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

Class AbstractParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>

java.lang.Object

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

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

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

All Implemented Interfaces:

Iterable<P>, Collection<P>, EventListener, EntityInteractorChangeListener, Entity<F>, Participant<I,F>, ParticipantPool<I,F,P>

Direct Known Subclasses:

DefaultExperimentalParticipantPool, DefaultModelledParticipantPool, DefaultParticipantPool

public abstract class AbstractParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>
extends AbstractParticipant<I,F>
implements ParticipantPool<I,F,P>, EntityInteractorChangeListener

Abstract class for Participant pool

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
AbstractParticipantPool(String poolName)	Constructor for AbstractParticipantPool.
AbstractParticipantPool(String poolName, CvTerm bioRole)	Constructor for AbstractParticipantPool.
AbstractParticipantPool(String poolName, CvTerm bioRole, Stoichiometry stoichiometry)	Constructor for AbstractParticipantPool.
AbstractParticipantPool(String poolName, Stoichiometry stoichiometry)	Constructor for AbstractParticipantPool.

Method Summary

Modifier and Type	Method	Description
boolean	add(P interactor)	add
boolean	addAll(Collection<? extends P> interactors)
void	clear()	clear
boolean	contains(Object o)
boolean	containsAll(Collection<?> objects)
InteractorPool	getInteractor()	Getter for the field interactor.
CvTerm	getType()	Getter for the field type.
protected void	initialiseComponentCandidatesSet()	initialiseComponentCandidatesSet
protected void	initialiseComponentCandidatesSetWith(Collection<P> candidates)	initialiseComponentCandidatesSetWith
boolean	isEmpty()	isEmpty
Iterator<P>	iterator()	iterator
void	onInteractorUpdate(Entity entity, Interactor oldInteractor)	onInteractorUpdate
boolean	remove(Object o)
boolean	removeAll(Collection<?> objects)
boolean	retainAll(Collection<?> objects)
void	setInteractor(Interactor interactor)	Sets the interactor
void	setType(CvTerm type)	Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304)
int	size()	size
Object[]	toArray()	toArray
<T> T[]	toArray(T[] ts)	toArray
String	toString()

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

addAllFeatures, addFeature, getAliases, getAnnotations, getBiologicalEffect, getBiologicalRole, getInteraction, getXrefs, initialiseAliases, initialiseAliasesWith, initialiseAnnotations, initialiseAnnotationsWith, initialiseXrefs, initialiseXrefsWith, removeAllFeatures, removeFeature, setBiologicalEffect, setBiologicalRole, setInteraction, setInteractionAndAddParticipant

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

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection

equals, hashCode, parallelStream, removeIf, spliterator, stream, toArray

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

addAllFeatures, addFeature, getCausalRelationships, getChangeListener, getFeatures, getStoichiometry, removeAllFeatures, removeFeature, setChangeListener, setStoichiometry, setStoichiometry

Methods inherited from interface java.lang.Iterable

forEach

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

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

Constructor Detail

AbstractParticipantPool

public AbstractParticipantPool(String poolName)

Constructor for AbstractParticipantPool.

Parameters:

poolName - a String object.

AbstractParticipantPool

public AbstractParticipantPool(String poolName,
                               CvTerm bioRole)

Constructor for AbstractParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

AbstractParticipantPool

public AbstractParticipantPool(String poolName,
                               Stoichiometry stoichiometry)

Constructor for AbstractParticipantPool.

Parameters:

poolName - a String object.

stoichiometry - a Stoichiometry object.

AbstractParticipantPool

public AbstractParticipantPool(String poolName,
                               CvTerm bioRole,
                               Stoichiometry stoichiometry)

Constructor for AbstractParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

Method Detail

initialiseComponentCandidatesSet

protected void initialiseComponentCandidatesSet()

initialiseComponentCandidatesSet

initialiseComponentCandidatesSetWith

protected void initialiseComponentCandidatesSetWith(Collection<P> candidates)

initialiseComponentCandidatesSetWith

Parameters:

candidates - a Collection object.

getInteractor

public InteractorPool getInteractor()

Getter for the field interactor.

Specified by:

getInteractor in interface Entity<I extends Interaction>

Overrides:

getInteractor in class AbstractEntity<F extends Feature>

Returns:

a Interactor object.

setInteractor

public void setInteractor(Interactor interactor)

Sets the interactor

Specified by:

setInteractor in interface Entity<I extends Interaction>

Overrides:

setInteractor in class AbstractEntity<F extends Feature>

Parameters:

interactor - : interactor

getType

public CvTerm getType()

Getter for the field type.

Specified by:

getType in interface ParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>

Returns:

a CvTerm object.

setType

public void setType(CvTerm type)

Sets the pool type for this participant pool If the given type is null, this method automatically sets the interactor type to 'molecule set' (MI:1304) Sets the component set type. Sets the type to molecule set (MI:1304) if the given type is null

Specified by:

setType in interface ParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate>

Parameters:

type - : molecule type

size

public int size()

size

Specified by:

size in interface Collection<I extends Interaction>

Returns:

a int.

isEmpty

public boolean isEmpty()

isEmpty

Specified by:

isEmpty in interface Collection<I extends Interaction>

Returns:

a boolean.

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<I extends Interaction>

iterator

public Iterator<P> iterator()

iterator

Specified by:

iterator in interface Collection<I extends Interaction>

Specified by:

iterator in interface Iterable<I extends Interaction>

Returns:

a Iterator object.

toArray

public Object[] toArray()

toArray

Specified by:

toArray in interface Collection<I extends Interaction>

Returns:

an array of Object objects.

toArray

public <T> T[] toArray(T[] ts)

toArray

Specified by:

toArray in interface Collection<I extends Interaction>

Type Parameters:

T - a T object.

Parameters:

ts - an array of T objects.

Returns:

an array of T objects.

add

public boolean add(P interactor)

add

Specified by:

add in interface Collection<I extends Interaction>

Parameters:

interactor - a P object.

Returns:

a boolean.

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<I extends Interaction>

containsAll

public boolean containsAll(Collection<?> objects)

Specified by:

containsAll in interface Collection<I extends Interaction>

addAll

public boolean addAll(Collection<? extends P> interactors)

Specified by:

addAll in interface Collection<I extends Interaction>

retainAll

public boolean retainAll(Collection<?> objects)

Specified by:

retainAll in interface Collection<I extends Interaction>

removeAll

public boolean removeAll(Collection<?> objects)

Specified by:

removeAll in interface Collection<I extends Interaction>

clear

public void clear()

clear

Specified by:

clear in interface Collection<I extends Interaction>

onInteractorUpdate

public void onInteractorUpdate(Entity entity,
                               Interactor oldInteractor)

onInteractorUpdate

Specified by:

onInteractorUpdate in interface EntityInteractorChangeListener

Parameters:

entity - : updated entity

oldInteractor - : old interactor

toString

public String toString()

Overrides:

toString in class AbstractParticipant<I extends Interaction,F extends Feature>