Package psidev.psi.mi.jami.model

Interface ParticipantEvidence

All Superinterfaces:

Entity<FeatureEvidence>, ExperimentalEntity, Participant<InteractionEvidence,FeatureEvidence>

All Known Subinterfaces:

ExperimentalParticipantPool, ExtendedPsiXmlParticipantEvidence

All Known Implementing Classes:

CsvExperimentalParticipantPool, CsvParticipantEvidence, DefaultExperimentalParticipantPool, DefaultNamedParticipantEvidence, DefaultParticipantEvidence, MitabParticipantEvidence, XmlExperimentalParticipantPool, XmlExperimentalParticipantPool, XmlExperimentalParticipantPool, XmlParticipantEvidence, XmlParticipantEvidence, XmlParticipantEvidence

public interface ParticipantEvidence
extends Participant<InteractionEvidence,FeatureEvidence>, ExperimentalEntity

Participant of an interaction which is supported by experimental evidences

Since:

07/12/12

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

Method Summary

Modifier and Type	Method	Description
<C extends Confidence> Collection<C>	getConfidences()	The confidences for this participant.
<C extends CvTerm> Collection<C>	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.
<C extends CvTerm> Collection<C>	getIdentificationMethods()	The identification methods for this participant.
<P extends Parameter> Collection<P>	getParameters()	Numerical parameters associated with this participant.
void	setExperimentalRole(CvTerm expRole)	Sets the experimental role.
void	setExpressedInOrganism(Organism organism)	Sets the expressed in organism

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.model.Participant

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

Method Detail

getExperimentalRole

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, ...

Returns:

the experimental role

setExperimentalRole

void setExperimentalRole(CvTerm expRole)

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

Parameters:

expRole - : experimental role

getIdentificationMethods

<C extends CvTerm> Collection<C> 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, ...

Type Parameters:

C - a C object

Returns:

the participant identification method

getExperimentalPreparations

<C extends CvTerm> Collection<C> 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, ...

Type Parameters:

C - a C object

Returns:

the experimental preparations.

getExpressedInOrganism

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, ...

Returns:

the expressed in organism

setExpressedInOrganism

void setExpressedInOrganism(Organism organism)

Sets the expressed in organism

Parameters:

organism - : expressed in organism

getConfidences

<C extends Confidence> Collection<C> 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, ...

Type Parameters:

C - a C object

Returns:

the confidences

getParameters

<P extends Parameter> Collection<P> 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.

Type Parameters:

P - a P object

Returns:

the parameters