Package psidev.psi.mi.jami.model.impl

Class AbstractParticipant<I extends Interaction,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.model.impl.AbstractEntity<F>

psidev.psi.mi.jami.model.impl.AbstractParticipant<I,F>

All Implemented Interfaces:

Entity<F>, Participant<I,F>

Direct Known Subclasses:

AbstractParticipantPool, DefaultModelledParticipant, DefaultParticipant, DefaultParticipantEvidence

public abstract class AbstractParticipant<I extends Interaction,F extends Feature>
extends AbstractEntity<F>
implements Participant<I,F>

Abstract class for Participant

Since:

09/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

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

Method Summary

Modifier and Type	Method	Description
boolean	addAllFeatures(Collection<? extends F> features)	This method will add all features and set the entity of the new features to this current entity
boolean	addFeature(F feature)	addFeature
Collection<Alias>	getAliases()	Getter for the field aliases.
Collection<Annotation>	getAnnotations()	Getter for the field annotations.
CvTerm	getBiologicalEffect()	Getter for the field biologicalEffect.
CvTerm	getBiologicalRole()	Getter for the field biologicalRole.
I	getInteraction()	Getter for the field interaction.
Collection<Xref>	getXrefs()	Getter for the field xrefs.
protected void	initialiseAliases()	initialiseAliases
protected void	initialiseAliasesWith(Collection<Alias> aliases)	initialiseAliasesWith
protected void	initialiseAnnotations()	initialiseAnnotations
protected void	initialiseAnnotationsWith(Collection<Annotation> annotations)	initialiseAnnotationsWith
protected void	initialiseXrefs()	initialiseXrefs
protected void	initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
boolean	removeAllFeatures(Collection<? extends F> features)	This method will remove all the features and set the entity of the removed features to null.
boolean	removeFeature(F feature)	removeFeature
void	setBiologicalEffect(CvTerm biologicalEffect)	setBiologicalEffect
void	setBiologicalRole(CvTerm bioRole)	Sets the biological role.
void	setInteraction(I interaction)	Setter for the field interaction.
void	setInteractionAndAddParticipant(I interaction)	setInteractionAndAddParticipant
String	toString()

Methods inherited from class psidev.psi.mi.jami.model.impl.AbstractEntity

getCausalRelationships, getChangeListener, getFeatures, getInteractor, getStoichiometry, initialiseCausalRelationships, initialiseCausalRelationshipsWith, initialiseFeatures, initialiseFeaturesWith, setChangeListener, setInteractor, setStoichiometry, setStoichiometry

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, getChangeListener, getFeatures, getInteractor, getStoichiometry, setChangeListener, setInteractor, setStoichiometry, setStoichiometry

Constructor Detail

AbstractParticipant

public AbstractParticipant(Interactor interactor)

Constructor for AbstractParticipant.

Parameters:

interactor - a Interactor object.

AbstractParticipant

public AbstractParticipant(Interactor interactor,
                           CvTerm bioRole)

Constructor for AbstractParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

AbstractParticipant

public AbstractParticipant(Interactor interactor,
                           Stoichiometry stoichiometry)

Constructor for AbstractParticipant.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

AbstractParticipant

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

Constructor for AbstractParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

AbstractParticipant

public AbstractParticipant(Interactor interactor,
                           CvTerm bioRole,
                           CvTerm biologicalEffect,
                           Stoichiometry stoichiometry)

Constructor for AbstractParticipant.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

biologicalEffect - a CvTerm object.

Method Detail

initialiseXrefs

protected void initialiseXrefs()

initialiseXrefs

initialiseAnnotations

protected void initialiseAnnotations()

initialiseAnnotations

initialiseAliases

protected void initialiseAliases()

initialiseAliases

initialiseXrefsWith

protected void initialiseXrefsWith(Collection<Xref> xrefs)

initialiseXrefsWith

Parameters:

xrefs - a Collection object.

initialiseAnnotationsWith

protected void initialiseAnnotationsWith(Collection<Annotation> annotations)

initialiseAnnotationsWith

Parameters:

annotations - a Collection object.

initialiseAliasesWith

protected void initialiseAliasesWith(Collection<Alias> aliases)

initialiseAliasesWith

Parameters:

aliases - a Collection object.

getBiologicalRole

public CvTerm getBiologicalRole()

Getter for the field biologicalRole.

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

Specified by:

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

Parameters:

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

getBiologicalEffect

public CvTerm getBiologicalEffect()

Getter for the field biologicalEffect.

Specified by:

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

Returns:

a CvTerm object.

setBiologicalEffect

public void setBiologicalEffect(CvTerm biologicalEffect)

setBiologicalEffect

Specified by:

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

Parameters:

biologicalEffect - a CvTerm object.

getXrefs

public Collection<Xref> getXrefs()

Getter for the field xrefs.

Specified by:

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

Returns:

a Collection object.

getAnnotations

public Collection<Annotation> getAnnotations()

Getter for the field annotations.

Specified by:

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

Returns:

a Collection object.

getAliases

public Collection<Alias> getAliases()

Getter for the field aliases.

Specified by:

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

Returns:

a Collection object.

addFeature

public boolean addFeature(F feature)

addFeature

Specified by:

addFeature in interface Entity<I extends Interaction>

Overrides:

addFeature in class AbstractEntity<F extends Feature>

Parameters:

feature - a F object.

Returns:

a boolean.

removeFeature

public boolean removeFeature(F feature)

removeFeature

Specified by:

removeFeature in interface Entity<I extends Interaction>

Overrides:

removeFeature in class AbstractEntity<F extends Feature>

Parameters:

feature - a F object.

Returns:

a boolean.

addAllFeatures

public boolean addAllFeatures(Collection<? extends F> 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 AbstractEntity<F extends Feature>

Parameters:

features - : features to add

Returns:

true if features are added to the list of features

removeAllFeatures

public boolean removeAllFeatures(Collection<? extends F> 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 AbstractEntity<F extends Feature>

Parameters:

features - : features to remove

Returns:

true if features are removed from the list of features

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.

toString

public String toString()

Overrides:

toString in class AbstractEntity<F extends Feature>