Package psidev.psi.mi.jami.xml.model.reference.xml254

Class AbstractParticipantRef<I extends Interaction,T extends Feature>

java.lang.Object

psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

psidev.psi.mi.jami.xml.model.reference.xml254.AbstractEntityRef<T>

psidev.psi.mi.jami.xml.model.reference.xml254.AbstractParticipantRef<I,T>

All Implemented Interfaces:

FileSourceContext, Entity<T>, NamedParticipant<I,T>, Participant<I,T>, ExtendedPsiXmlEntity<T>, XmlIdReference

public abstract class AbstractParticipantRef<I extends Interaction,T extends Feature>
extends AbstractEntityRef<T>
implements ExtendedPsiXmlEntity<T>, NamedParticipant<I,T>

Abstract participant reference

Since:

11/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

ref

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
AbstractParticipantRef(int ref)	Constructor for AbstractParticipantRef.

Method Summary

Modifier and Type	Method	Description
boolean	addAllFeatures(Collection<? extends T> features)	This method will add all features and set the entity of the new features to this current entity
boolean	addFeature(T feature)	addFeature.
Collection<Alias>	getAliases()	getAliases.
Collection<Annotation>	getAnnotations()	getAnnotations.
CvTerm	getBiologicalEffect()	The biological effect of the participant in a causal interaction.
CvTerm	getBiologicalRole()	getBiologicalRole.
EntityInteractorChangeListener	getChangeListener()	getChangeListener.
protected ExtendedPsiXmlParticipant<I,T>	getDelegate()	Getter for the field delegate.
Collection<T>	getFeatures()	getFeatures.
String	getFullName()	The full name of the entity.
int	getId()	getId.
I	getInteraction()	The interaction in which the participant is involved.
String	getShortName()	The short name of the entity.
Stoichiometry	getStoichiometry()	getStoichiometry.
Collection<Xref>	getXrefs()	getXrefs.
boolean	removeAllFeatures(Collection<? extends T> features)	This method will remove all the features and set the entity of the removed features to null.
boolean	removeFeature(T feature)	removeFeature.
void	setBiologicalEffect(CvTerm biologicalEffect)	Sets the biological effect of the participant in a causal interaction.
void	setBiologicalRole(CvTerm bioRole)	Sets the biological role.
void	setChangeListener(EntityInteractorChangeListener listener)	Sets the entity change listener
void	setFullName(String name)	Sets the full name of the entity
void	setId(int id)	setId.
void	setInteraction(I interaction)	Sets the interaction.
void	setInteractionAndAddParticipant(I interaction)	Sets the Interaction and add the new Participant to its list of Participants.
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)	setStoichiometry.
String	toString()	toString

Methods inherited from class psidev.psi.mi.jami.xml.model.reference.xml254.AbstractEntityRef

getCausalRelationships, getInteractor, initialiseParticipantDelegate, setDelegate, setInteractor

Methods inherited from class psidev.psi.mi.jami.xml.model.reference.AbstractXmlIdReference

getRef, registerForResolution

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

getCausalRelationships, getInteractor, setInteractor

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

getSourceLocator, setSourceLocator

Methods inherited from interface psidev.psi.mi.jami.xml.model.reference.XmlIdReference

resolve

Constructor Detail

AbstractParticipantRef

public AbstractParticipantRef(int ref)

Constructor for AbstractParticipantRef.

Parameters:

ref - a int.

Method Detail

setInteractionAndAddParticipant

public void setInteractionAndAddParticipant(I interaction)

Sets the Interaction and add the new Participant to its list of Participants. If the given interaction is null, it will remove the Participant from the previous interaction it was attached to

Specified by:

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

Parameters:

interaction - : interaction

getInteraction

public I getInteraction()

The interaction in which the participant is involved. It can be null if the participant is not attached to any interactions. It can happen if the participant has been removed from an interaction and is now invalid.

Specified by:

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

Returns:

the interaction

setInteraction

public void setInteraction(I interaction)

Sets the interaction.

Specified by:

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

Parameters:

interaction - : interaction

getBiologicalRole

public CvTerm getBiologicalRole()

getBiologicalRole.

Specified by:

getBiologicalRole in interface Participant<I extends Interaction,T 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

Specified by:

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

Parameters:

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

getBiologicalEffect

public CvTerm getBiologicalEffect()

The biological effect of the participant in a causal interaction. It is a controlled vocabulary term and can be null.

Specified by:

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

Returns:

the biological effect

setBiologicalEffect

public void setBiologicalEffect(CvTerm biologicalEffect)

Sets the biological effect of the participant in a causal interaction.

Specified by:

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

Parameters:

biologicalEffect - : biological effect

getXrefs

public Collection<Xref> getXrefs()

getXrefs.

Specified by:

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

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

getAnnotations.

Specified by:

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

Returns:

a Collection object.

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

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

Returns:

a Collection object.

getStoichiometry

public Stoichiometry getStoichiometry()

getStoichiometry.

Specified by:

getStoichiometry in interface Entity<I extends Interaction>

Overrides:

getStoichiometry in class AbstractEntityRef<T 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 AbstractEntityRef<T extends Feature>

Parameters:

stoichiometry - : mean stoichiometry value

setStoichiometry

public void setStoichiometry(Stoichiometry stoichiometry)

setStoichiometry.

Specified by:

setStoichiometry in interface Entity<I extends Interaction>

Overrides:

setStoichiometry in class AbstractEntityRef<T extends Feature>

Parameters:

stoichiometry - a Stoichiometry object.

getFeatures

public Collection<T> getFeatures()

getFeatures.

Specified by:

getFeatures in interface Entity<I extends Interaction>

Overrides:

getFeatures in class AbstractEntityRef<T extends Feature>

Returns:

a Collection object.

getChangeListener

public EntityInteractorChangeListener getChangeListener()

getChangeListener.

Specified by:

getChangeListener in interface Entity<I extends Interaction>

Overrides:

getChangeListener in class AbstractEntityRef<T extends Feature>

Returns:

a EntityInteractorChangeListener object.

setChangeListener

public void setChangeListener(EntityInteractorChangeListener listener)

Sets the entity change listener

Specified by:

setChangeListener in interface Entity<I extends Interaction>

Overrides:

setChangeListener in class AbstractEntityRef<T extends Feature>

Parameters:

listener - : the entity change listener

addFeature

public boolean addFeature(T feature)

addFeature.

Specified by:

addFeature in interface Entity<I extends Interaction>

Overrides:

addFeature in class AbstractEntityRef<T extends Feature>

Parameters:

feature - a T object.

Returns:

a boolean.

removeFeature

public boolean removeFeature(T feature)

removeFeature.

Specified by:

removeFeature in interface Entity<I extends Interaction>

Overrides:

removeFeature in class AbstractEntityRef<T extends Feature>

Parameters:

feature - a T object.

Returns:

a boolean.

addAllFeatures

public boolean addAllFeatures(Collection<? extends T> features)

This method will add all features and set the entity of the new features to this current entity

Specified by:

addAllFeatures in interface Entity<I extends Interaction>

Overrides:

addAllFeatures in class AbstractEntityRef<T extends Feature>

Parameters:

features - : features to add

Returns:

true if features are added to the list of features

removeAllFeatures

public boolean removeAllFeatures(Collection<? extends T> features)

This method will remove all the features and set the entity of the removed features to null.

Specified by:

removeAllFeatures in interface Entity<I extends Interaction>

Overrides:

removeAllFeatures in class AbstractEntityRef<T extends Feature>

Parameters:

features - : features to remove

Returns:

true if features are removed from the list of features

setId

public void setId(int id)

setId.

Specified by:

setId in interface ExtendedPsiXmlEntity<I extends Interaction>

Overrides:

setId in class AbstractEntityRef<T extends Feature>

Parameters:

id - a int.

getId

public int getId()

getId.

Specified by:

getId in interface ExtendedPsiXmlEntity<I extends Interaction>

Overrides:

getId in class AbstractEntityRef<T extends Feature>

Returns:

a int.

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,T 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,T 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,T 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,T extends Feature>

Parameters:

name - : full name

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractEntityRef<T extends Feature>

Returns:

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

getDelegate

protected ExtendedPsiXmlParticipant<I,T> getDelegate()

Getter for the field delegate.

Overrides:

getDelegate in class AbstractEntityRef<T extends Feature>

Returns:

a ExtendedPsiXmlSource object.