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

Class CsvExperimentalParticipantPool

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<InteractionEvidence,FeatureEvidence,ExperimentalParticipantCandidate>

psidev.psi.mi.jami.model.impl.DefaultExperimentalParticipantPool

psidev.psi.mi.jami.crosslink.extension.CsvExperimentalParticipantPool

All Implemented Interfaces:

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

public class CsvExperimentalParticipantPool
extends DefaultExperimentalParticipantPool
implements FileSourceContext

Crosslink CSV extension of ParticipantEvidencePool. 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
CsvExperimentalParticipantPool(String poolName)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, Stoichiometry stoichiometry)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, CvTerm expRole, Stoichiometry stoichiometry, Organism expressedIn, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, CvTerm bioRole, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.
CsvExperimentalParticipantPool(InteractionEvidence interaction, String poolName, Stoichiometry stoichiometry, CvTerm participantIdentificationMethod)	Constructor for CsvExperimentalParticipantPool.

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.DefaultExperimentalParticipantPool

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.AbstractParticipantPool

add, addAll, clear, contains, containsAll, getInteractor, getType, initialiseComponentCandidatesSet, initialiseComponentCandidatesSetWith, isEmpty, iterator, onInteractorUpdate, remove, removeAll, retainAll, setInteractor, setType, size, toArray, toArray

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

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 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

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm bioRole,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

bioRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      Stoichiometry stoichiometry,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      Stoichiometry stoichiometry)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

stoichiometry - a Stoichiometry object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      Stoichiometry stoichiometry,
                                      Organism expressedIn,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      Organism expressedIn,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      Stoichiometry stoichiometry,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      Stoichiometry stoichiometry,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      CvTerm bioRole,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

bioRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(String poolName,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

poolName - a String object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm bioRole,
                                      Stoichiometry stoichiometry,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

bioRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      Stoichiometry stoichiometry,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      Organism expressedIn,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm object.

CsvExperimentalParticipantPool

public CsvExperimentalParticipantPool(InteractionEvidence interaction,
                                      String poolName,
                                      CvTerm bioRole,
                                      CvTerm expRole,
                                      Stoichiometry stoichiometry,
                                      Organism expressedIn,
                                      CvTerm participantIdentificationMethod)

Constructor for CsvExperimentalParticipantPool.

Parameters:

interaction - a InteractionEvidence object.

poolName - a String object.

bioRole - a CvTerm object.

expRole - a CvTerm object.

stoichiometry - a Stoichiometry object.

expressedIn - a Organism object.

participantIdentificationMethod - a CvTerm 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 DefaultExperimentalParticipantPool

Returns:

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