Uses of Interface
psidev.psi.mi.jami.model.Xref

Packages that use Xref

Package	Description
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.bridges.obo
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher.impl.full
psidev.psi.mi.jami.enricher.impl.minimal
psidev.psi.mi.jami.enricher.listener.impl
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.enricher.util
psidev.psi.mi.jami.factory
psidev.psi.mi.jami.imex.listener
psidev.psi.mi.jami.imex.listener.impl
psidev.psi.mi.jami.json
psidev.psi.mi.jami.json.binary.elements
psidev.psi.mi.jami.json.elements
psidev.psi.mi.jami.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.tab.io.writer.feeder
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.comparator
psidev.psi.mi.jami.utils.comparator.cv
psidev.psi.mi.jami.utils.comparator.feature
psidev.psi.mi.jami.utils.comparator.interaction
psidev.psi.mi.jami.utils.comparator.interactor
psidev.psi.mi.jami.utils.comparator.publication
psidev.psi.mi.jami.utils.comparator.xref
psidev.psi.mi.jami.xml.io.writer.elements.impl
psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended
psidev.psi.mi.jami.xml.model.extension
psidev.psi.mi.jami.xml.model.extension.binary
psidev.psi.mi.jami.xml.model.extension.binary.xml30
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300
psidev.psi.mi.jami.xml.model.reference
psidev.psi.mi.jami.xml.model.reference.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300

Uses of Xref in psidev.psi.mi.jami.binary.impl

Methods in psidev.psi.mi.jami.binary.impl that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractBinaryInteractionWrapper.getIdentifiers()	getIdentifiers
Collection<Xref>	AbstractBinaryInteractionWrapper.getXrefs()	getXrefs

Methods in psidev.psi.mi.jami.binary.impl with parameters of type Xref

Modifier and Type	Method	Description
protected void	DefaultBinaryInteractionEvidence.processAddedXrefEvent(Xref added)	processAddedXrefEvent
protected void	DefaultBinaryInteractionEvidence.processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent

Uses of Xref in psidev.psi.mi.jami.bridges.obo

Methods in psidev.psi.mi.jami.bridges.obo with parameters of type Xref

Modifier and Type	Method	Description
protected abstract T	AbstractOboLoader.instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.
protected CvTerm	CvOboLoader.instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.
protected OntologyTerm	OntologyOboLoader.instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.
protected Source	SourceOboLoader.instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.

Uses of Xref in psidev.psi.mi.jami.bridges.ols

Methods in psidev.psi.mi.jami.bridges.ols that return Xref

Modifier and Type	Method	Description
protected Xref	AbstractOlsFetcher.createXref(String identifier, String miOntologyName)	createXref.
protected Xref	LazyCvTerm.getOriginalXref()	Getter for the field originalXref.

Methods in psidev.psi.mi.jami.bridges.ols that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	LazyCvTerm.getXrefs()	getXrefs.

Methods in psidev.psi.mi.jami.bridges.ols with parameters of type Xref

Modifier and Type	Method	Description
protected void	LazyCvTerm.initialiseMetaData(Xref xref)	Retrieve the metadata for an entry.
protected abstract T	AbstractOlsFetcher.instantiateCvTerm(String termName, Xref identity, String olsOntologyName)	instantiateCvTerm.
protected CvTerm	OlsCvTermFetcher.instantiateCvTerm(String termName, Xref identity, String ontologyName)	instantiateCvTerm.
protected OntologyTerm	OlsOntologyTermFetcher.instantiateCvTerm(String termName, Xref identity, String ontologyName)	instantiateCvTerm.
protected Source	OlsSourceFetcher.instantiateCvTerm(String termName, Xref identity, String ontologyName)	instantiateCvTerm.

Constructors in psidev.psi.mi.jami.bridges.ols with parameters of type Xref

Constructor	Description
LazyCvTerm(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient olsClient, String fullName, Xref identityRef, String ontologyName)	Constructor for LazyCvTerm.
LazyOntologyTerm(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient olsClient, String fullName, Xref identityRef, String ontologyName)	Constructor for LazyOntologyTerm.
LazySource(uk.ac.ebi.pride.utilities.ols.web.service.client.OLSClient olsClient, String fullName, Xref identityRef, String ontologyName)	Constructor for LazySource.

Uses of Xref in psidev.psi.mi.jami.crosslink.extension

Classes in psidev.psi.mi.jami.crosslink.extension that implement Xref

Modifier and Type	Class	Description
class	CsvXref	CSV extension for Xref.

Constructors in psidev.psi.mi.jami.crosslink.extension with parameters of type Xref

Constructor	Description
CsvInteractionEvidence(String shortName, CvTerm type, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(String shortName, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Xref imexId)	Constructor for CsvInteractionEvidence.
CsvProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, String fullName, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, CvTerm type, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, Organism organism, Xref uniqueId)	Constructor for CsvProtein.
CsvProtein(String name, Xref uniqueId)	Constructor for CsvProtein.

Uses of Xref in psidev.psi.mi.jami.enricher.impl.full

Methods in psidev.psi.mi.jami.enricher.impl.full with parameters of type Xref

Modifier and Type	Method	Description
void	FullFeatureEvidenceEnricher.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FullFeatureEvidenceUpdater.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FullFeatureUpdater.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FullFeatureEvidenceEnricher.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FullFeatureEvidenceUpdater.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FullFeatureUpdater.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FullFeatureEvidenceEnricher.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FullFeatureEvidenceUpdater.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FullFeatureUpdater.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FullFeatureEvidenceEnricher.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FullFeatureEvidenceUpdater.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FullFeatureUpdater.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Xref in psidev.psi.mi.jami.enricher.impl.minimal

Methods in psidev.psi.mi.jami.enricher.impl.minimal with parameters of type Xref

Modifier and Type	Method	Description
void	MinimalFeatureEnricher.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	MinimalFeatureEvidenceUpdater.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	MinimalFeatureEnricher.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	MinimalFeatureEvidenceUpdater.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	MinimalFeatureEnricher.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	MinimalFeatureEvidenceUpdater.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	MinimalFeatureEnricher.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	MinimalFeatureEvidenceUpdater.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
protected void	MinimalProteinEnricher.processDeadUniprotIdentity(Protein proteinToEnrich, Xref uniprotIdentity)	processDeadUniprotIdentity.

Uses of Xref in psidev.psi.mi.jami.enricher.listener.impl

Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type Xref

Modifier and Type	Method	Description
void	CvTermEnricherListenerManager.onAddedIdentifier(CvTerm cv, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FeatureEnricherListenerManager.onAddedIdentifier(T feature, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	InteractionEnricherListenerManager.onAddedIdentifier(I o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	InteractorEnricherListenerManager.onAddedIdentifier(T interactor, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	PublicationEnricherListenerManager.onAddedIdentifier(Publication publication, Xref addedXref)	Listen to the event where an identifier has been added to the protein identifiers.
void	CvTermEnricherListenerManager.onAddedXref(CvTerm cv, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	ExperimentEnricherListenerManager.onAddedXref(Experiment experiment, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FeatureEnricherListenerManager.onAddedXref(T feature, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractionEnricherListenerManager.onAddedXref(I o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractorEnricherListenerManager.onAddedXref(T interactor, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	ParticipantEnricherListenerManager.onAddedXref(P o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationEnricherListenerManager.onAddedXref(Publication publication, Xref addedXref)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationEnricherListenerManager.onImexIdentifierUpdate(Publication publication, Xref addedXref)	onImexIdentifierUpdate
void	CvTermEnricherListenerManager.onRemovedIdentifier(CvTerm cv, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FeatureEnricherListenerManager.onRemovedIdentifier(T feature, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	InteractionEnricherListenerManager.onRemovedIdentifier(I o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	InteractorEnricherListenerManager.onRemovedIdentifier(T interactor, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	PublicationEnricherListenerManager.onRemovedIdentifier(Publication publication, Xref removedXref)	Listen to the event where an identifier has been removed from the protein identifiers.
void	CvTermEnricherListenerManager.onRemovedXref(CvTerm cv, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	ExperimentEnricherListenerManager.onRemovedXref(Experiment experiment, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FeatureEnricherListenerManager.onRemovedXref(T feature, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	InteractionEnricherListenerManager.onRemovedXref(I o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	InteractorEnricherListenerManager.onRemovedXref(T interactor, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	ParticipantEnricherListenerManager.onRemovedXref(P o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	PublicationEnricherListenerManager.onRemovedXref(Publication publication, Xref removedXref)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Xref in psidev.psi.mi.jami.enricher.listener.impl.writer

Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type Xref

Modifier and Type	Method	Description
void	CvTermEnricherStatisticsWriter.onAddedIdentifier(CvTerm cv, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FeatureEnricherStatisticsWriter.onAddedIdentifier(T feature, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	InteractionEnricherStatisticsWriter.onAddedIdentifier(I o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	InteractorEnricherStatisticsWriter.onAddedIdentifier(T interactor, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	PublicationEnricherStatisticsWriter.onAddedIdentifier(Publication publication, Xref addedXref)	Listen to the event where an identifier has been added to the protein identifiers.
void	CvTermEnricherStatisticsWriter.onAddedXref(CvTerm cv, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	ExperimentEnricherStatisticsWriter.onAddedXref(Experiment o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FeatureEnricherStatisticsWriter.onAddedXref(T feature, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractionEnricherStatisticsWriter.onAddedXref(I o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractorEnricherStatisticsWriter.onAddedXref(T interactor, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	ParticipantEnricherStatisticsWriter.onAddedXref(P o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationEnricherStatisticsWriter.onAddedXref(Publication publication, Xref addedXref)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationEnricherStatisticsWriter.onImexIdentifierUpdate(Publication publication, Xref addedXref)	onImexIdentifierUpdate
void	CvTermEnricherStatisticsWriter.onRemovedIdentifier(CvTerm cv, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FeatureEnricherStatisticsWriter.onRemovedIdentifier(T feature, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	InteractionEnricherStatisticsWriter.onRemovedIdentifier(I o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	InteractorEnricherStatisticsWriter.onRemovedIdentifier(T interactor, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	PublicationEnricherStatisticsWriter.onRemovedIdentifier(Publication publication, Xref removedXref)	Listen to the event where an identifier has been removed from the protein identifiers.
void	CvTermEnricherStatisticsWriter.onRemovedXref(CvTerm cv, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	ExperimentEnricherStatisticsWriter.onRemovedXref(Experiment o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FeatureEnricherStatisticsWriter.onRemovedXref(T feature, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	InteractionEnricherStatisticsWriter.onRemovedXref(I o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	InteractorEnricherStatisticsWriter.onRemovedXref(T interactor, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	ParticipantEnricherStatisticsWriter.onRemovedXref(P o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	PublicationEnricherStatisticsWriter.onRemovedXref(Publication publication, Xref removedXref)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Xref in psidev.psi.mi.jami.enricher.util

Method parameters in psidev.psi.mi.jami.enricher.util with type arguments of type Xref

Modifier and Type	Method	Description
static <T> void	EnricherUtils.mergeXrefs(T termToEnrich, Collection<Xref> toEnrichXrefs, Collection<Xref> fetchedXrefs, boolean remove, boolean isIdentifier, XrefsChangeListener<T> xrefListener, IdentifiersChangeListener<T> identifierListener)	Takes two lists of Xrefs and produces a list of those to add and those to remove.

Uses of Xref in psidev.psi.mi.jami.factory

Method parameters in psidev.psi.mi.jami.factory with type arguments of type Xref

Modifier and Type	Method	Description
Interactor	DefaultInteractorFactory.createInteractorFromIdentityXrefs(Collection<? extends Xref> xrefs, String name)	Return the proper instance of the interactor if the database is recognized (the interactor will be returned on the first database which is recognized).
Interactor	InteractorFactory.createInteractorFromIdentityXrefs(Collection<? extends Xref> xrefs, String name)	Return the proper instance of the interactor if the database is recognized (the interactor will be returned on the first database which is recognized).

Uses of Xref in psidev.psi.mi.jami.imex.listener

Method parameters in psidev.psi.mi.jami.imex.listener with type arguments of type Xref

Modifier and Type	Method	Description
void	ExperimentImexEnricherListener.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	InteractionImexEnricherListener.onImexIdConflicts(InteractionEvidence originalInteraction, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	PublicationImexEnricherListener.onImexIdConflicts(Publication originalPublication, Collection<Xref> conflictingXrefs)	onImexIdConflicts.

Uses of Xref in psidev.psi.mi.jami.imex.listener.impl

Method parameters in psidev.psi.mi.jami.imex.listener.impl with type arguments of type Xref

Modifier and Type	Method	Description
void	ExperimentImexEnricherListenerManager.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	ExperimentImexEnricherLogger.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	ExperimentImexEnricherStatisticsWriter.onImexIdConflicts(Experiment originalExperiment, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	InteractionEvidenceImexEnricherListenerManager.onImexIdConflicts(InteractionEvidence originalInteraction, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	InteractionEvidenceImexEnricherLogger.onImexIdConflicts(InteractionEvidence interactionEvidence, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	InteractionEvidenceImexEnricherStatisticsWriter.onImexIdConflicts(InteractionEvidence interaction, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	PublicationImexEnricherListenerManager.onImexIdConflicts(Publication originalPublication, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	PublicationImexEnricherLogger.onImexIdConflicts(Publication originalPublication, Collection<Xref> conflictingXrefs)	onImexIdConflicts.
void	PublicationImexEnricherStatisticsWriter.onImexIdConflicts(Publication originalPublication, Collection<Xref> conflictingXrefs)	onImexIdConflicts.

Uses of Xref in psidev.psi.mi.jami.json

Methods in psidev.psi.mi.jami.json with parameters of type Xref

Modifier and Type	Method	Description
static String[]	MIJsonUtils.extractBinaryInteractionId(Xref ref, BinaryInteraction interaction, Integer number)	extractBinaryInteractionId.
static String[]	MIJsonUtils.extractInteractionId(Xref ref, Interaction interaction)	extractInteractionId.
static String[]	MIJsonUtils.extractInteractorId(Xref ref, Interactor interactor)	extractInteractorId.

Uses of Xref in psidev.psi.mi.jami.json.binary.elements

Methods in psidev.psi.mi.jami.json.binary.elements with parameters of type Xref

Modifier and Type	Method	Description
protected String[]	SimpleJsonBinaryInteractionEvidenceWriter.generateInteractionIdentifier(BinaryInteractionEvidence object, Xref preferredIdentifier)	generateInteractionIdentifier.
protected String[]	SimpleJsonBinaryInteractionWriter.generateInteractionIdentifier(I object, Xref preferredIdentifier)	generateInteractionIdentifier.
protected String[]	SimpleJsonModelledBinaryInteractionWriter.generateInteractionIdentifier(ModelledBinaryInteraction object, Xref preferredIdentifier)	generateInteractionIdentifier.

Uses of Xref in psidev.psi.mi.jami.json.elements

Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type Xref

Modifier and Type	Method	Description
JsonElementWriter<Xref>	SimpleJsonFeatureWriter.getIdentifierWriter()	Getter for the field identifierWriter.
JsonElementWriter<Xref>	SimpleJsonInteractionWriter.getIdentifierWriter()	Getter for the field identifierWriter.
JsonElementWriter<Xref>	SimpleJsonInteractorWriter.getIdentifierWriter()	Getter for the field identifierWriter.
JsonElementWriter<Xref>	SimpleJsonPublicationWriter.getIdentifierWriter()	Getter for the field identifierWriter.

Methods in psidev.psi.mi.jami.json.elements with parameters of type Xref

Modifier and Type	Method	Description
protected String[]	SimpleJsonInteractionWriter.generateInteractionIdentifier(I object, Xref preferredIdentifier)	generateInteractionIdentifier.
void	SimpleJsonIdentifierWriter.write(Xref object)	write.

Method parameters in psidev.psi.mi.jami.json.elements with type arguments of type Xref

Modifier and Type	Method	Description
void	SimpleJsonFeatureWriter.setIdentifierWriter(JsonElementWriter<Xref> identifierWriter)	Setter for the field identifierWriter.
void	SimpleJsonInteractionWriter.setIdentifierWriter(JsonElementWriter<Xref> identifierWriter)	Setter for the field identifierWriter.
void	SimpleJsonInteractorWriter.setIdentifierWriter(JsonElementWriter<Xref> identifierWriter)	Setter for the field identifierWriter.
void	SimpleJsonPublicationWriter.setIdentifierWriter(JsonElementWriter<Xref> identifierWriter)	Setter for the field identifierWriter.

Uses of Xref in psidev.psi.mi.jami.listener

Methods in psidev.psi.mi.jami.listener with parameters of type Xref

Modifier and Type	Method	Description
void	IdentifiersChangeListener.onAddedIdentifier(T o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	XrefsChangeListener.onAddedXref(T o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationChangeListener.onImexIdentifierUpdate(Publication publication, Xref addedXref)	onImexIdentifierUpdate
void	IdentifiersChangeListener.onRemovedIdentifier(T o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	XrefsChangeListener.onRemovedXref(T o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Xref in psidev.psi.mi.jami.listener.impl

Methods in psidev.psi.mi.jami.listener.impl with parameters of type Xref

Modifier and Type	Method	Description
void	CvTermChangeLogger.onAddedIdentifier(CvTerm cv, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FeatureChangeLogger.onAddedIdentifier(T protein, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	InteractionChangeLogger.onAddedIdentifier(T interaction, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	InteractorChangeLogger.onAddedIdentifier(T protein, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	PublicationChangeLogger.onAddedIdentifier(Publication publication, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	CvTermChangeLogger.onAddedXref(CvTerm cv, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	ExperimentChangeLogger.onAddedXref(Experiment experiment, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FeatureChangeLogger.onAddedXref(T protein, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractionChangeLogger.onAddedXref(T interaction, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	InteractorChangeLogger.onAddedXref(T protein, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	ParticipantChangeLogger.onAddedXref(T protein, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationChangeLogger.onAddedXref(Publication publication, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	PublicationChangeLogger.onImexIdentifierUpdate(Publication publication, Xref oldId)	onImexIdentifierUpdate
void	CvTermChangeLogger.onRemovedIdentifier(CvTerm cv, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FeatureChangeLogger.onRemovedIdentifier(T protein, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	InteractionChangeLogger.onRemovedIdentifier(T interaction, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	InteractorChangeLogger.onRemovedIdentifier(T protein, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	PublicationChangeLogger.onRemovedIdentifier(Publication publication, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	CvTermChangeLogger.onRemovedXref(CvTerm cv, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	ExperimentChangeLogger.onRemovedXref(Experiment experiment, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FeatureChangeLogger.onRemovedXref(T protein, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	InteractionChangeLogger.onRemovedXref(T interaction, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	InteractorChangeLogger.onRemovedXref(T protein, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	ParticipantChangeLogger.onRemovedXref(T protein, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	PublicationChangeLogger.onRemovedXref(Publication publication, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.

Uses of Xref in psidev.psi.mi.jami.model

Methods in psidev.psi.mi.jami.model with type parameters of type Xref

Modifier and Type	Method	Description
<X extends Xref> Collection<X>	CvTerm.getIdentifiers()	The collection of identifiers which identifies this CvTerm.
<X extends Xref> Collection<X>	Feature.getIdentifiers()	Collection of External identifiers which describes this feature.
<X extends Xref> Collection<X>	Interaction.getIdentifiers()	The identifiers for an interaction.
<X extends Xref> Collection<X>	Interactor.getIdentifiers()	Set of identifiers for this interactor.
<X extends Xref> Collection<X>	Publication.getIdentifiers()	The publication identifiers.
<X extends Xref> Collection<X>	CvTerm.getXrefs()	Collection of cross references describing the CvTerm.
<X extends Xref> Collection<X>	Experiment.getXrefs()	Collection of cross references for an experiment which can give more information about the experiment.
<X extends Xref> Collection<X>	Feature.getXrefs()	Collection of cross references which give more information about the feature.
<X extends Xref> Collection<X>	Interaction.getXrefs()	The external cross references for an interaction.
<X extends Xref> Collection<X>	Interactor.getXrefs()	Collection of other xrefs that give more information about the interactor.
<X extends Xref> Collection<X>	Participant.getXrefs()	Collection of cross references which give more information about the participant.
<X extends Xref> Collection<X>	Publication.getXrefs()	Other cross references which give more information about the publication.
<X extends Xref> Collection<X>	ResultingSequence.getXrefs()	The collection of external database cross-references for this resulting sequence portion.

Methods in psidev.psi.mi.jami.model that return Xref

Modifier and Type	Method	Description
Xref	Interactor.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.

Uses of Xref in psidev.psi.mi.jami.model.impl

Classes in psidev.psi.mi.jami.model.impl that implement Xref

Modifier and Type	Class	Description
class	DefaultXref	Default implementation for Xref Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousXrefComparator

Methods in psidev.psi.mi.jami.model.impl that return Xref

Modifier and Type	Method	Description
Xref	DefaultBioactiveEntity.getPreferredIdentifier()	getPreferredIdentifier
Xref	DefaultGene.getPreferredIdentifier()	getPreferredIdentifier
Xref	DefaultInteractor.getPreferredIdentifier()	getPreferredIdentifier
Xref	DefaultNucleicAcid.getPreferredIdentifier()	getPreferredIdentifier
Xref	DefaultProtein.getPreferredIdentifier()	getPreferredIdentifier

Methods in psidev.psi.mi.jami.model.impl that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractFeature.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	AbstractInteraction.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	DefaultComplex.getIdentifiers()	getIdentifiers
Collection<Xref>	DefaultCvTerm.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	DefaultInteractor.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	DefaultPublication.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	AbstractFeature.getXrefs()	Getter for the field xrefs.
Collection<Xref>	AbstractInteraction.getXrefs()	Getter for the field xrefs.
Collection<Xref>	AbstractParticipant.getXrefs()	Getter for the field xrefs.
Collection<Xref>	DefaultComplex.getXrefs()	getXrefs
Collection<Xref>	DefaultCvTerm.getXrefs()	Getter for the field xrefs.
Collection<Xref>	DefaultExperiment.getXrefs()	Getter for the field xrefs.
Collection<Xref>	DefaultInteractor.getXrefs()	Getter for the field xrefs.
Collection<Xref>	DefaultPublication.getXrefs()	Getter for the field xrefs.
Collection<Xref>	DefaultResultingSequence.getXrefs()	Getter for the field xrefs.

Methods in psidev.psi.mi.jami.model.impl with parameters of type Xref

Modifier and Type	Method	Description
protected void	AbstractFeature.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	DefaultBioactiveEntity.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	DefaultCvTerm.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	DefaultGene.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	DefaultProtein.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	DefaultPublication.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent
protected void	DefaultNucleicAcid.processAddedIdentifiersEvent(Xref added)	processAddedIdentifiersEvent
protected void	AbstractFeature.FeatureIdentifierList.processAddedObjectEvent(Xref added)
protected void	DefaultComplex.processAddedXrefEvent(Xref added)	processAddedXrefEvent
protected void	DefaultInteractionEvidence.processAddedXrefEvent(Xref added)	processAddedXrefEvent
protected void	DefaultPublication.processAddedXrefEvent(Xref added)	processAddedXrefEvent
protected void	AbstractFeature.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
protected void	DefaultBioactiveEntity.processRemovedIdentifierEvent(Xref removed)
protected void	DefaultCvTerm.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
protected void	DefaultGene.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
protected void	DefaultNucleicAcid.processRemovedIdentifierEvent(Xref removed)
protected void	DefaultProtein.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
protected void	DefaultPublication.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent
protected void	AbstractFeature.FeatureIdentifierList.processRemovedObjectEvent(Xref removed)
protected void	DefaultComplex.processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent
protected void	DefaultInteractionEvidence.processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent
protected void	DefaultPublication.processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent

Method parameters in psidev.psi.mi.jami.model.impl with type arguments of type Xref

Modifier and Type	Method	Description
protected void	AbstractFeature.initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	AbstractInteraction.initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	DefaultCvTerm.initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	DefaultInteractor.initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	DefaultPublication.initialiseIdentifiersWith(Collection<Xref> identifiers)	initialiseIdentifiersWith
protected void	AbstractFeature.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	AbstractInteraction.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	AbstractParticipant.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	DefaultCvTerm.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	DefaultExperiment.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	DefaultInteractor.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	DefaultPublication.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith
protected void	DefaultResultingSequence.initialiseXrefsWith(Collection<Xref> xrefs)	initialiseXrefsWith

Constructors in psidev.psi.mi.jami.model.impl with parameters of type Xref

Constructor	Description
DefaultBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, String fullName, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, Organism organism, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultBioactiveEntity(String name, Xref uniqueId)	Constructor for DefaultBioactiveEntity.
DefaultComplex(String name, String fullName, CvTerm interactorType, Organism organism, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, String fullName, CvTerm interactorType, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, String fullName, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, CvTerm interactorType, Organism organism, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, CvTerm interactorType, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, Organism organism, Xref uniqueId)	Constructor for DefaultComplex.
DefaultComplex(String name, Xref uniqueId)	Constructor for DefaultComplex.
DefaultCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultCvTerm.
DefaultCvTerm(String shortName, Xref ontologyId)	Constructor for DefaultCvTerm.
DefaultGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultGene.
DefaultGene(String name, String fullName, Xref uniqueId)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Organism organism, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for DefaultGene.
DefaultGene(String name, Organism organism, Xref uniqueId)	Constructor for DefaultGene.
DefaultGene(String name, Xref uniqueId)	Constructor for DefaultGene.
DefaultInteractionEvidence(String shortName, CvTerm type, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(String shortName, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, String fullName, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, Organism organism, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractor(String name, Xref uniqueId)	Constructor for DefaultInteractor.
DefaultInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, String fullName, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, Organism organism, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultInteractorPool(String name, Xref uniqueId)	Constructor for DefaultInteractorPool.
DefaultMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, String fullName, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, Organism organism, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultMolecule(String name, Xref uniqueId)	Constructor for DefaultMolecule.
DefaultNamedInteractionEvidence(String shortName, CvTerm type, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(String shortName, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, String fullName, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, Organism organism, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultNucleicAcid(String name, Xref uniqueId)	Constructor for DefaultNucleicAcid.
DefaultOntologyTerm(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultOntologyTerm.
DefaultOntologyTerm(String shortName, String fullName, Xref ontologyId, String def)	Constructor for DefaultOntologyTerm.
DefaultOntologyTerm(String shortName, Xref ontologyId)	Constructor for DefaultOntologyTerm.
DefaultPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, String fullName, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, Organism organism, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultPolymer(String name, Xref uniqueId)	Constructor for DefaultPolymer.
DefaultProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, String fullName, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, Organism organism, Xref uniqueId)	Constructor for DefaultProtein.
DefaultProtein(String name, Xref uniqueId)	Constructor for DefaultProtein.
DefaultPublication(Xref identifier)	Constructor for DefaultPublication.
DefaultPublication(Xref identifier, String imexId, Source source)	Constructor for DefaultPublication.
DefaultPublication(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for DefaultPublication.
DefaultSource(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultSource.
DefaultSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultSource.
DefaultSource(String shortName, Xref ontologyId)	Constructor for DefaultSource.
DefaultSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultSource.

Uses of Xref in psidev.psi.mi.jami.tab.extension

Classes in psidev.psi.mi.jami.tab.extension that implement Xref

Modifier and Type	Class	Description
class	MitabXref	Mitab extension for Xref.

Constructors in psidev.psi.mi.jami.tab.extension with parameters of type Xref

Constructor	Description
MitabBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, String fullName, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, CvTerm type, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, Organism organism, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabBioactiveEntity(String name, Xref uniqueId)	Constructor for MitabBioactiveEntity.
MitabComplex(String name, String fullName, CvTerm interactorType, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, CvTerm interactorType, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, String fullName, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, CvTerm interactorType, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, CvTerm interactorType, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, Organism organism, Xref uniqueId)	Constructor for MitabComplex.
MitabComplex(String name, Xref uniqueId)	Constructor for MitabComplex.
MitabCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for MitabCvTerm.
MitabCvTerm(String shortName, Xref ontologyId)	Constructor for MitabCvTerm.
MitabGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabGene.
MitabGene(String name, String fullName, Xref uniqueId)	Constructor for MitabGene.
MitabGene(String name, Organism organism, Xref uniqueId)	Constructor for MitabGene.
MitabGene(String name, Xref uniqueId)	Constructor for MitabGene.
MitabInteractionEvidence(String shortName, CvTerm type, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(String shortName, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, CvTerm type, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, String fullName, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, Organism organism, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractor(String name, Xref uniqueId)	Constructor for MitabInteractor.
MitabInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, String fullName, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, CvTerm type, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, Organism organism, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabInteractorPool(String name, Xref uniqueId)	Constructor for MitabInteractorPool.
MitabMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, String fullName, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, CvTerm type, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, Organism organism, Xref uniqueId)	Constructor for MitabMolecule.
MitabMolecule(String name, Xref uniqueId)	Constructor for MitabMolecule.
MitabNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, String fullName, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, CvTerm type, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, Organism organism, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabNucleicAcid(String name, Xref uniqueId)	Constructor for MitabNucleicAcid.
MitabPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, String fullName, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, CvTerm type, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, Organism organism, Xref uniqueId)	Constructor for MitabPolymer.
MitabPolymer(String name, Xref uniqueId)	Constructor for MitabPolymer.
MitabProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, String fullName, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, CvTerm type, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, Organism organism, Xref uniqueId)	Constructor for MitabProtein.
MitabProtein(String name, Xref uniqueId)	Constructor for MitabProtein.
MitabPublication(Xref identifier)	Constructor for MitabPublication.
MitabPublication(Xref identifier, String imexId, Source source)	Constructor for MitabPublication.
MitabPublication(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for MitabPublication.
MitabSource(String shortName, String fullName, Xref ontologyId)	Constructor for MitabSource.
MitabSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for MitabSource.
MitabSource(String shortName, Xref ontologyId)	Constructor for MitabSource.
MitabSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for MitabSource.

Uses of Xref in psidev.psi.mi.jami.tab.io.writer.feeder

Methods in psidev.psi.mi.jami.tab.io.writer.feeder with parameters of type Xref

Modifier and Type	Method	Description
void	AbstractMitabColumnFeeder.writeIdentifier(Xref identifier)	This methods write the database, id and version of an identifier
void	MitabColumnFeeder.writeIdentifier(Xref identifier)	This methods write the database, id and version of an identifier
void	AbstractMitabColumnFeeder.writeXref(Xref xref)	This methods write the database, id, version and qualifier of an xref
void	MitabColumnFeeder.writeXref(Xref xref)	This methods write the database, id, version and qualifier of an xref

Uses of Xref in psidev.psi.mi.jami.utils

Methods in psidev.psi.mi.jami.utils that return Xref

Modifier and Type	Method	Description
static Xref	XrefUtils.collectFirstIdentifierWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName)	This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name
static Xref	XrefUtils.collectFirstIdentifierWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)	This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name
static Xref	XrefUtils.createChebiIdentity(String id)	createChebiIdentity
static Xref	XrefUtils.createChebiSecondary(String id)	createChebiSecondary
static Xref	XrefUtils.createDdbjEmblGenbankIdentity(String id)	createDdbjEmblGenbankIdentity
static Xref	XrefUtils.createDdbjEmblGenbankSecondary(String id)	createDdbjEmblGenbankSecondary
static Xref	XrefUtils.createDoiIdentity(String id)	createDoiIdentity
static Xref	XrefUtils.createEnsemblGenomesIdentity(String ensembl)	createEnsemblGenomesIdentity
static Xref	XrefUtils.createEnsemblGenomesSecondary(String ensembl)	createEnsemblGenomesSecondary
static Xref	XrefUtils.createEnsemblIdentity(String ensembl)	createEnsemblIdentity
static Xref	XrefUtils.createEnsemblSecondary(String ensembl)	createEnsemblSecondary
static Xref	XrefUtils.createEntrezGeneIdIdentity(String geneId)	createEntrezGeneIdIdentity
static Xref	XrefUtils.createEntrezGeneIdSecondary(String geneId)	createEntrezGeneIdSecondary
static Xref	XrefUtils.createIdentityXref(String databaseName, String id)	createIdentityXref
static Xref	XrefUtils.createIdentityXref(String databaseName, String databaseMi, String id)	createIdentityXref
static Xref	XrefUtils.createPrimaryXref(String databaseName, String id)	createPrimaryXref
static Xref	XrefUtils.createPrimaryXref(String databaseName, String databaseMi, String id)	createPrimaryXref
static Xref	XrefUtils.createPsiMiIdentity(String id)	createPsiMiIdentity
static Xref	XrefUtils.createPsiMiSecondary(String id)	createPsiMiSecondary
static Xref	XrefUtils.createPsiModIdentity(String id)	createPsiModIdentity
static Xref	XrefUtils.createPsiModSecondary(String id)	createPsiModSecondary
static Xref	XrefUtils.createPubmedIdentity(String id)	createPubmedIdentity
static Xref	XrefUtils.createRefseqIdentity(String refseq)	createRefseqIdentity
static Xref	XrefUtils.createRefseqSecondary(String refseq)	createRefseqSecondary
static Xref	XrefUtils.createSecondaryXref(String databaseName, String id)	createSecondaryXref
static Xref	XrefUtils.createSecondaryXref(String databaseName, String databaseMi, String id)	createSecondaryXref
static Xref	XrefUtils.createUniprotIdentity(String uniprot)	createUniprotIdentity
static Xref	XrefUtils.createUniprotSecondary(String uniprot)	createUniprotSecondary
static Xref	XrefUtils.createXref(String databaseName, String id)	createXref
static Xref	XrefUtils.createXref(String databaseName, String databaseMi, String id)	createXref
static Xref	XrefUtils.createXrefWithQualifier(String databaseName, String id, String qualifierName)	createXrefWithQualifier
static Xref	XrefUtils.createXrefWithQualifier(String databaseName, String databaseMi, String id, String qualifierName, String qualifierMi)	createXrefWithQualifier
static Xref	XrefUtils.createXrefWithQualifier(String databaseName, String databaseMi, String id, String version, String qualifierName, String qualifierMi)	createXrefWithQualifierAndVersion
static Xref	ExperimentUtils.getDoiReference(Experiment exp)	getDoiReference
static Xref	PublicationUtils.getDoiReference(Publication pub)	getDoiReference
static Xref	CvTermUtils.getPsiMiReference(CvTerm term)	getPsiMiReference
static Xref	CvTermUtils.getPsiModReference(CvTerm term)	getPsiModReference
static Xref	CvTermUtils.getPsiParReference(CvTerm term)	getPsiParReference
static Xref	ExperimentUtils.getPubmedReference(Experiment exp)	getPubmedReference
static Xref	PublicationUtils.getPubmedReference(Publication pub)	getPubmedReference

Methods in psidev.psi.mi.jami.utils that return types with arguments of type Xref

Modifier and Type	Method	Description
static Collection<Xref>	XrefUtils.collectAllIdentifiersFrom(Collection<? extends Xref> refs)	Method to return a sub collection of identifiers (qualifier identity or secondary) in a list of Xrefs
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabase(Collection<? extends Xref> refs, String dbId, String dbName)	Collect all cross references having a specific database
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)	Collect all cross references having a specific database
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(Collection<? extends Xref> refs, String dbId, String dbName, String qualifierId, String qualifierName)	Collect all cross references having a specific database and qualifier
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabaseQualifierAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id, String qualifierId, String qualifierName)	Collect all cross references having a specific database and qualifier
static Collection<Xref>	XrefUtils.collectAllXrefsHavingQualifier(Collection<? extends Xref> refs, String qualifierId, String qualifierName)	Collect all cross references having a specific qualifier
static Collection<Xref>	XrefUtils.collectAllXrefsHavingQualifierAndId(Collection<? extends Xref> refs, String qualifierId, String qualifierName, String id)	Collect all cross references having a specific qualifier
static Collection<Xref>	XrefUtils.searchAllXrefsHavingDatabaseAndQualifier(Collection<Xref> xrefs, Collection<String> dbMiRefs, Collection<String> dbRefs, Collection<String> typeMiRefs, Collection<String> typeRefs)	Collect all cross references having specific databases and qualifiers
static Collection<Xref>	XrefUtils.searchAllXrefsHavingDatabases(Collection<Xref> xrefs, Collection<String> dbMiRefs, Collection<String> dbRefs)	Collect all Xrefs having specific databases

Methods in psidev.psi.mi.jami.utils with parameters of type Xref

Modifier and Type	Method	Description
static boolean	XrefUtils.doesXrefHaveDatabaseAndId(Xref ref, String dbId, String dbName, String id)	Method to know if a Xref is from the same database (dbId is the MI identifier and dbName is the database shortname)
static boolean	XrefUtils.doesXrefHaveQualifier(Xref ref, String qualifierId, String qualifierName)	Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname)
static boolean	XrefUtils.doesXrefHaveQualifierAndId(Xref ref, String qualifierId, String qualifierName, String id)	Method to know if a Xref has the same qualifier (qualifierId is the MI identifier and qualifierName is the qualifier shortname)
static boolean	XrefUtils.isXrefAnIdentifier(Xref ref)	Method to know if a Xref is a potential identifier.
static boolean	XrefUtils.isXrefFromDatabase(Xref ref, String dbId, String dbName)	Method to know if a Xref is from the same database (dbId is the MI identifier and dbName is the database shortname)

Method parameters in psidev.psi.mi.jami.utils with type arguments of type Xref

Modifier and Type	Method	Description
static Collection<Xref>	XrefUtils.collectAllIdentifiersFrom(Collection<? extends Xref> refs)	Method to return a sub collection of identifiers (qualifier identity or secondary) in a list of Xrefs
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabase(Collection<? extends Xref> refs, String dbId, String dbName)	Collect all cross references having a specific database
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)	Collect all cross references having a specific database
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(Collection<? extends Xref> refs, String dbId, String dbName, String qualifierId, String qualifierName)	Collect all cross references having a specific database and qualifier
static Collection<Xref>	XrefUtils.collectAllXrefsHavingDatabaseQualifierAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id, String qualifierId, String qualifierName)	Collect all cross references having a specific database and qualifier
static Collection<Xref>	XrefUtils.collectAllXrefsHavingQualifier(Collection<? extends Xref> refs, String qualifierId, String qualifierName)	Collect all cross references having a specific qualifier
static Collection<Xref>	XrefUtils.collectAllXrefsHavingQualifierAndId(Collection<? extends Xref> refs, String qualifierId, String qualifierName, String id)	Collect all cross references having a specific qualifier
static Xref	XrefUtils.collectFirstIdentifierWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName)	This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name
static Xref	XrefUtils.collectFirstIdentifierWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)	This method will return the first Xref from this database having : - identity qualifier - secondary identifier if no identity qualifier - first Xref from this database if no identity or secondary qualifier It will return null if there are no Xrefs with this database id/name
static String	CommonUtils.extractIntactAcFromIdentifier(Collection<Xref> identifiers)
static void	XrefUtils.removeAllXrefsWithDatabase(Collection<? extends Xref> refs, String dbId, String dbName)	Remove all Xrefs having this database name/database id from the collection of xrefs
static void	XrefUtils.removeAllXrefsWithDatabaseAndId(Collection<? extends Xref> refs, String dbId, String dbName, String id)	Remove all Xrefs having this database name/database id from the collection of xrefs
static Collection<Xref>	XrefUtils.searchAllXrefsHavingDatabaseAndQualifier(Collection<Xref> xrefs, Collection<String> dbMiRefs, Collection<String> dbRefs, Collection<String> typeMiRefs, Collection<String> typeRefs)	Collect all cross references having specific databases and qualifiers
static Collection<Xref>	XrefUtils.searchAllXrefsHavingDatabases(Collection<Xref> xrefs, Collection<String> dbMiRefs, Collection<String> dbRefs)	Collect all Xrefs having specific databases

Uses of Xref in psidev.psi.mi.jami.utils.comparator

Method parameters in psidev.psi.mi.jami.utils.comparator with type arguments of type Xref

Modifier and Type	Method	Description
static boolean	ComparatorUtils.findAtLeastOneMatchingIdentifier(Collection<? extends Xref> identifiers1, Collection<? extends Xref> identifiers2)	True if there is at least one identifier in identifiers1 that is identical to at least one identifier in identfiers2 ( equality based on DefaultExternalIdentifierComparator.areEquals)

Uses of Xref in psidev.psi.mi.jami.utils.comparator.cv

Methods in psidev.psi.mi.jami.utils.comparator.cv that return types with arguments of type Xref

Modifier and Type	Method	Description
CollectionComparator<Xref>	CvTermComparator.getIdentifierCollectionComparator()	Getter for the field identifierCollectionComparator.
Comparator<Xref>	CvTermComparator.getIdentifierComparator()	Getter for the field identifierComparator.
Comparator<Xref>	CvTermIdentifierComparator.getIdentifierComparator()	Getter for the field identifierComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.cv with type arguments of type Xref

Constructor	Description
CvTermComparator(Comparator<Xref> identifierComparator)	Creates a new CvTermComparator with UnambiguousExternalIdentifierComparator
CvTermComparator(CollectionComparator<Xref> identifierComparator)	Constructor for CvTermComparator.
CvTermIdentifierComparator(Comparator<Xref> identifierComparator)	Constructor for CvTermIdentifierComparator.
CvTermIdentifierComparator(CollectionComparator<Xref> identifierComparator)	Constructor for CvTermIdentifierComparator.

Uses of Xref in psidev.psi.mi.jami.utils.comparator.feature

Methods in psidev.psi.mi.jami.utils.comparator.feature that return types with arguments of type Xref

Modifier and Type	Method	Description
CollectionComparator<Xref>	FeatureBaseComparator.getExternalIdentifierCollectionComparator()	Getter for the field externalIdentifierCollectionComparator.
Comparator<Xref>	FeatureBaseComparator.getIdentifierComparator()	Getter for the field identifierComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.feature with type arguments of type Xref

Constructor	Description
FeatureBaseComparator(Comparator<CvTerm> cvComparator, CollectionComparator<Xref> identifierComparator, CollectionComparator<Range> rangeComparator)	Constructor for FeatureBaseComparator.

Uses of Xref in psidev.psi.mi.jami.utils.comparator.interaction

Methods in psidev.psi.mi.jami.utils.comparator.interaction that return types with arguments of type Xref

Modifier and Type	Method	Description
CollectionComparator<Xref>	InteractionBaseComparator.getIdentifierCollectionComparator()	Getter for the field identifierCollectionComparator.
Comparator<Xref>	InteractionBaseComparator.getIdentifierComparator()	Getter for the field identifierComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.interaction with type arguments of type Xref

Constructor	Description
InteractionBaseComparator(Comparator<Xref> identifierComparator, Comparator<CvTerm> cvTermComparator)	Constructor for InteractionBaseComparator.
InteractionBaseComparator(CollectionComparator<Xref> identifierComparator, Comparator<CvTerm> cvTermComparator)	Constructor for InteractionBaseComparator.

Uses of Xref in psidev.psi.mi.jami.utils.comparator.interactor

Methods in psidev.psi.mi.jami.utils.comparator.interactor that return types with arguments of type Xref

Modifier and Type	Method	Description
CollectionComparator<Xref>	InteractorBaseComparator.getIdentifierCollectionComparator()	Getter for the field identifierCollectionComparator.
Comparator<Xref>	InteractorBaseComparator.getIdentifierComparator()	Getter for the field identifierComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.interactor with type arguments of type Xref

Constructor	Description
InteractorBaseComparator(Comparator<Xref> identifierComparator, AliasComparator aliasComparator)	Constructor for InteractorBaseComparator.
InteractorBaseComparator(CollectionComparator<Xref> identifierComparator, CollectionComparator<Alias> aliasComparator)	Constructor for InteractorBaseComparator.

Uses of Xref in psidev.psi.mi.jami.utils.comparator.publication

Methods in psidev.psi.mi.jami.utils.comparator.publication that return types with arguments of type Xref

Modifier and Type	Method	Description
CollectionComparator<Xref>	PublicationComparator.getIdentifierCollectionComparator()	Getter for the field identifierCollectionComparator.
Comparator<Xref>	PublicationComparator.getIdentifierComparator()	Getter for the field identifierComparator.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.publication with type arguments of type Xref

Constructor	Description
PublicationComparator(Comparator<Xref> identifierComparator)	Constructor for PublicationComparator.
PublicationComparator(CollectionComparator<Xref> identifiersComparator)	Constructor for PublicationComparator.

Uses of Xref in psidev.psi.mi.jami.utils.comparator.xref

Methods in psidev.psi.mi.jami.utils.comparator.xref that return types with arguments of type Xref

Modifier and Type	Method	Description
Comparator<Xref>	XrefsCollectionComparator.getObjectComparator()	Getter for the field objectComparator.

Methods in psidev.psi.mi.jami.utils.comparator.xref with parameters of type Xref

Modifier and Type	Method	Description
static boolean	DefaultExternalIdentifierComparator.areEquals(Xref externalIdentifier1, Xref externalIdentifier2)	Use DefaultIdentifierComparator to know if two external identifiers are equals.
static boolean	DefaultXrefComparator.areEquals(Xref xref1, Xref xref2)	Use DefaultXrefComparator to know if two xrefs are equals.
static boolean	ExactExternalIdentifierComparator.areEquals(Xref externalIdentifier1, Xref externalIdentifier2)	Use ExactExternalIdentifierComparator to know if two external identifiers are equals.
static boolean	ExactXrefComparator.areEquals(Xref xref1, Xref xref2)	Use ExactXrefComparator to know if two xrefs are equals.
static boolean	UnambiguousExternalIdentifierComparator.areEquals(Xref externalIdentifier1, Xref externalIdentifier2)	Use UnambiguousIdentifierComparator to know if two external identifiers are equals.
static boolean	UnambiguousXrefComparator.areEquals(Xref xref1, Xref xref2)	Use UnambiguousXrefComparator to know if two xrefs are equals.
int	ExactExternalIdentifierComparator.compare(Xref externalIdentifier1, Xref externalIdentifier2)	It compares first the databases using UnambiguousCvTermComparator, then the ids (case sensitive) and then the version.
int	ExactXrefComparator.compare(Xref xref1, Xref xref2)	It compares first the databases and then the ids (case sensitive) but ignores the version.
int	UnambiguousExternalIdentifierComparator.compare(Xref externalIdentifier1, Xref externalIdentifier2)	It compares first the databases and then the ids (case sensitive) but ignores the version.
int	UnambiguousXrefComparator.compare(Xref xref1, Xref xref2)	It compares first the databases and then the ids (case sensitive) but ignores the version.
static int	ExactExternalIdentifierComparator.hashCode(Xref externalIdentifier1)
static int	ExactXrefComparator.hashCode(Xref xref)
static int	UnambiguousExternalIdentifierComparator.hashCode(Xref externalIdentifier1)	hashCode
static int	UnambiguousXrefComparator.hashCode(Xref xref)	hashCode

Constructor parameters in psidev.psi.mi.jami.utils.comparator.xref with type arguments of type Xref

Constructor	Description
XrefsCollectionComparator(Comparator<Xref> xrefComparator)	Creates a new xref CollectionComparator.

Uses of Xref in psidev.psi.mi.jami.xml.io.writer.elements.impl

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl with parameters of type Xref

Modifier and Type	Method	Description
void	XmlDbXrefWriter.write(Xref object, String nodeName)	write.
protected void	XmlInteractorWriter.writeNewXref(Xref preferredIdentifier, String nodeName)
protected void	XmlDbXrefWriter.writeOtherProperties(Xref object)	writeOtherProperties.

Uses of Xref in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with parameters of type Xref

Modifier and Type	Method	Description
protected void	AbstractXmlPublicationWriter.writePrimaryRef(PsiXmlXrefWriter writer, Xref ref, String name)	writePrimaryRef.

Uses of Xref in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended with parameters of type Xref

Modifier and Type	Method	Description
protected void	XmlDbXrefWriter.writeOtherProperties(Xref object)	writeOtherProperties.

Uses of Xref in psidev.psi.mi.jami.xml.model.extension

Subinterfaces of Xref in psidev.psi.mi.jami.xml.model.extension

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlXref	PSI-XML extension of an xref

Methods in psidev.psi.mi.jami.xml.model.extension that return Xref

Modifier and Type	Method	Description
Xref	AbstractBaseXmlInteractor.getPreferredIdentifier()	getPreferredIdentifier.

Methods in psidev.psi.mi.jami.xml.model.extension that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractBaseXmlInteractor.getIdentifiers()	getIdentifiers.
Collection<Xref>	IInteractorXrefContainer.getIdentifiers()
Collection<Xref>	AbstractBaseXmlInteractor.getXrefs()	getXrefs.
List<Xref>	IInteractorXrefContainer.getXrefs()

Constructors in psidev.psi.mi.jami.xml.model.extension with parameters of type Xref

Constructor	Description
AbstractBaseXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.
AbstractBaseXmlInteractor(String name, Xref uniqueId)	Constructor for AbstractBaseXmlInteractor.

Uses of Xref in psidev.psi.mi.jami.xml.model.extension.binary

Methods in psidev.psi.mi.jami.xml.model.extension.binary that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	XmlBinaryInteractionEvidenceWrapper.getIdentifiers()	The identifiers for an interaction.
Collection<Xref>	XmlBinaryInteractionWrapper.getIdentifiers()	The identifiers for an interaction.
Collection<Xref>	XmlModelledBinaryInteractionWrapper.getIdentifiers()	The identifiers for an interaction.
Collection<Xref>	XmlBinaryInteractionEvidenceWrapper.getXrefs()	The external cross references for an interaction.
Collection<Xref>	XmlBinaryInteractionWrapper.getXrefs()	The external cross references for an interaction.
Collection<Xref>	XmlModelledBinaryInteractionWrapper.getXrefs()	The external cross references for an interaction.

Methods in psidev.psi.mi.jami.xml.model.extension.binary with parameters of type Xref

Modifier and Type	Method	Description
protected void	AbstractXmlBinaryInteractionEvidence.ExperimentalBinaryInteractionXrefList.processAddedObjectEvent(Xref added)
protected void	AbstractXmlBinaryInteractionEvidence.processAddedXrefEvent(Xref added)	processAddedXrefEvent.
protected void	AbstractXmlBinaryInteractionEvidence.ExperimentalBinaryInteractionXrefList.processRemovedObjectEvent(Xref removed)
protected void	AbstractXmlBinaryInteractionEvidence.processRemovedXrefEvent(Xref removed)	processRemovedXrefEvent.
void	AbstractXmlBinaryInteractionEvidence.setImexId(Xref imexId)

Uses of Xref in psidev.psi.mi.jami.xml.model.extension.binary.xml30

Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that return Xref

Modifier and Type	Method	Description
Xref	XmlModelledBinaryInteraction.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlModelledBinaryInteractionWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.

Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	XmlModelledBinaryInteraction.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	XmlModelledBinaryInteractionWrapper.getIdentifiers()	The identifiers for an interaction.
Collection<Xref>	XmlModelledBinaryInteraction.getXrefs()	Getter for the field xrefs.
Collection<Xref>	XmlModelledBinaryInteractionWrapper.getXrefs()	The external cross references for an interaction.

Uses of Xref in psidev.psi.mi.jami.xml.model.extension.xml253

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Xref

Modifier and Type	Class	Description
class	XmlXref	Refers to a unique object in an external database.

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return Xref

Modifier and Type	Method	Description
Xref	AbstractXmlComplex.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	InteractorXrefContainer.getPreferredIdentifier()	getPreferredIdentifier.
Xref	XmlBasicInteractionComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlInteractionEvidenceComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlModelledInteractionComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractXmlComplex.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlCvTerm.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlFeature.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlInteraction.getIdentifiers()	getIdentifiers.
Collection<Xref>	BibRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	CvTermXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	FeatureXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	InteractionXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	InteractorXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	PublicationXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	XmlBasicInteractionComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
Collection<Xref>	XmlFeatureEvidenceWrapper.getIdentifiers()	Collection of External identifiers which describes this feature.
Collection<Xref>	XmlFeatureWrapper.getIdentifiers()	Collection of External identifiers which describes this feature.
Collection<Xref>	XmlInteractionEvidenceComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
Collection<Xref>	XmlModelledInteractionComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
List<Xref>	XrefContainer.getJAXBSecondaryRefs()	Gets the value of the secondaryReves property.
Collection<Xref>	AbstractXmlComplex.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlCvTerm.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlExperiment.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlFeature.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlInteraction.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlParticipant.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlParticipantPool.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	BibRef.getXrefs()	getXrefs.
Collection<Xref>	XmlBasicInteractionComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlFeatureEvidenceWrapper.getXrefs()	Collection of cross references which give more information about the feature.
Collection<Xref>	XmlFeatureWrapper.getXrefs()	Collection of cross references which give more information about the feature.
Collection<Xref>	XmlInteractionEvidenceComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlModelledInteractionComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlParticipantEvidenceWrapper.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	XmlParticipantWrapper.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	XmlResultingSequence.getXrefs()	getXrefs.
List<Xref>	XrefContainer.getXrefs()	Getter for the field xrefs.

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Xref

Modifier and Type	Method	Description
void	XrefContainer.JAXBSecondaryXrefList.add(int index, Xref element)
boolean	XrefContainer.JAXBSecondaryXrefList.add(Xref xref)
protected boolean	XrefContainer.JAXBSecondaryXrefList.addXref(Integer index, Xref xref)
protected boolean	CvTermXrefContainer.isAnIdentifier(Xref ref)	isAnIdentifier.
protected boolean	FeatureXrefContainer.isAnIdentifier(Xref ref)	isAnIdentifier.
protected void	CvTermXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	FeatureXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	PublicationXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	InteractionXrefContainer.processAddedPotentialComplexAc(Xref added)
protected void	ExperimentXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	InteractionXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	PublicationXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	CvTermXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	FeatureXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	InteractionXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	InteractorXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	PublicationXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	XrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	CvTermXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	FeatureXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	PublicationXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	InteractionXrefContainer.processRemovedPotentialComplexAc(Xref removed)
protected void	ExperimentXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
protected void	InteractionXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
protected void	PublicationXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
void	XrefContainer.setJAXBPrimaryRef(Xref value)	Sets the value of the primaryRef property.

Method parameters in psidev.psi.mi.jami.xml.model.extension.xml253 with type arguments of type Xref

Modifier and Type	Method	Description
boolean	XrefContainer.JAXBSecondaryXrefList.addAll(int index, Collection<? extends Xref> c)
boolean	XrefContainer.JAXBSecondaryXrefList.addAll(Collection<? extends Xref> c)
protected void	XrefContainer.initialiseXrefsWith(List<Xref> list)	initialiseXrefsWith.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Xref

Constructor	Description
AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, Xref ontologyId)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for AbstractXmlSource.
BibRef(Xref identifier)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.
DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, Xref ontologyId)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultXmlSource.
ExperimentalCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for ExperimentalCvTerm.
ExperimentalCvTerm(String shortName, Xref ontologyId)	Constructor for ExperimentalCvTerm.
XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, CvTerm type, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, Xref uniqueId)	Constructor for XmlComplex.
XmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for XmlCvTerm.
XmlCvTerm(String shortName, Xref ontologyId)	Constructor for XmlCvTerm.
XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, String fullName, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Organism organism, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, Organism organism, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, Xref uniqueId)	Constructor for XmlGene.
XmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, CvTerm type, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, CvTerm type, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, Xref uniqueId)	Constructor for XmlMolecule.
XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, CvTerm type, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlOpenCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for XmlOpenCvTerm.
XmlOpenCvTerm(String shortName, Xref ontologyId)	Constructor for XmlOpenCvTerm.
XmlPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, CvTerm type, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, Xref uniqueId)	Constructor for XmlPolymer.
XmlProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, CvTerm type, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, Xref uniqueId)	Constructor for XmlProtein.
XmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for XmlSource.
XmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for XmlSource.
XmlSource(String shortName, Xref ontologyId)	Constructor for XmlSource.
XmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for XmlSource.

Uses of Xref in psidev.psi.mi.jami.xml.model.extension.xml254

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Xref

Modifier and Type	Class	Description
class	XmlXref	Refers to a unique object in an external database.

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return Xref

Modifier and Type	Method	Description
Xref	AbstractXmlComplex.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	InteractorXrefContainer.getPreferredIdentifier()	getPreferredIdentifier.
Xref	XmlBasicInteractionComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlInteractionEvidenceComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlModelledInteractionComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractXmlComplex.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlCvTerm.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlFeature.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlInteraction.getIdentifiers()	getIdentifiers.
Collection<Xref>	BibRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	CvTermXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	FeatureXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	InteractionXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	InteractorXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	PublicationXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	XmlBasicInteractionComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
Collection<Xref>	XmlFeatureEvidenceWrapper.getIdentifiers()	Collection of External identifiers which describes this feature.
Collection<Xref>	XmlFeatureWrapper.getIdentifiers()	Collection of External identifiers which describes this feature.
Collection<Xref>	XmlInteractionEvidenceComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
Collection<Xref>	XmlModelledInteractionComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
List<Xref>	XrefContainer.getJAXBSecondaryRefs()	Gets the value of the secondaryReves property.
Collection<Xref>	AbstractXmlComplex.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlCvTerm.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlExperiment.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlFeature.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlInteraction.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlParticipant.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlParticipantPool.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	BibRef.getXrefs()	getXrefs.
Collection<Xref>	XmlBasicInteractionComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlFeatureEvidenceWrapper.getXrefs()	Collection of cross references which give more information about the feature.
Collection<Xref>	XmlFeatureWrapper.getXrefs()	Collection of cross references which give more information about the feature.
Collection<Xref>	XmlInteractionEvidenceComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlModelledInteractionComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlParticipantEvidenceWrapper.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	XmlParticipantWrapper.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	XmlResultingSequence.getXrefs()	getXrefs.
List<Xref>	XrefContainer.getXrefs()	Getter for the field xrefs.

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Xref

Modifier and Type	Method	Description
void	XrefContainer.JAXBSecondaryXrefList.add(int index, Xref element)
boolean	XrefContainer.JAXBSecondaryXrefList.add(Xref xref)
protected boolean	XrefContainer.JAXBSecondaryXrefList.addXref(Integer index, Xref xref)
protected boolean	CvTermXrefContainer.isAnIdentifier(Xref ref)	isAnIdentifier.
protected boolean	FeatureXrefContainer.isAnIdentifier(Xref ref)	isAnIdentifier.
protected void	CvTermXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	FeatureXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	PublicationXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	InteractionXrefContainer.processAddedPotentialComplexAc(Xref added)
protected void	ExperimentXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	InteractionXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	PublicationXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	CvTermXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	FeatureXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	InteractionXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	InteractorXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	PublicationXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	XrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	CvTermXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	FeatureXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	PublicationXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	InteractionXrefContainer.processRemovedPotentialComplexAc(Xref removed)
protected void	ExperimentXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
protected void	InteractionXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
protected void	PublicationXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
void	XrefContainer.setJAXBPrimaryRef(Xref value)	Sets the value of the primaryRef property.

Method parameters in psidev.psi.mi.jami.xml.model.extension.xml254 with type arguments of type Xref

Modifier and Type	Method	Description
boolean	XrefContainer.JAXBSecondaryXrefList.addAll(int index, Collection<? extends Xref> c)
boolean	XrefContainer.JAXBSecondaryXrefList.addAll(Collection<? extends Xref> c)
protected void	XrefContainer.initialiseXrefsWith(List<Xref> list)	initialiseXrefsWith.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Xref

Constructor	Description
AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, Xref ontologyId)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for AbstractXmlSource.
BibRef(Xref identifier)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.
DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, Xref ontologyId)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultXmlSource.
ExperimentalCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for ExperimentalCvTerm.
ExperimentalCvTerm(String shortName, Xref ontologyId)	Constructor for ExperimentalCvTerm.
XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, CvTerm type, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, Xref uniqueId)	Constructor for XmlComplex.
XmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for XmlCvTerm.
XmlCvTerm(String shortName, Xref ontologyId)	Constructor for XmlCvTerm.
XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, String fullName, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Organism organism, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, Organism organism, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, Xref uniqueId)	Constructor for XmlGene.
XmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, CvTerm type, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, CvTerm type, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, Xref uniqueId)	Constructor for XmlMolecule.
XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, CvTerm type, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlOpenCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for XmlOpenCvTerm.
XmlOpenCvTerm(String shortName, Xref ontologyId)	Constructor for XmlOpenCvTerm.
XmlPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, CvTerm type, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, Xref uniqueId)	Constructor for XmlPolymer.
XmlProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, CvTerm type, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, Xref uniqueId)	Constructor for XmlProtein.
XmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for XmlSource.
XmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for XmlSource.
XmlSource(String shortName, Xref ontologyId)	Constructor for XmlSource.
XmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for XmlSource.

Uses of Xref in psidev.psi.mi.jami.xml.model.extension.xml300

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Xref

Modifier and Type	Class	Description
class	XmlXref	Refers to a unique object in an external database.

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return Xref

Modifier and Type	Method	Description
Xref	AbstractXmlComplex.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	InteractorXrefContainer.getPreferredIdentifier()	getPreferredIdentifier.
Xref	XmlBasicInteractionComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlInteractionEvidenceComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlModelledInteraction.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.
Xref	XmlModelledInteractionComplexWrapper.getPreferredIdentifier()	The identifier in the list of identifiers which is the preferred identifier.

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractXmlComplex.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlCvTerm.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlFeature.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractXmlInteraction.getIdentifiers()	getIdentifiers.
Collection<Xref>	BibRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	CvTermXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	FeatureXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	InteractionXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	InteractorXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	PublicationXrefContainer.getIdentifiers()	Getter for the field identifiers.
Collection<Xref>	XmlBasicInteractionComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
Collection<Xref>	XmlFeatureEvidenceWrapper.getIdentifiers()	Collection of External identifiers which describes this feature.
Collection<Xref>	XmlFeatureWrapper.getIdentifiers()	Collection of External identifiers which describes this feature.
Collection<Xref>	XmlInteractionEvidenceComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
Collection<Xref>	XmlModelledInteraction.getIdentifiers()	getIdentifiers.
Collection<Xref>	XmlModelledInteractionComplexWrapper.getIdentifiers()	Set of identifiers for this interactor.
List<Xref>	XrefContainer.getJAXBSecondaryRefs()	Gets the value of the secondaryReves property.
Collection<Xref>	AbstractXmlComplex.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlCvTerm.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlExperiment.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlFeature.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlInteraction.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlParticipant.getXrefs()	getXrefs.
Collection<Xref>	AbstractXmlParticipantPool.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	BibRef.getXrefs()	getXrefs.
Collection<Xref>	XmlBasicInteractionComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlFeatureEvidenceWrapper.getXrefs()	Collection of cross references which give more information about the feature.
Collection<Xref>	XmlFeatureWrapper.getXrefs()	Collection of cross references which give more information about the feature.
Collection<Xref>	XmlInteractionEvidenceComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlModelledInteraction.getXrefs()	getXrefs.
Collection<Xref>	XmlModelledInteractionComplexWrapper.getXrefs()	Collection of other xrefs that give more information about the interactor.
Collection<Xref>	XmlParticipantEvidenceWrapper.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	XmlParticipantWrapper.getXrefs()	Collection of cross references which give more information about the participant.
Collection<Xref>	XmlResultingSequence.getXrefs()	getXrefs.
List<Xref>	XrefContainer.getXrefs()	Getter for the field xrefs.

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Xref

Modifier and Type	Method	Description
void	XrefContainer.JAXBSecondaryXrefList.add(int index, Xref element)
boolean	XrefContainer.JAXBSecondaryXrefList.add(Xref xref)
protected boolean	XrefContainer.JAXBSecondaryXrefList.addXref(Integer index, Xref xref)
protected boolean	CvTermXrefContainer.isAnIdentifier(Xref ref)	isAnIdentifier.
protected boolean	FeatureXrefContainer.isAnIdentifier(Xref ref)	isAnIdentifier.
protected void	CvTermXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	FeatureXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	PublicationXrefContainer.processAddedIdentifierEvent(Xref added)	processAddedIdentifierEvent.
protected void	InteractionXrefContainer.processAddedPotentialComplexAc(Xref added)
protected void	ExperimentXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	InteractionXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	PublicationXrefContainer.processAddedPotentialImex(Xref added)	processAddedPotentialImex.
protected void	CvTermXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	FeatureXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	InteractionXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	InteractorXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	PublicationXrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	XrefContainer.processAddedPrimaryRef(Xref added)	processAddedPrimaryRef.
protected void	CvTermXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	FeatureXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	PublicationXrefContainer.processRemovedIdentifierEvent(Xref removed)	processRemovedIdentifierEvent.
protected void	InteractionXrefContainer.processRemovedPotentialComplexAc(Xref removed)
protected void	ExperimentXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
protected void	InteractionXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
protected void	PublicationXrefContainer.processRemovedPotentialImex(Xref removed)	processRemovedPotentialImex.
void	XrefContainer.setJAXBPrimaryRef(Xref value)	Sets the value of the primaryRef property.

Method parameters in psidev.psi.mi.jami.xml.model.extension.xml300 with type arguments of type Xref

Modifier and Type	Method	Description
boolean	XrefContainer.JAXBSecondaryXrefList.addAll(int index, Collection<? extends Xref> c)
boolean	XrefContainer.JAXBSecondaryXrefList.addAll(Collection<? extends Xref> c)
protected void	XrefContainer.initialiseXrefsWith(List<Xref> list)	initialiseXrefsWith.

Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Xref

Constructor	Description
AbstractXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlComplex(String name, Xref uniqueId)	Constructor for AbstractXmlComplex.
AbstractXmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlCvTerm(String shortName, Xref ontologyId)	Constructor for AbstractXmlCvTerm.
AbstractXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlInteractor(String name, Xref uniqueId)	Constructor for AbstractXmlInteractor.
AbstractXmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, Xref ontologyId)	Constructor for AbstractXmlSource.
AbstractXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for AbstractXmlSource.
BibRef(Xref identifier)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.
DefaultXmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, String fullName, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlComplex(String name, Xref uniqueId)	Constructor for DefaultXmlComplex.
DefaultXmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlInteractor(String name, Xref uniqueId)	Constructor for DefaultXmlInteractor.
DefaultXmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, Xref ontologyId)	Constructor for DefaultXmlSource.
DefaultXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for DefaultXmlSource.
ExperimentalCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for ExperimentalCvTerm.
ExperimentalCvTerm(String shortName, Xref ontologyId)	Constructor for ExperimentalCvTerm.
XmlBioactiveEntity(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, String fullName, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, CvTerm type, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, Organism organism, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlBioactiveEntity(String name, Xref uniqueId)	Constructor for XmlBioactiveEntity.
XmlComplex(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, String fullName, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, CvTerm type, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, Organism organism, Xref uniqueId)	Constructor for XmlComplex.
XmlComplex(String name, Xref uniqueId)	Constructor for XmlComplex.
XmlCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for XmlCvTerm.
XmlCvTerm(String shortName, Xref ontologyId)	Constructor for XmlCvTerm.
XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, String fullName, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Organism organism, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Organism organism, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, CvTerm type, Xref uniqueId, Xref ensembl)	Constructor for XmlGene.
XmlGene(String name, Organism organism, Xref uniqueId)	Constructor for XmlGene.
XmlGene(String name, Xref uniqueId)	Constructor for XmlGene.
XmlInteractor(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, String fullName, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, CvTerm type, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, Organism organism, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractor(String name, Xref uniqueId)	Constructor for XmlInteractor.
XmlInteractorPool(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, String fullName, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, CvTerm type, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, Organism organism, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlInteractorPool(String name, Xref uniqueId)	Constructor for XmlInteractorPool.
XmlMolecule(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, String fullName, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, CvTerm type, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, Organism organism, Xref uniqueId)	Constructor for XmlMolecule.
XmlMolecule(String name, Xref uniqueId)	Constructor for XmlMolecule.
XmlNucleicAcid(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, String fullName, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, CvTerm type, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, Organism organism, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlNucleicAcid(String name, Xref uniqueId)	Constructor for XmlNucleicAcid.
XmlOpenCvTerm(String shortName, String fullName, Xref ontologyId)	Constructor for XmlOpenCvTerm.
XmlOpenCvTerm(String shortName, Xref ontologyId)	Constructor for XmlOpenCvTerm.
XmlPolymer(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, String fullName, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, CvTerm type, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, Organism organism, Xref uniqueId)	Constructor for XmlPolymer.
XmlPolymer(String name, Xref uniqueId)	Constructor for XmlPolymer.
XmlProtein(String name, String fullName, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, CvTerm type, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, String fullName, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, CvTerm type, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, CvTerm type, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, Organism organism, Xref uniqueId)	Constructor for XmlProtein.
XmlProtein(String name, Xref uniqueId)	Constructor for XmlProtein.
XmlSource(String shortName, String fullName, Xref ontologyId)	Constructor for XmlSource.
XmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for XmlSource.
XmlSource(String shortName, Xref ontologyId)	Constructor for XmlSource.
XmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)	Constructor for XmlSource.

Uses of Xref in psidev.psi.mi.jami.xml.model.reference

Methods in psidev.psi.mi.jami.xml.model.reference that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractFeatureRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractFeatureRef.getXrefs()	getXrefs.

Uses of Xref in psidev.psi.mi.jami.xml.model.reference.xml253

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return Xref

Modifier and Type	Method	Description
Xref	AbstractInteractorRef.getPreferredIdentifier()	getPreferredIdentifier.

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractComplexRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractInteractorRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractComplexRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractExperimentRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractInteractorRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractParticipantRef.getXrefs()	getXrefs.

Uses of Xref in psidev.psi.mi.jami.xml.model.reference.xml254

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return Xref

Modifier and Type	Method	Description
Xref	AbstractInteractorRef.getPreferredIdentifier()	getPreferredIdentifier.

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractComplexRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractInteractorRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractComplexRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractExperimentRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractInteractorRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractParticipantRef.getXrefs()	getXrefs.

Uses of Xref in psidev.psi.mi.jami.xml.model.reference.xml300

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return Xref

Modifier and Type	Method	Description
Xref	AbstractInteractorRef.getPreferredIdentifier()	getPreferredIdentifier.

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return types with arguments of type Xref

Modifier and Type	Method	Description
Collection<Xref>	AbstractComplexRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractInteractorRef.getIdentifiers()	getIdentifiers.
Collection<Xref>	AbstractComplexRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractExperimentRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractInteractorRef.getXrefs()	getXrefs.
Collection<Xref>	AbstractParticipantRef.getXrefs()	getXrefs.