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

Class XmlExperimentalParticipantPool

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlParticipantPool<InteractionEvidence,FeatureEvidence,ExperimentalParticipantCandidate>

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

All Implemented Interfaces:

Iterable<ExperimentalParticipantCandidate>, Collection<ExperimentalParticipantCandidate>, EventListener, FileSourceContext, EntityInteractorChangeListener, Entity<FeatureEvidence>, ExperimentalEntity, ExperimentalParticipantPool, NamedParticipant<InteractionEvidence,FeatureEvidence>, Participant<InteractionEvidence,FeatureEvidence>, ParticipantEvidence, ParticipantPool<InteractionEvidence,FeatureEvidence,ExperimentalParticipantCandidate>, ExtendedPsiXmlEntity<FeatureEvidence>

public class XmlExperimentalParticipantPool
extends AbstractXmlParticipantPool<InteractionEvidence,FeatureEvidence,ExperimentalParticipantCandidate>
implements ExperimentalParticipantPool

Xml implementation of participant pool

Since:

02/09/14

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
XmlExperimentalParticipantPool()	Constructor for XmlExperimentalParticipantPool.
XmlExperimentalParticipantPool(AbstractXmlParticipant<InteractionEvidence,FeatureEvidence> delegate)	Constructor for XmlExperimentalParticipantPool.

Method Summary

Modifier and Type	Method	Description
Collection<Confidence>	getConfidences()	The confidences for this participant.
Collection<CvTerm>	getExperimentalPreparations()	The experimental preparations for this participant.
CvTerm	getExperimentalRole()	The experimental role of the participant.
Organism	getExpressedInOrganism()	The organisms in which the participant has been expressed.
Collection<CvTerm>	getIdentificationMethods()	The identification methods for this participant.
Collection<Parameter>	getParameters()	Numerical parameters associated with this participant.
protected void	initialiseDefaultDelegate()	initialiseDefaultDelegate.
void	setExperimentalRole(CvTerm expRole)	Sets the experimental role.
void	setExpressedInOrganism(Organism organism)	Sets the expressed in organism

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

add, addAll, addAllFeatures, addFeature, clear, contains, containsAll, getAliases, getAnnotations, getBiologicalEffect, getBiologicalRole, getCausalRelationships, getChangeListener, getDelegate, getFeatures, getFullName, getId, getInteraction, getInteractor, getJAXBInteractorCandidates, getShortName, getSourceLocator, getStoichiometry, getType, getXrefs, initialiseComponentCandidatesSet, initialiseComponentCandidatesSetWith, isEmpty, iterator, onInteractorUpdate, remove, removeAll, removeAllFeatures, removeFeature, retainAll, setBiologicalEffect, setBiologicalRole, setChangeListener, setDelegate, setFullName, setId, setInteraction, setInteractionAndAddParticipant, setInteractor, setJAXBType, setShortName, setSourceLocator, setStoichiometry, setStoichiometry, setType, size, toArray, toArray

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Collection

add, addAll, clear, contains, containsAll, equals, hashCode, isEmpty, iterator, parallelStream, remove, removeAll, removeIf, retainAll, size, spliterator, stream, toArray, toArray, 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 psidev.psi.mi.jami.datasource.FileSourceContext

toString

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

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

getType, setType

Constructor Detail

XmlExperimentalParticipantPool

public XmlExperimentalParticipantPool()

Constructor for XmlExperimentalParticipantPool.

XmlExperimentalParticipantPool

public XmlExperimentalParticipantPool(AbstractXmlParticipant<InteractionEvidence,FeatureEvidence> delegate)

Constructor for XmlExperimentalParticipantPool.

Parameters:

delegate - a AbstractXmlParticipant object.

Method Detail

initialiseDefaultDelegate

protected void initialiseDefaultDelegate()

initialiseDefaultDelegate.

Specified by:

initialiseDefaultDelegate in class AbstractXmlParticipantPool<InteractionEvidence,FeatureEvidence,ExperimentalParticipantCandidate>

getExperimentalRole

public CvTerm getExperimentalRole()

The experimental role of the participant. It is a controlled vocabulary term and cannot be null. It the experimental role role of a participant is not known or not relevant, the method should return unspecified role (MI:0499) Ex: bait, prey, ...

Specified by:

getExperimentalRole in interface ParticipantEvidence

Returns:

the experimental role

setExperimentalRole

public void setExperimentalRole(CvTerm expRole)

Sets the experimental role. If expRole is null, it should create a unspecified role (MI:0499)

Specified by:

setExperimentalRole in interface ParticipantEvidence

Parameters:

expRole - : experimental role

getIdentificationMethods

public Collection<CvTerm> getIdentificationMethods()

The identification methods for this participant. Each identification method is a controlled vocabulary term. The collection cannot be null. If the participant does not have any identification methods, this method should return an empty collection Ex: western blot, immunostaining, ...

Specified by:

getIdentificationMethods in interface ParticipantEvidence

Returns:

the participant identification method

getExperimentalPreparations

public Collection<CvTerm> getExperimentalPreparations()

The experimental preparations for this participant. Each experimental preparation is a controlled vocabulary term. The Collection cannot be null. If the participant does not have any experimental preparations, the method should return an empty Collection. Ex: engineered, cDNA library, ...

Specified by:

getExperimentalPreparations in interface ParticipantEvidence

Returns:

the experimental preparations.

getExpressedInOrganism

public Organism getExpressedInOrganism()

The organisms in which the participant has been expressed. It can be null if not relevant or same as the original source organism of the interactor Ex: human-hela cells, ...

Specified by:

getExpressedInOrganism in interface ParticipantEvidence

Returns:

the expressed in organism

setExpressedInOrganism

public void setExpressedInOrganism(Organism organism)

Sets the expressed in organism

Specified by:

setExpressedInOrganism in interface ParticipantEvidence

Parameters:

organism - : expressed in organism

getConfidences

public Collection<Confidence> getConfidences()

The confidences for this participant. The Collection cannot be null. If the participant does not have any confidences, the method should return an empty Collection. Ex: author based scores, statistical confidences, ...

Specified by:

getConfidences in interface ParticipantEvidence

Returns:

the confidences

getParameters

public Collection<Parameter> getParameters()

Numerical parameters associated with this participant. The Collection cannot be null. If the participant does not have any parameters, the method should return an empty Collection.

Specified by:

getParameters in interface ParticipantEvidence

Returns:

the parameters