Package psidev.psi.mi.jami.crosslink.extension

Class CsvParticipantEvidence

java.lang.Object

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

psidev.psi.mi.jami.model.impl.AbstractParticipant<InteractionEvidence,FeatureEvidence>

psidev.psi.mi.jami.model.impl.DefaultParticipantEvidence

psidev.psi.mi.jami.crosslink.extension.CsvParticipantEvidence

All Implemented Interfaces:

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

public class CsvParticipantEvidence
extends DefaultParticipantEvidence
implements FileSourceContext

Crosslink CSV extension of ParticipantEvidence. It contains a FileSourceLocator

Since:

11/06/13

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
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(InteractionEvidence interaction, Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry)	Constructor for CsvParticipantEvidence.
CsvParticipantEvidence(Interactor interactor, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvParticipantEvidence.

Method Summary

Modifier and Type	Method	Description
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

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

getConfidences, getExperimentalPreparations, getExperimentalRole, getExpressedInOrganism, getIdentificationMethods, getParameters, initialiseConfidences, initialiseConfidencesWith, initialiseExperimentalPreparations, initialiseExperimentalPreparationsWith, initialiseIdentificationMethods, initialiseIdentificationMethodsWith, initialiseParameters, initialiseParametersWith, setExperimentalRole, setExpressedInOrganism

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, 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

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

Constructor Detail

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm bioRole,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

bioRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              Stoichiometry stoichiometry,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm bioRole,
                              Stoichiometry stoichiometry,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              Stoichiometry stoichiometry,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              Organism expressedIn,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(InteractionEvidence interaction,
                              Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              Stoichiometry stoichiometry,
                              Organism expressedIn,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interaction - a InteractionEvidence object.

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              CvTerm bioRole,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              Stoichiometry stoichiometry,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              Stoichiometry stoichiometry,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              Organism expressedIn,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              CvTerm bioRole,
                              CvTerm expRole,
                              Stoichiometry stoichiometry,
                              Organism expressedIn,
                              CvTerm participantIdentificationMethod)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

CsvParticipantEvidence

public CsvParticipantEvidence(Interactor interactor,
                              Stoichiometry stoichiometry)

Constructor for CsvParticipantEvidence.

Parameters:

interactor - a Interactor object.

stoichiometry - a Stoichiometry object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class DefaultParticipantEvidence

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties