidence

Returns:

a Collection object.

getExpressedInOrganism

public Organism getExpressedInOrganism()

getExpressedInOrganism.

Specified by:

getExpressedInOrganism in interface ParticipantEvidence

Returns:

a Organism object.

setExpressedInOrganism

public void setExpressedInOrganism(Organism organism)

Sets the expressed in organism

Specified by:

setExpressedInOrganism in interface ParticipantEvidence

Parameters:

organism - : expressed in organism

getConfidences

public Collection<Confidence> getConfidences()

getConfidences.

Specified by:

getConfidences in interface ParticipantEvidence

Returns:

a Collection object.

getParameters

public Collection<Parameter> getParameters()

getParameters.

Specified by:

getParameters in interface ParticipantEvidence

Returns:

a Collection object.

getHostOrganisms

public List<Organism> getHostOrganisms()

getHostOrganisms.

Specified by:

getHostOrganisms in interface ExtendedPsiXmlParticipantEvidence

Returns:

a List object.

getExperimentalInteractors

public List<AbstractExperimentalInteractor> getExperimentalInteractors()

getExperimentalInteractors.

Specified by:

getExperimentalInteractors in interface ExtendedPsiXmlParticipantEvidence

Returns:

a List object.

getExperimentalRoles

public List<CvTerm> getExperimentalRoles()

getExperimentalRoles.

Specified by:

getExperimentalRoles in interface ExtendedPsiXmlParticipantEvidence

Returns:

a List object.

setJAXBNames

public void setJAXBNames(NamesContainer value)

Sets the value of the namesContainer property.

Overrides:

setJAXBNames in class AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

Parameters:

value - allowed object is NamesContainer

setJAXBXref

public void setJAXBXref(XrefContainer value)

Sets the value of the xrefContainer property.

Overrides:

setJAXBXref in class AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

Parameters:

value - allowed object is XrefContainer

setJAXBInteractor

public void setJAXBInteractor(DefaultXmlInteractor interactor)

setJAXBInteractor.

Overrides:

setJAXBInteractor in class AbstractXmlEntity<FeatureEvidence>

Parameters:

interactor - a DefaultXmlInteractor object.

setJAXBInteractionRef

public void setJAXBInteractionRef(Integer value)

Sets the value of the interactionRef property.

Overrides:

setJAXBInteractionRef in class AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

Parameters:

value - allowed object is Integer

setJAXBInteractorRef

public void setJAXBInteractorRef(Integer value)

Sets the value of the interactorRef property.

Overrides:

setJAXBInteractorRef in class AbstractXmlEntity<FeatureEvidence>

Parameters:

value - allowed object is Integer

setJAXBBiologicalRole

public void setJAXBBiologicalRole(XmlCvTerm bioRole)

Sets the value of the biologicalRole property.

Overrides:

setJAXBBiologicalRole in class AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

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<InteractionEvidence,FeatureEvidence>

Parameters:

jaxbAttributeWrapper - a AbstractXmlParticipant.JAXBAttributeWrapper object.

setFeatureWrapper

public void setFeatureWrapper(XmlParticipantEvidence.JAXBFeatureWrapper jaxbFeatureWrapper)

setFeatureWrapper.

Parameters:

jaxbFeatureWrapper - a XmlParticipantEvidence.JAXBFeatureWrapper object.

setJAXBParticipantIdentificationMethodWrapper

public void setJAXBParticipantIdentificationMethodWrapper(XmlParticipantEvidence.JAXBParticipantIdentificationWrapper wrapper)

setJAXBParticipantIdentificationMethodWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBParticipantIdentificationWrapper object.

setJAXBExperimentalRoleWrapper

public void setJAXBExperimentalRoleWrapper(XmlParticipantEvidence.JAXBExperimentalRoleWrapper wrapper)

setJAXBExperimentalRoleWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBExperimentalRoleWrapper object.

setJAXBExperimentalPreparationWrapper

public void setJAXBExperimentalPreparationWrapper(XmlParticipantEvidence.JAXBExperimentalPreparationWrapper wrapper)

setJAXBExperimentalPreparationWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBExperimentalPreparationWrapper object.

setExperimentalInteractorWrapper

public void setExperimentalInteractorWrapper(XmlParticipantEvidence.JAXBExperimentalInteractorWrapper wrapper)

setExperimentalInteractorWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBExperimentalInteractorWrapper object.

setJAXBHostOrganismWrapper

public void setJAXBHostOrganismWrapper(XmlParticipantEvidence.JAXBHostOrganismWrapper wrapper)

setJAXBHostOrganismWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBHostOrganismWrapper object.

setJAXBParameterWrapper

public void setJAXBParameterWrapper(XmlParticipantEvidence.JAXBParameterWrapper wrapper)

setJAXBParameterWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBParameterWrapper object.

setJAXBConfidenceWrapper

public void setJAXBConfidenceWrapper(XmlParticipantEvidence.JAXBConfidenceWrapper wrapper)

setJAXBConfidenceWrapper.

Parameters:

wrapper - a XmlParticipantEvidence.JAXBConfidenceWrapper object.

setJAXBStoichiometry

public void setJAXBStoichiometry(XmlStoichiometry stoichiometry)

setJAXBStoichiometry.

Overrides:

setJAXBStoichiometry in class AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

Parameters:

stoichiometry - a XmlStoichiometry object.

setJAXBInteractorCandidates

public void setJAXBInteractorCandidates(XmlParticipantEvidence.JAXBInteractorCandidatesWrapper pool)

setJAXBInteractorCandidates.

Parameters:

pool - a XmlParticipantEvidence.JAXBInteractorCandidatesWrapper object.

setJAXBStoichiometryRange

public void setJAXBStoichiometryRange(XmlStoichiometryRange stoichiometry)

setJAXBStoichiometryRange.

Overrides:

setJAXBStoichiometryRange in class AbstractXmlParticipant<InteractionEvidence,FeatureEvidence>

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<FeatureEvidence>

Returns:

a FileSourceLocator object.

processAddedFeature

public void processAddedFeature(FeatureEvidence feature)

processAddedFeature.

Overrides:

processAddedFeature in class AbstractXmlEntity<FeatureEvidence>

Parameters:

feature - a F object.

setOriginalXmlInteraction

protected void setOriginalXmlInteraction(ExtendedPsiXmlInteractionEvidence i)

setOriginalXmlInteraction.

Parameters:

i - a ExtendedPsiXmlInteractionEvidence object.

getOriginalInteraction

protected ExtendedPsiXmlInteractionEvidence getOriginalInteraction()

Getter for the field originalInteraction.

Returns:

a ExtendedPsiXmlInteractionEvidence object.

initialiseFeatureWrapper

protected void initialiseFeatureWrapper()

initialiseFeatureWrapper.

Overrides:

initialiseFeatureWrapper in class AbstractXmlEntity<FeatureEvidence>