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

Class AbstractXmlParticipant<I extends Interaction,F extends Feature>

java.lang.Object

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

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlParticipant<I,F>

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Entity<F>, NamedParticipant<I,F>, Participant<I,F>, ExtendedPsiXmlEntity<F>

Direct Known Subclasses:

XmlModelledParticipant, XmlParticipant, XmlParticipantEvidence

public abstract class AbstractXmlParticipant<I extends Interaction,F extends Feature>
extends AbstractXmlEntity<F>
implements FileSourceContext, com.sun.xml.bind.Locatable, ExtendedPsiXmlEntity<F>, NamedParticipant<I,F>

Abstract class for XmlParticipant

Since:

07/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbstractXmlParticipant.JAXBAttributeWrapper
static class	AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate>

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

AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature>

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

Method Summary

Modifier and Type	Method	Description
List<Alias>	getAliases()	Collection of aliases which give more information about the participant.
Collection<Annotation>	getAnnotations()	getAnnotations.
CvTerm	getBiologicalEffect()	Gets the value of the biologicalEffect property.
CvTerm	getBiologicalRole()	Gets the value of the biologicalRole property.
String	getFullName()	The full name of the entity.
I	getInteraction()	Getter for the field interaction.
AbstractXmlParticipantPool<I,F,? extends ParticipantCandidate>	getParticipantPool()	getParticipantPool.
String	getShortName()	The short name of the entity.
Stoichiometry	getStoichiometry()	getStoichiometry.
Collection<Xref>	getXrefs()	getXrefs.
protected void	initialiseAnnotationWrapper()	initialiseAnnotationWrapper.
protected void	initialiseStoichiometry()	initialiseStoichiometry.
void	setBiologicalEffect(CvTerm biologicalEffect)	Sets the biological effect of the participant in a causal interaction.
void	setBiologicalRole(CvTerm bioRole)	Sets the biological role.
void	setFullName(String name)	Sets the full name of the entity
void	setInteraction(I interaction)	Setter for the field interaction.
void	setInteractionAndAddParticipant(I interaction)	setInteractionAndAddParticipant.
void	setJAXBAttributeWrapper(AbstractXmlParticipant.JAXBAttributeWrapper jaxbAttributeWrapper)	setJAXBAttributeWrapper.
void	setJAXBBiologicalRole(XmlCvTerm bioRole)	Sets the value of the biologicalRole property.
void	setJAXBInteractionRef(Integer value)	Sets the value of the interactionRef property.
protected void	setJAXBInteractorCandidates(AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I,F,? extends ParticipantCandidate> value)	Sets the value of the interactor candidates 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.
void	setShortName(String name)	Sets the short name of an entity
void	setStoichiometry(Integer stoichiometry)	Sets the mean stoichiometry for this participant.
void	setStoichiometry(Stoichiometry stoichiometry)	Setter for the field stoichiometry.

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

addAllFeatures, addFeature, getCausalRelationships, getChangeListener, getFeatures, getId, getInteractor, getParticipantLocator, getSourceLocator, initialiseFeatureWrapper, initialiseUnspecifiedInteractor, processAddedFeature, removeAllFeatures, removeFeature, setChangeListener, setFeatureWrapper, setId, setInteractor, setJAXBInteractor, setJAXBInteractorRef, 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

getSourceLocator, setSourceLocator, toString

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

sourceLocation

Constructor Detail

AbstractXmlParticipant

public AbstractXmlParticipant()

Constructor for AbstractXmlParticipant.

AbstractXmlParticipant

public AbstractXmlParticipant(Interactor interactor)

Constructor for AbstractXmlParticipant.

Parameters:

interactor - a Interactor object.

AbstractXmlParticipant

public AbstractXmlParticipant(Interactor interactor,
                              CvTerm bioRole)

Constructor for AbstractXmlParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

AbstractXmlParticipant

public AbstractXmlParticipant(Interactor interactor,
                              Stoichiometry stoichiometry)

Constructor for AbstractXmlParticipant.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

AbstractXmlParticipant

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

Constructor for AbstractXmlParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

Method Detail

setInteractionAndAddParticipant

public void setInteractionAndAddParticipant(I interaction)

setInteractionAndAddParticipant.

Specified by:

setInteractionAndAddParticipant in interface Participant<I extends Interaction,F extends Feature>

Parameters:

interaction - a I object.

getInteraction

public I getInteraction()

Getter for the field interaction.

Specified by:

getInteraction in interface Participant<I extends Interaction,F extends Feature>

Returns:

a I object.

setInteraction

public void setInteraction(I interaction)

Setter for the field interaction.

Specified by:

setInteraction in interface Participant<I extends Interaction,F extends Feature>

Parameters:

interaction - a I object.

getShortName

public String getShortName()

The short name of the entity. It can be null or empty.

Specified by:

getShortName in interface NamedParticipant<I extends Interaction,F extends Feature>

Returns:

the short name

setShortName

public void setShortName(String name)

Sets the short name of an entity

Specified by:

setShortName in interface NamedParticipant<I extends Interaction,F extends Feature>

Parameters:

name - : short name

getFullName

public String getFullName()

The full name of the entity. It can be null

Specified by:

getFullName in interface NamedParticipant<I extends Interaction,F extends Feature>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the entity

Specified by:

setFullName in interface NamedParticipant<I extends Interaction,F extends Feature>

Parameters:

name - : full name

getAliases

public List<Alias> getAliases()

Collection of aliases which give more information about the participant. The set of aliases cannot be null. If the participant does not have any aliases, the method should return an empty Collection. Ex: author assigned name, ...

Specified by:

getAliases in interface Participant<I extends Interaction,F extends Feature>

Returns:

the xrefs

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

getXrefs in interface Participant<I extends Interaction,F extends Feature>

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

getAnnotations in interface Participant<I extends Interaction,F extends Feature>

Returns:

a Collection object.

getStoichiometry

public Stoichiometry getStoichiometry()

getStoichiometry.

Specified by:

getStoichiometry in interface Entity<I extends Interaction>

Overrides:

getStoichiometry in class AbstractXmlEntity<F extends Feature>

Returns:

a Stoichiometry object.

setStoichiometry

public void setStoichiometry(Integer stoichiometry)

Sets the mean stoichiometry for this participant.

Specified by:

setStoichiometry in interface Entity<I extends Interaction>

Overrides:

setStoichiometry in class AbstractXmlEntity<F extends Feature>

Parameters:

stoichiometry - : mean stoichiometry value

setStoichiometry

public void setStoichiometry(Stoichiometry stoichiometry)

Setter for the field stoichiometry.

Specified by:

setStoichiometry in interface Entity<I extends Interaction>

Overrides:

setStoichiometry in class AbstractXmlEntity<F extends Feature>

Parameters:

stoichiometry - a Stoichiometry object.

getBiologicalRole

public CvTerm getBiologicalRole()

Gets the value of the biologicalRole property.

Specified by:

getBiologicalRole in interface Participant<I extends Interaction,F extends Feature>

Returns:

a CvTerm object.

setBiologicalRole

public void setBiologicalRole(CvTerm bioRole)

Sets the biological role. If the bioRole is null, should create a bioRole Sets the value of the biologicalRole property.

Specified by:

setBiologicalRole in interface Participant<I extends Interaction,F extends Feature>

Parameters:

bioRole - : biological role unspecified role (MI:0499)

getBiologicalEffect

public CvTerm getBiologicalEffect()

Gets the value of the biologicalEffect property.

Specified by:

getBiologicalEffect in interface Participant<I extends Interaction,F extends Feature>

Returns:

a CvTerm object.

setBiologicalEffect

public void setBiologicalEffect(CvTerm biologicalEffect)

Sets the biological effect of the participant in a causal interaction. Sets the value of the biologicalEffect property.

Specified by:

setBiologicalEffect in interface Participant<I extends Interaction,F extends Feature>

Parameters:

biologicalEffect - : biological effect

setJAXBNames

public void setJAXBNames(NamesContainer value)

Sets the value of the namesContainer property.

Parameters:

value - allowed object is NamesContainer

setJAXBXref

public void setJAXBXref(XrefContainer value)

Sets the value of the xrefContainer property.

Parameters:

value - allowed object is XrefContainer

setJAXBBiologicalRole

public void setJAXBBiologicalRole(XmlCvTerm bioRole)

Sets the value of the biologicalRole property.

Parameters:

bioRole - allowed object is XmlCvTerm

setJAXBStoichiometry

public void setJAXBStoichiometry(XmlStoichiometry stoichiometry)

setJAXBStoichiometry.

Parameters:

stoichiometry - a XmlStoichiometry object.

setJAXBStoichiometryRange

public void setJAXBStoichiometryRange(XmlStoichiometryRange stoichiometry)

setJAXBStoichiometryRange.

Parameters:

stoichiometry - a XmlStoichiometryRange object.

setJAXBInteractionRef

public void setJAXBInteractionRef(Integer value)

Sets the value of the interactionRef property.

Parameters:

value - allowed object is Integer

getParticipantPool

public AbstractXmlParticipantPool<I,F,? extends ParticipantCandidate> getParticipantPool()

getParticipantPool.

Returns:

a AbstractXmlParticipantPool object.

setJAXBInteractorCandidates

protected void setJAXBInteractorCandidates(AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I,F,? extends ParticipantCandidate> value)

Sets the value of the interactor candidates property.

Parameters:

value - allowed object is Integer

setJAXBAttributeWrapper

public void setJAXBAttributeWrapper(AbstractXmlParticipant.JAXBAttributeWrapper jaxbAttributeWrapper)

setJAXBAttributeWrapper.

Parameters:

jaxbAttributeWrapper - a AbstractXmlParticipant.JAXBAttributeWrapper object.

initialiseStoichiometry

protected void initialiseStoichiometry()

initialiseStoichiometry.

initialiseAnnotationWrapper

protected void initialiseAnnotationWrapper()

initialiseAnnotationWrapper.