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

Class XmlExperimentalParticipantPoolWrapper

java.lang.Object

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

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

All Implemented Interfaces:

Iterable<ModelledParticipantCandidate>, Collection<ModelledParticipantCandidate>, FileSourceContext, Entity<ModelledFeature>, ModelledEntity, ModelledParticipant, ModelledParticipantPool, NamedParticipant<ModelledInteraction,ModelledFeature>, Participant<ModelledInteraction,ModelledFeature>, ParticipantPool<ModelledInteraction,ModelledFeature,ModelledParticipantCandidate>, ExtendedPsiXmlEntity<ModelledFeature>

public class XmlExperimentalParticipantPoolWrapper
extends XmlParticipantEvidenceWrapper
implements ModelledParticipantPool

Wrapper for Xml participants pools Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.

Since:

11/10/13

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
XmlExperimentalParticipantPoolWrapper(ExperimentalParticipantPool part, XmlInteractionEvidenceComplexWrapper wrapper)	Constructor for XmlExperimentalParticipantPoolWrapper.

Method Summary

Modifier and Type	Method	Description
boolean	add(ModelledParticipantCandidate modelledParticipantCandidate)
boolean	addAll(Collection<? extends ModelledParticipantCandidate> modelledParticipantCandidates)
void	clear()
boolean	contains(Object o)
boolean	containsAll(Collection<?> objects)
protected Collection<ModelledParticipantCandidate>	getCandidates()	getCandidates.
CvTerm	getType()	The pool type of this participant pool.
protected void	initialiseCandidates()	initialiseCandidates.
boolean	isEmpty()
Iterator<ModelledParticipantCandidate>	iterator()
boolean	remove(Object o)
boolean	removeAll(Collection<?> objects)
boolean	retainAll(Collection<?> objects)
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()
Object[]	toArray()
<T> T[]	toArray(T[] ts)

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

addAllFeatures, addFeature, getAliases, getAnnotations, getBiologicalEffect, getBiologicalRole, getCausalRelationships, getChangeListener, getFeatures, getFullName, getId, getInteraction, getInteractor, getShortName, getSourceLocator, getStoichiometry, getWrappedParticipant, getXrefs, initialiseFeatures, removeAllFeatures, removeFeature, setBiologicalEffect, setBiologicalRole, setChangeListener, setFullName, setId, setInteraction, setInteractionAndAddParticipant, setInteractor, setShortName, setSourceLocator, setStoichiometry, setStoichiometry, toString

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, getInteractor, getStoichiometry, removeAllFeatures, removeFeature, setChangeListener, setInteractor, 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

XmlExperimentalParticipantPoolWrapper

public XmlExperimentalParticipantPoolWrapper(ExperimentalParticipantPool part,
                                             XmlInteractionEvidenceComplexWrapper wrapper)

Constructor for XmlExperimentalParticipantPoolWrapper.

Parameters:

part - a ExperimentalParticipantPool object.

wrapper - a XmlInteractionEvidenceComplexWrapper object.

Method Detail

getCandidates

protected Collection<ModelledParticipantCandidate> getCandidates()

getCandidates.

Returns:

a Collection object.

initialiseCandidates

protected void initialiseCandidates()

initialiseCandidates.

getType

public CvTerm getType()

The pool type of this participant pool. It is a controlled vocabulary term and cannot be null. Ex: molecule set, candidate set, defined set, ...

Specified by:

getType in interface ParticipantPool<ModelledInteraction,ModelledFeature,ModelledParticipantCandidate>

Returns:

pool type

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)

Specified by:

setType in interface ParticipantPool<ModelledInteraction,ModelledFeature,ModelledParticipantCandidate>

Parameters:

type - : molecule type

size

public int size()

Specified by:

size in interface Collection<ModelledParticipantCandidate>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<ModelledParticipantCandidate>

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<ModelledParticipantCandidate>

iterator

public Iterator<ModelledParticipantCandidate> iterator()

Specified by:

iterator in interface Collection<ModelledParticipantCandidate>

Specified by:

iterator in interface Iterable<ModelledParticipantCandidate>

toArray

public Object[] toArray()

Specified by:

toArray in interface Collection<ModelledParticipantCandidate>

toArray

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

Specified by:

toArray in interface Collection<ModelledParticipantCandidate>

add

public boolean add(ModelledParticipantCandidate modelledParticipantCandidate)

Specified by:

add in interface Collection<ModelledParticipantCandidate>

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<ModelledParticipantCandidate>

containsAll

public boolean containsAll(Collection<?> objects)

Specified by:

containsAll in interface Collection<ModelledParticipantCandidate>

addAll

public boolean addAll(Collection<? extends ModelledParticipantCandidate> modelledParticipantCandidates)

Specified by:

addAll in interface Collection<ModelledParticipantCandidate>

removeAll

public boolean removeAll(Collection<?> objects)

Specified by:

removeAll in interface Collection<ModelledParticipantCandidate>

retainAll

public boolean retainAll(Collection<?> objects)

Specified by:

retainAll in interface Collection<ModelledParticipantCandidate>

clear

public void clear()

Specified by:

clear in interface Collection<ModelledParticipantCandidate>