Uses of Interface psidev.psi.mi.jami.model.Publication (PSI :: JAMI - Java framework for molecular interactions 3.3.0 API)

Packages that use Publication
Package	Description
psidev.psi.mi.jami.bridges.europubmedcentral
psidev.psi.mi.jami.bridges.fetcher
psidev.psi.mi.jami.bridges.fetcher.mock
psidev.psi.mi.jami.bridges.imex
psidev.psi.mi.jami.bridges.imex.extension
psidev.psi.mi.jami.bridges.imex.mock
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.datasource
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.log
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.html
psidev.psi.mi.jami.imex
psidev.psi.mi.jami.imex.actions
psidev.psi.mi.jami.imex.actions.impl
psidev.psi.mi.jami.imex.listener
psidev.psi.mi.jami.imex.listener.impl
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.clone
psidev.psi.mi.jami.utils.comparator.cooperativity
psidev.psi.mi.jami.utils.comparator.experiment
psidev.psi.mi.jami.utils.comparator.publication
psidev.psi.mi.jami.xml.io.writer.elements
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.xml25
psidev.psi.mi.jami.xml.io.writer.elements.impl.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.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300

Uses of Publication in psidev.psi.mi.jami.bridges.europubmedcentral

Methods in psidev.psi.mi.jami.bridges.europubmedcentral that return Publication
Modifier and Type	Method	Description
`Publication`	CachedEuroPubmedCentralFetcher.`fetchByIdentifier(String identifier, String source)`	Uses the identifier to search for a publication and return a completed record.
`Publication`	EuroPubmedCentralFetcher.`fetchByIdentifier(String id, String source)`	Uses the identifier to search for a publication and return a completed record.

Methods in psidev.psi.mi.jami.bridges.europubmedcentral that return types with arguments of type Publication
Modifier and Type	Method	Description
`Collection<Publication>`	CachedEuroPubmedCentralFetcher.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.
`Collection<Publication>`	EuroPubmedCentralFetcher.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.

Uses of Publication in psidev.psi.mi.jami.bridges.fetcher

Methods in psidev.psi.mi.jami.bridges.fetcher that return Publication
Modifier and Type	Method	Description
`Publication`	PublicationFetcher.`fetchByIdentifier(String identifier, String source)`	Uses the identifier to search for a publication and return a completed record.

Methods in psidev.psi.mi.jami.bridges.fetcher that return types with arguments of type Publication
Modifier and Type	Method	Description
`Collection<Publication>`	PublicationFetcher.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.

Uses of Publication in psidev.psi.mi.jami.bridges.fetcher.mock

Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return Publication
Modifier and Type	Method	Description
`Publication`	FailingPublicationFetcher.`fetchByIdentifier(String pubmedID, String source)`	Uses the identifier to search for a publication and return a completed record.
`Publication`	MockPublicationFetcher.`fetchByIdentifier(String pubmedID, String source)`	Uses the identifier to search for a publication and return a completed record.

Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return types with arguments of type Publication
Modifier and Type	Method	Description
`Collection<Publication>`	FailingPublicationFetcher.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.
`Collection<Publication>`	MockPublicationFetcher.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.

Uses of Publication in psidev.psi.mi.jami.bridges.imex

Methods in psidev.psi.mi.jami.bridges.imex that return Publication
Modifier and Type	Method	Description
`Publication`	DefaultImexCentralClient.`createPublicationById(String identifier, String source)`	Creates a publication given a valid pubmed id.
`Publication`	ImexCentralClient.`createPublicationById(String identifier, String source)`	Creates a publication given a valid pubmed id.
`Publication`	DefaultImexCentralClient.`fetchByIdentifier(String identifier, String source)`	Uses the identifier to search for a publication and return a completed record.
`Publication`	DefaultImexCentralClient.`fetchPublicationImexAccession(String identifier, String source, boolean aBoolean)`	Create a new IMEx id if requested for a given pubmed id
`Publication`	ImexCentralClient.`fetchPublicationImexAccession(String identifier, String source, boolean assign)`	Create a new IMEx id if requested for a given pubmed id
`Publication`	DefaultImexCentralClient.`updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)`	Update the publication admin group given a valid pubmed identifier and a valid operator.
`Publication`	ImexCentralClient.`updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)`	Update the publication admin group given a valid pubmed identifier and a valid operator.
`Publication`	DefaultImexCentralClient.`updatePublicationAdminUser(String identifier, String source, Operation operation, String user)`	Update the publication admin user given a valid pubmed identifier and a valid operator.
`Publication`	ImexCentralClient.`updatePublicationAdminUser(String identifier, String source, Operation operation, String user)`	Update the publication admin user given a valid pubmed identifier and a valid operator.
`Publication`	DefaultImexCentralClient.`updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)`	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
`Publication`	ImexCentralClient.`updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)`	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
`Publication`	DefaultImexCentralClient.`updatePublicationStatus(String identifier, String source, PublicationStatus status)`	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central
`Publication`	ImexCentralClient.`updatePublicationStatus(String identifier, String source, PublicationStatus status)`	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central

Methods in psidev.psi.mi.jami.bridges.imex that return types with arguments of type Publication
Modifier and Type	Method	Description
`Collection<Publication>`	DefaultImexCentralClient.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.
`List<Publication>`	DefaultImexCentralClient.`fetchPublicationsByOwner(String owner, int first, int max)`	Collect a list of publications associated with a specific owner.
`Collection<Publication>`	ImexCentralClient.`fetchPublicationsByOwner(String owner, int first, int max)`	Collect a list of publications associated with a specific owner.
`List<Publication>`	DefaultImexCentralClient.`fetchPublicationsByStatus(String status, int first, int max)`	Collect a list of publications having a specific status.
`Collection<Publication>`	ImexCentralClient.`fetchPublicationsByStatus(String status, int first, int max)`	Collect a list of publications having a specific status.

Methods in psidev.psi.mi.jami.bridges.imex with parameters of type Publication
Modifier and Type	Method	Description
`void`	DefaultImexCentralClient.`createPublication(Publication publication)`	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)
`void`	ImexCentralClient.`createPublication(Publication publication)`	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)

Uses of Publication in psidev.psi.mi.jami.bridges.imex.extension

Classes in psidev.psi.mi.jami.bridges.imex.extension that implement Publication
Modifier and Type	Class	Description
`class`	`ImexPublication`	Extension of publication for imex central

Uses of Publication in psidev.psi.mi.jami.bridges.imex.mock

Methods in psidev.psi.mi.jami.bridges.imex.mock that return Publication
Modifier and Type	Method	Description
`Publication`	MockImexCentralClient.`createPublicationById(String identifier, String source)`	Creates a publication given a valid pubmed id.
`Publication`	MockImexCentralClient.`fetchByIdentifier(String identifier, String source)`	Uses the identifier to search for a publication and return a completed record.
`Publication`	MockImexCentralClient.`fetchPublicationImexAccession(String identifier, String source, boolean create)`	Create a new IMEx id if requested for a given pubmed id
`Publication`	MockImexCentralClient.`updatePublicationAdminGroup(String identifier, String source, Operation operation, String group)`	Update the publication admin group given a valid pubmed identifier and a valid operator.
`Publication`	MockImexCentralClient.`updatePublicationAdminUser(String identifier, String source, Operation operation, String user)`	Update the publication admin user given a valid pubmed identifier and a valid operator.
`Publication`	MockImexCentralClient.`updatePublicationIdentifier(String oldIdentifier, String oldSource, String newIdentifier, String source)`	Update publication pubmed identifier, DOI number or internal identifier of an existing record in IMEx central.
`Publication`	MockImexCentralClient.`updatePublicationStatus(String identifier, String source, PublicationStatus status)`	Update the status of a publication associated with a valid pubmed identifier already registered in IMEx central

Methods in psidev.psi.mi.jami.bridges.imex.mock that return types with arguments of type Publication
Modifier and Type	Method	Description
`Collection<Publication>`	MockImexCentralClient.`fetchByIdentifiers(Map<String,Collection<String>> identifiers)`	Uses the identifiers to search for publications and return completed records.
`List<Publication>`	MockImexCentralClient.`fetchPublicationsByOwner(String owner, int first, int max)`	Collect a list of publications associated with a specific owner.
`List<Publication>`	MockImexCentralClient.`fetchPublicationsByStatus(String status, int first, int max)`	Collect a list of publications having a specific status.

Methods in psidev.psi.mi.jami.bridges.imex.mock with parameters of type Publication
Modifier and Type	Method	Description
`void`	MockImexCentralClient.`addPublication(Publication p)`	addPublication.
`void`	MockImexCentralClient.`createPublication(Publication publication)`	Create a new publication record in IMEx central (not implemented yet in production but can be used in test with the MockImexCentralClient)

Method parameters in psidev.psi.mi.jami.bridges.imex.mock with type arguments of type Publication
Modifier and Type	Method	Description
`void`	MockImexCentralClient.`initPublications(List<Publication> allPublications)`	initPublications.

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

Methods in psidev.psi.mi.jami.bridges.ols that return Publication
Modifier and Type	Method	Description
`Publication`	LazySource.`getPublication()`	getPublication.

Methods in psidev.psi.mi.jami.bridges.ols with parameters of type Publication
Modifier and Type	Method	Description
`void`	LazySource.`setPublication(Publication ref)`	Set the bibliographical reference

Uses of Publication in psidev.psi.mi.jami.datasource

Methods in psidev.psi.mi.jami.datasource that return types with arguments of type Publication
Modifier and Type	Method	Description
`Iterator<Publication>`	PublicationStream.`getPublicationsIterator()`	The publications iterator for this datasource.

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

Methods in psidev.psi.mi.jami.enricher.impl.full that return Publication
Modifier and Type	Method	Description
`Publication`	FullCuratedPublicationUpdater.`find(Publication publicationToEnrich)`	find.
`Publication`	FullPublicationUpdater.`find(Publication publicationToEnrich)`	find.

Methods in psidev.psi.mi.jami.enricher.impl.full with parameters of type Publication
Modifier and Type	Method	Description
`Publication`	FullCuratedPublicationUpdater.`find(Publication publicationToEnrich)`	find.
`Publication`	FullPublicationUpdater.`find(Publication publicationToEnrich)`	find.
`protected void`	FullPublicationEnricher.`processAnnotations(Publication publicationToEnrich, Publication fetched)`	processAnnotations.
`protected void`	FullPublicationUpdater.`processAnnotations(Publication publicationToEnrich, Publication fetched)`	processAnnotations.
`protected void`	FullCuratedPublicationEnricher.`processCurationDepth(Publication publicationToEnrich, Publication fetched)`	processCurationDepth.
`protected void`	FullCuratedPublicationUpdater.`processCurationDepth(Publication publicationToEnrich, Publication fetched)`	processCurationDepth.
`protected void`	FullPublicationEnricher.`processCurationDepth(Publication publicationToEnrich, Publication fetched)`	processCurationDepth.
`protected void`	FullPublicationEnricher.`processJournal(Publication publicationToEnrich, Publication fetched)`	processJournal.
`protected void`	FullPublicationUpdater.`processJournal(Publication publicationToEnrich, Publication fetched)`	processJournal.
`protected void`	FullCuratedPublicationEnricher.`processOtherProperties(Publication publicationToEnrich, Publication fetched)`	processOtherProperties.
`protected void`	FullPublicationEnricher.`processOtherProperties(Publication publicationToEnrich, Publication fetched)`	processOtherProperties.
`void`	FullCuratedPublicationUpdater.`processPublication(Publication publicationToEnrich, Publication fetchedPublication)`	The strategy for the enrichment of the publication.
`void`	FullPublicationUpdater.`processPublication(Publication publicationToEnrich, Publication fetchedPublication)`	The strategy for the enrichment of the publication.
`protected void`	FullPublicationEnricher.`processPublicationTitle(Publication publicationToEnrich, Publication fetched)`	processPublicationTitle.
`protected void`	FullPublicationUpdater.`processPublicationTitle(Publication publicationToEnrich, Publication fetched)`	processPublicationTitle.
`protected void`	FullCuratedPublicationEnricher.`processReleasedDate(Publication publicationToEnrich, Publication fetched)`	processReleasedDate.
`protected void`	FullCuratedPublicationUpdater.`processReleasedDate(Publication publicationToEnrich, Publication fetched)`	processReleasedDate.
`protected void`	FullPublicationEnricher.`processReleasedDate(Publication publicationToEnrich, Publication fetched)`	processReleasedDate.
`protected void`	FullPublicationEnricher.`processXrefs(Publication publicationToEnrich, Publication fetched)`	processXrefs.
`protected void`	FullPublicationUpdater.`processXrefs(Publication publicationToEnrich, Publication fetched)`	processXrefs.

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

Methods in psidev.psi.mi.jami.enricher.impl.minimal that return Publication
Modifier and Type	Method	Description
`Publication`	MinimalCuratedPublicationEnricher.`find(Publication objectToEnrich)`	find.
`Publication`	MinimalPublicationEnricher.`find(Publication publicationToEnrich)`	find.

Methods in psidev.psi.mi.jami.enricher.impl.minimal with parameters of type Publication
Modifier and Type	Method	Description
`void`	MinimalCuratedPublicationEnricher.`enrich(Publication objectToEnrich, Publication fetchedObject)`	enrich.
`void`	MinimalPublicationEnricher.`enrich(Publication publicationToEnrich, Publication publicationFetched)`	enrich.
`Publication`	MinimalCuratedPublicationEnricher.`find(Publication objectToEnrich)`	find.
`Publication`	MinimalPublicationEnricher.`find(Publication publicationToEnrich)`	find.
`protected void`	MinimalCuratedPublicationEnricher.`onEnrichedVersionNotFound(Publication objectToEnrich)`	onEnrichedVersionNotFound.
`protected void`	MinimalPublicationEnricher.`onEnrichedVersionNotFound(Publication publicationToEnrich)`	onEnrichedVersionNotFound.
`protected void`	MinimalPublicationEnricher.`processAuthors(Publication publicationToEnrich, Publication fetched)`	processAuthors.
`protected void`	MinimalPublicationUpdater.`processAuthors(Publication publicationToEnrich, Publication fetched)`	processAuthors.
`protected void`	MinimalPublicationEnricher.`processIdentifiers(Publication publicationToEnrich, Publication fetched)`	processIdentifiers.
`protected void`	MinimalPublicationUpdater.`processIdentifiers(Publication publicationToEnrich, Publication fetched)`	processIdentifiers.
`protected void`	MinimalCuratedPublicationEnricher.`processOtherProperties(Publication publicationToEnrich, Publication fetchedPublication)`	processOtherProperties.
`protected void`	MinimalPublicationEnricher.`processOtherProperties(Publication publicationToEnrich, Publication fetchedPublication)`	processOtherProperties.
`void`	MinimalCuratedPublicationEnricher.`processPublication(Publication publicationToEnrich, Publication fetchedPublication)`	The strategy for the enrichment of the publication.
`void`	MinimalPublicationEnricher.`processPublication(Publication publicationToEnrich, Publication fetchedPublication)`	The strategy for the enrichment of the publication.
`protected void`	MinimalPublicationEnricher.`processPublicationDate(Publication publicationToEnrich, Publication fetched)`	processPublicationDate.
`protected void`	MinimalPublicationUpdater.`processPublicationDate(Publication publicationToEnrich, Publication fetched)`	processPublicationDate.
`protected void`	MinimalCuratedPublicationEnricher.`processSource(Publication publicationToEnrich, Publication fetchedPublication)`	processSource.
`protected void`	MinimalCuratedPublicationUpdater.`processSource(Publication publicationToEnrich, Publication fetchedPublication)`	processSource.

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

Methods in psidev.psi.mi.jami.enricher.listener.impl with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationEnricherListenerManager.`onAddedAnnotation(Publication publication, Annotation annotationAdded)`	Listen to the event where an annotation has been added to the object annotations.
`void`	PublicationEnricherListenerManager.`onAddedIdentifier(Publication publication, Xref addedXref)`	Listen to the event where an identifier has been added to the protein identifiers.
`void`	PublicationEnricherListenerManager.`onAddedXref(Publication publication, Xref addedXref)`	Listen to the event where a xref has been added to the protein xrefs.
`void`	PublicationEnricherListenerManager.`onAuthorAdded(Publication publication, String addedAuthor)`	onAuthorAdded
`void`	PublicationEnricherListenerManager.`onAuthorRemoved(Publication publication, String removedAuthor)`	onAuthorRemoved
`void`	PublicationEnricherListenerManager.`onCurationDepthUpdate(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdate
`void`	PublicationEnricherListenerManager.`onDoiUpdate(Publication publication, String oldDoi)`	onDoiUpdate
`void`	PublicationEnricherListenerManager.`onImexIdentifierUpdate(Publication publication, Xref addedXref)`	onImexIdentifierUpdate
`void`	PublicationEnricherListenerManager.`onJournalUpdated(Publication publication, String oldJournal)`	onJournalUpdated
`void`	PublicationEnricherListenerManager.`onPublicationDateUpdated(Publication publication, Date oldDate)`	onPublicationDateUpdated
`void`	ExperimentEnricherListenerManager.`onPublicationUpdate(Experiment experiment, Publication oldPublication)`	onPublicationUpdate
`void`	SourceEnricherListenerManager.`onPublicationUpdate(Source cv, Publication oldPublication)`	Listen to the event where the publication of a source has been changed.
`void`	PublicationEnricherListenerManager.`onPubmedIdUpdate(Publication publication, String oldPubmedId)`	onPubmedIdUpdate
`void`	PublicationEnricherListenerManager.`onReleaseDateUpdated(Publication publication, Date oldDate)`	onReleaseDateUpdated
`void`	PublicationEnricherListenerManager.`onRemovedAnnotation(Publication publication, Annotation annotationRemoved)`	Listen to the event where an annotation has been removed from the object annotations.
`void`	PublicationEnricherListenerManager.`onRemovedIdentifier(Publication publication, Xref removedXref)`	Listen to the event where an identifier has been removed from the protein identifiers.
`void`	PublicationEnricherListenerManager.`onRemovedXref(Publication publication, Xref removedXref)`	Listen to the event where a xref has been removed from the interactor xrefs.
`void`	PublicationEnricherListenerManager.`onSourceUpdated(Publication publication, Source oldSource)`	onSourceUpdated
`void`	PublicationEnricherListenerManager.`onTitleUpdated(Publication publication, String oldTitle)`	onTitleUpdated

Uses of Publication in psidev.psi.mi.jami.enricher.listener.impl.log

Methods in psidev.psi.mi.jami.enricher.listener.impl.log with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationEnricherLogger.`onEnrichmentComplete(Publication publication, EnrichmentStatus status, String message)`	onEnrichmentComplete.
`void`	PublicationEnricherLogger.`onEnrichmentError(Publication object, String message, Exception e)`	onEnrichmentError.

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

Methods in psidev.psi.mi.jami.enricher.listener.impl.writer with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationEnricherStatisticsWriter.`onAddedAnnotation(Publication publication, Annotation annotationAdded)`	Listen to the event where an annotation has been added to the object annotations.
`void`	PublicationEnricherStatisticsWriter.`onAddedIdentifier(Publication publication, Xref addedXref)`	Listen to the event where an identifier has been added to the protein identifiers.
`void`	PublicationEnricherStatisticsWriter.`onAddedXref(Publication publication, Xref addedXref)`	Listen to the event where a xref has been added to the protein xrefs.
`void`	PublicationEnricherStatisticsWriter.`onAuthorAdded(Publication publication, String addedAuthor)`	onAuthorAdded
`void`	PublicationEnricherStatisticsWriter.`onAuthorRemoved(Publication publication, String removedAuthor)`	onAuthorRemoved
`void`	PublicationEnricherStatisticsWriter.`onCurationDepthUpdate(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdate
`void`	PublicationEnricherStatisticsWriter.`onDoiUpdate(Publication publication, String oldDoi)`	onDoiUpdate
`void`	PublicationEnricherStatisticsWriter.`onImexIdentifierUpdate(Publication publication, Xref addedXref)`	onImexIdentifierUpdate
`void`	PublicationEnricherStatisticsWriter.`onJournalUpdated(Publication publication, String oldJournal)`	onJournalUpdated
`void`	PublicationEnricherStatisticsWriter.`onPublicationDateUpdated(Publication publication, Date oldDate)`	onPublicationDateUpdated
`void`	ExperimentEnricherStatisticsWriter.`onPublicationUpdate(Experiment experiment, Publication oldPublication)`	onPublicationUpdate
`void`	SourceEnricherStatisticsWriter.`onPublicationUpdate(Source cv, Publication oldPublication)`	Listen to the event where the publication of a source has been changed.
`void`	PublicationEnricherStatisticsWriter.`onPubmedIdUpdate(Publication publication, String oldPubmedId)`	onPubmedIdUpdate
`void`	PublicationEnricherStatisticsWriter.`onReleaseDateUpdated(Publication publication, Date oldDate)`	onReleaseDateUpdated
`void`	PublicationEnricherStatisticsWriter.`onRemovedAnnotation(Publication publication, Annotation annotationRemoved)`	Listen to the event where an annotation has been removed from the object annotations.
`void`	PublicationEnricherStatisticsWriter.`onRemovedIdentifier(Publication publication, Xref removedXref)`	Listen to the event where an identifier has been removed from the protein identifiers.
`void`	PublicationEnricherStatisticsWriter.`onRemovedXref(Publication publication, Xref removedXref)`	Listen to the event where a xref has been removed from the interactor xrefs.
`void`	PublicationEnricherStatisticsWriter.`onSourceUpdated(Publication publication, Source oldSource)`	onSourceUpdated
`void`	PublicationEnricherStatisticsWriter.`onTitleUpdated(Publication publication, String oldTitle)`	onTitleUpdated

Uses of Publication in psidev.psi.mi.jami.html

Methods in psidev.psi.mi.jami.html with parameters of type Publication
Modifier and Type	Method	Description
`protected void`	MIEvidenceHtmlWriter.`writePublication(Publication publication)`	writePublication
`protected void`	MIModelledHtmlWriter.`writePublication(Publication publication)`	writePublication

Uses of Publication in psidev.psi.mi.jami.imex

Methods in psidev.psi.mi.jami.imex with parameters of type Publication
Modifier and Type	Method	Description
`protected String`	ImexPublicationUpdater.`collectAndCleanUpImexPrimaryReferenceFrom(Publication publication)`	collectAndCleanUpImexPrimaryReferenceFrom.
`ImexPublication`	ImexPublicationAssigner.`find(Publication publicationToEnrich)`	find.
`ImexPublication`	ImexPublicationRegister.`find(Publication publicationToEnrich)`	find.
`ImexPublication`	ImexPublicationUpdater.`find(Publication publicationToEnrich)`	find.
`protected boolean`	ImexPublicationAssigner.`isEntitledToAssignImexId(Publication publicationToEnrich, ImexPublication imexPublication)`	isEntitledToAssignImexId.
`protected void`	ImexPublicationUpdater.`onEnrichedVersionNotFound(Publication publicationToEnrich)`	onEnrichedVersionNotFound.
`protected void`	ImexPublicationAssigner.`processAnnotations(Publication publicationToEnrich, Publication fetched)`	processAnnotations.
`protected void`	ImexPublicationRegister.`processAnnotations(Publication publicationToEnrich, Publication fetched)`	processAnnotations.
`protected void`	ImexPublicationUpdater.`processAnnotations(Publication publicationToEnrich, Publication fetched)`	processAnnotations.
`protected void`	ImexPublicationAssigner.`processAuthors(Publication publicationToEnrich, Publication fetched)`	processAuthors.
`protected void`	ImexPublicationRegister.`processAuthors(Publication publicationToEnrich, Publication fetched)`	processAuthors.
`protected void`	ImexPublicationUpdater.`processAuthors(Publication publicationToEnrich, Publication fetched)`	processAuthors.
`protected void`	ImexPublicationAssigner.`processCurationDepth(Publication publicationToEnrich, Publication fetched)`	processCurationDepth.
`protected void`	ImexPublicationRegister.`processCurationDepth(Publication publicationToEnrich, Publication fetched)`	processCurationDepth.
`protected void`	ImexPublicationUpdater.`processCurationDepth(Publication publicationToEnrich, Publication fetched)`	processCurationDepth.
`protected void`	ImexPublicationAssigner.`processIdentifiers(Publication publicationToEnrich, Publication fetched)`	processIdentifiers.
`protected void`	ImexPublicationRegister.`processIdentifiers(Publication publicationToEnrich, Publication fetched)`	processIdentifiers.
`protected void`	ImexPublicationUpdater.`processIdentifiers(Publication publicationToEnrich, Publication fetched)`	processIdentifiers.
`protected void`	ImexPublicationAssigner.`processJournal(Publication publicationToEnrich, Publication fetched)`	processJournal.
`protected void`	ImexPublicationRegister.`processJournal(Publication publicationToEnrich, Publication fetched)`	processJournal.
`protected void`	ImexPublicationUpdater.`processJournal(Publication publicationToEnrich, Publication fetched)`	processJournal.
`protected void`	ImexPublicationAssigner.`processPublicationDate(Publication publicationToEnrich, Publication fetched)`	processPublicationDate.
`protected void`	ImexPublicationRegister.`processPublicationDate(Publication publicationToEnrich, Publication fetched)`	processPublicationDate.
`protected void`	ImexPublicationUpdater.`processPublicationDate(Publication publicationToEnrich, Publication fetched)`	processPublicationDate.
`protected void`	ImexPublicationAssigner.`processPublicationTitle(Publication publicationToEnrich, Publication fetched)`	processPublicationTitle.
`protected void`	ImexPublicationRegister.`processPublicationTitle(Publication publicationToEnrich, Publication fetched)`	processPublicationTitle.
`protected void`	ImexPublicationUpdater.`processPublicationTitle(Publication publicationToEnrich, Publication fetched)`	processPublicationTitle.
`protected void`	ImexPublicationAssigner.`processReleasedDate(Publication publicationToEnrich, Publication fetched)`	processReleasedDate.
`protected void`	ImexPublicationRegister.`processReleasedDate(Publication publicationToEnrich, Publication fetched)`	processReleasedDate.
`protected void`	ImexPublicationUpdater.`processReleasedDate(Publication publicationToEnrich, Publication fetched)`	processReleasedDate.
`protected void`	ImexPublicationAssigner.`processXrefs(Publication publicationToEnrich, Publication fetched)`	processXrefs.
`protected void`	ImexPublicationRegister.`processXrefs(Publication publicationToEnrich, Publication fetched)`	processXrefs.
`protected void`	ImexPublicationUpdater.`processXrefs(Publication publicationToEnrich, Publication fetched)`	processXrefs.

Uses of Publication in psidev.psi.mi.jami.imex.actions

Methods in psidev.psi.mi.jami.imex.actions that return Publication
Modifier and Type	Method	Description
`Publication`	ImexAssigner.`assignImexIdentifier(Publication publication, Publication imexPublication)`	Assign a new IMEx id to a publication that has not been assigned yet and update/clean up the annotations of the publication (full coverage and imex curation).
`Publication`	ImexCentralPublicationRegister.`getExistingPublicationInImexCentral(String publicationId, String source)`	Retrieve an existing record in IMEx central matching the publication identifier (pubmed, doi, jint or imex).
`Publication`	ImexCentralPublicationRegister.`registerPublicationInImexCentral(Publication publication)`	Register a publication in IMEx central which is not existing in IMEx central.

Methods in psidev.psi.mi.jami.imex.actions with parameters of type Publication
Modifier and Type	Method	Description
`Publication`	ImexAssigner.`assignImexIdentifier(Publication publication, Publication imexPublication)`	Assign a new IMEx id to a publication that has not been assigned yet and update/clean up the annotations of the publication (full coverage and imex curation).
`void`	PublicationStatusSynchronizer.`discardPublicationInImexCentral(Publication publication, ImexPublication imexPublication)`	Synchronize publication status with IMEx central and update the IMEx central record if necessary.
`int`	ImexAssigner.`getNextImexChunkNumberAndFilterValidImexIdsFrom(Publication publication)`	getNextImexChunkNumberAndFilterValidImexIdsFrom.
`PublicationStatus`	PublicationStatusSynchronizer.`getPublicationStatus(Publication publication)`	getPublicationStatus.
`Publication`	ImexCentralPublicationRegister.`registerPublicationInImexCentral(Publication publication)`	Register a publication in IMEx central which is not existing in IMEx central.
`void`	PublicationAdminGroupSynchronizer.`synchronizePublicationAdminGroup(Publication publication, ImexPublication imexPublication)`	Update IMEx central and synchronize the publication ADMIN group.
`void`	PublicationIdentifierSynchronizer.`synchronizePublicationIdentifier(Publication publication, Publication imexPublication)`	Update the IMEx record in case intact publication has a valid pubmed, unassigned or doi identifier that is not in IMEx central.
`void`	PublicationStatusSynchronizer.`synchronizePublicationStatusWithImexCentral(Publication intactPublication, ImexPublication imexPublication)`	Synchronize publication status with IMEx central and update the IMEx central record if necessary.

Uses of Publication in psidev.psi.mi.jami.imex.actions.impl

Methods in psidev.psi.mi.jami.imex.actions.impl that return Publication
Modifier and Type	Method	Description
`Publication`	ImexAssignerImpl.`assignImexIdentifier(Publication publication, Publication imexPublication)`	Assign a new IMEx id to a publication that has not been assigned yet and update/clean up the annotations of the publication (full coverage and imex curation).
`Publication`	ImexCentralPublicationRegisterImpl.`getExistingPublicationInImexCentral(String publicationId, String source)`	Retrieve an existing record in IMEx central matching the publication identifier (pubmed, doi, jint or imex).
`Publication`	ImexCentralPublicationRegisterImpl.`registerPublicationInImexCentral(Publication publication)`	Register a publication in IMEx central which is not existing in IMEx central.

Methods in psidev.psi.mi.jami.imex.actions.impl with parameters of type Publication
Modifier and Type	Method	Description
`Publication`	ImexAssignerImpl.`assignImexIdentifier(Publication publication, Publication imexPublication)`	Assign a new IMEx id to a publication that has not been assigned yet and update/clean up the annotations of the publication (full coverage and imex curation).
`void`	PublicationStatusSynchronizerImpl.`discardPublicationInImexCentral(Publication publication, ImexPublication imexPublication)`	Synchronize publication status with IMEx central and update the IMEx central record if necessary.
`int`	ImexAssignerImpl.`getNextImexChunkNumberAndFilterValidImexIdsFrom(Publication publication)`	getNextImexChunkNumberAndFilterValidImexIdsFrom.
`PublicationStatus`	PublicationStatusSynchronizerImpl.`getPublicationStatus(Publication publication)`	getPublicationStatus.
`Publication`	ImexCentralPublicationRegisterImpl.`registerPublicationInImexCentral(Publication publication)`	Register a publication in IMEx central which is not existing in IMEx central.
`void`	PublicationAdminGroupSynchronizerImpl.`synchronizePublicationAdminGroup(Publication publication, ImexPublication imexPublication)`	Update IMEx central and synchronize the publication ADMIN group.
`void`	PublicationIdentifierSynchronizerImpl.`synchronizePublicationIdentifier(Publication publication, Publication imexPublication)`	Update the IMEx record in case intact publication has a valid pubmed, unassigned or doi identifier that is not in IMEx central.
`void`	PublicationStatusSynchronizerImpl.`synchronizePublicationStatusWithImexCentral(Publication publication, ImexPublication imexPublication)`	Synchronize publication status with IMEx central and update the IMEx central record if necessary.

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

Methods in psidev.psi.mi.jami.imex.listener with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationImexEnricherListener.`onCurationDepthUpdated(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdated.
`void`	PublicationImexEnricherListener.`onImexAdminGroupUpdated(Publication publication, Source oldSource)`	onImexAdminGroupUpdated.
`void`	PublicationImexEnricherListener.`onImexIdAssigned(Publication publication, String imex)`	onImexIdAssigned.
`void`	PublicationImexEnricherListener.`onImexIdConflicts(Publication originalPublication, Collection<Xref> conflictingXrefs)`	onImexIdConflicts.
`void`	PublicationImexEnricherListener.`onImexIdNotRecognized(Publication publication, String imex)`	onImexIdNotRecognized.
`void`	PublicationImexEnricherListener.`onImexPublicationIdentifierSynchronized(Publication publication)`	onImexPublicationIdentifierSynchronized.
`void`	PublicationImexEnricherListener.`onImexStatusUpdated(Publication publication, PublicationStatus oldStatus)`	onImexStatusUpdated.
`void`	PublicationImexEnricherListener.`onMissingImexId(Publication publication)`	onMissingImexId.
`void`	PublicationImexEnricherListener.`onPublicationAlreadyRegisteredInImexCentral(Publication publication, String imex)`	onPublicationAlreadyRegisteredInImexCentral.
`void`	PublicationImexEnricherListener.`onPublicationNotEligibleForImex(Publication publication)`	onPublicationNotEligibleForImex.
`void`	PublicationImexEnricherListener.`onPublicationRegisteredInImexCentral(Publication publication)`	onPublicationRegisteredInImexCentral.
`void`	PublicationImexEnricherListener.`onPublicationWhichCannotBeRegistered(Publication publication)`	onPublicationWhichCannotBeRegistered.

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

Methods in psidev.psi.mi.jami.imex.listener.impl with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationImexEnricherListenerManager.`onCurationDepthUpdated(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdated.
`void`	PublicationImexEnricherLogger.`onCurationDepthUpdated(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdated.
`void`	PublicationImexEnricherStatisticsWriter.`onCurationDepthUpdated(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdated.
`void`	PublicationImexEnricherLogger.`onEnrichmentComplete(Publication publication, EnrichmentStatus status, String message)`	onEnrichmentComplete.
`void`	PublicationImexEnricherLogger.`onEnrichmentError(Publication object, String message, Exception e)`	onEnrichmentError.
`void`	PublicationImexEnricherListenerManager.`onImexAdminGroupUpdated(Publication publication, Source oldSource)`	onImexAdminGroupUpdated.
`void`	PublicationImexEnricherLogger.`onImexAdminGroupUpdated(Publication publication, Source oldSource)`	onImexAdminGroupUpdated.
`void`	PublicationImexEnricherStatisticsWriter.`onImexAdminGroupUpdated(Publication publication, Source oldSource)`	onImexAdminGroupUpdated.
`void`	PublicationImexEnricherListenerManager.`onImexIdAssigned(Publication publication, String imex)`	onImexIdAssigned.
`void`	PublicationImexEnricherLogger.`onImexIdAssigned(Publication publication, String imex)`	onImexIdAssigned.
`void`	PublicationImexEnricherStatisticsWriter.`onImexIdAssigned(Publication publication, String imex)`	onImexIdAssigned.
`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.
`void`	PublicationImexEnricherListenerManager.`onImexIdNotRecognized(Publication publication, String imex)`	onImexIdNotRecognized.
`void`	PublicationImexEnricherLogger.`onImexIdNotRecognized(Publication publication, String imex)`	onImexIdNotRecognized.
`void`	PublicationImexEnricherStatisticsWriter.`onImexIdNotRecognized(Publication publication, String imex)`	onImexIdNotRecognized.
`void`	PublicationImexEnricherListenerManager.`onImexPublicationIdentifierSynchronized(Publication publication)`	onImexPublicationIdentifierSynchronized.
`void`	PublicationImexEnricherLogger.`onImexPublicationIdentifierSynchronized(Publication publication)`	onImexPublicationIdentifierSynchronized.
`void`	PublicationImexEnricherStatisticsWriter.`onImexPublicationIdentifierSynchronized(Publication publication)`	onImexPublicationIdentifierSynchronized.
`void`	PublicationImexEnricherListenerManager.`onImexStatusUpdated(Publication publication, PublicationStatus oldStatus)`	onImexStatusUpdated.
`void`	PublicationImexEnricherLogger.`onImexStatusUpdated(Publication publication, PublicationStatus oldStatus)`	onImexStatusUpdated.
`void`	PublicationImexEnricherStatisticsWriter.`onImexStatusUpdated(Publication publication, PublicationStatus oldStatus)`	onImexStatusUpdated.
`void`	PublicationImexEnricherListenerManager.`onMissingImexId(Publication publication)`	onMissingImexId.
`void`	PublicationImexEnricherLogger.`onMissingImexId(Publication publication)`	onMissingImexId.
`void`	PublicationImexEnricherStatisticsWriter.`onMissingImexId(Publication publication)`	onMissingImexId.
`void`	PublicationImexEnricherListenerManager.`onPublicationAlreadyRegisteredInImexCentral(Publication publication, String imex)`	onPublicationAlreadyRegisteredInImexCentral.
`void`	PublicationImexEnricherLogger.`onPublicationAlreadyRegisteredInImexCentral(Publication publication, String imex)`	onPublicationAlreadyRegisteredInImexCentral.
`void`	PublicationImexEnricherStatisticsWriter.`onPublicationAlreadyRegisteredInImexCentral(Publication publication, String imex)`	onPublicationAlreadyRegisteredInImexCentral.
`void`	PublicationImexEnricherListenerManager.`onPublicationNotEligibleForImex(Publication publication)`	onPublicationNotEligibleForImex.
`void`	PublicationImexEnricherLogger.`onPublicationNotEligibleForImex(Publication publication)`	onPublicationNotEligibleForImex.
`void`	PublicationImexEnricherStatisticsWriter.`onPublicationNotEligibleForImex(Publication publication)`	onPublicationNotEligibleForImex.
`void`	PublicationImexEnricherListenerManager.`onPublicationRegisteredInImexCentral(Publication publication)`	onPublicationRegisteredInImexCentral.
`void`	PublicationImexEnricherLogger.`onPublicationRegisteredInImexCentral(Publication publication)`	onPublicationRegisteredInImexCentral.
`void`	PublicationImexEnricherStatisticsWriter.`onPublicationRegisteredInImexCentral(Publication publication)`	onPublicationRegisteredInImexCentral.
`void`	PublicationImexEnricherListenerManager.`onPublicationWhichCannotBeRegistered(Publication publication)`	onPublicationWhichCannotBeRegistered.
`void`	PublicationImexEnricherLogger.`onPublicationWhichCannotBeRegistered(Publication publication)`	onPublicationWhichCannotBeRegistered.
`void`	PublicationImexEnricherStatisticsWriter.`onPublicationWhichCannotBeRegistered(Publication publication)`	onPublicationWhichCannotBeRegistered.

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

Methods in psidev.psi.mi.jami.json.elements that return types with arguments of type Publication
Modifier and Type	Method	Description
`JsonElementWriter<Publication>`	SimpleJsonExperimentWriter.`getPublicationWriter()`	Getter for the field `publicationWriter`.

Methods in psidev.psi.mi.jami.json.elements with parameters of type Publication
Modifier and Type	Method	Description
`void`	SimpleJsonPublicationWriter.`write(Publication object)`	write.

Method parameters in psidev.psi.mi.jami.json.elements with type arguments of type Publication
Modifier and Type	Method	Description
`void`	SimpleJsonExperimentWriter.`setPublicationWriter(JsonElementWriter<Publication> publicationWriter)`	Setter for the field `publicationWriter`.

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

Methods in psidev.psi.mi.jami.listener with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationChangeListener.`onAuthorAdded(Publication publication, String addedAuthor)`	onAuthorAdded
`void`	PublicationChangeListener.`onAuthorRemoved(Publication publication, String removedAuthor)`	onAuthorRemoved
`void`	PublicationChangeListener.`onCurationDepthUpdate(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdate
`void`	PublicationChangeListener.`onDoiUpdate(Publication publication, String oldDoi)`	onDoiUpdate
`void`	PublicationChangeListener.`onImexIdentifierUpdate(Publication publication, Xref addedXref)`	onImexIdentifierUpdate
`void`	PublicationChangeListener.`onJournalUpdated(Publication publication, String oldJournal)`	onJournalUpdated
`void`	PublicationChangeListener.`onPublicationDateUpdated(Publication publication, Date oldDate)`	onPublicationDateUpdated
`void`	ExperimentChangeListener.`onPublicationUpdate(Experiment experiment, Publication oldPublication)`	onPublicationUpdate
`void`	SourceChangeListener.`onPublicationUpdate(Source cv, Publication oldPublication)`	Listen to the event where the publication of a source has been changed.
`void`	PublicationChangeListener.`onPubmedIdUpdate(Publication publication, String oldPubmedId)`	onPubmedIdUpdate
`void`	PublicationChangeListener.`onReleaseDateUpdated(Publication publication, Date oldDate)`	onReleaseDateUpdated
`void`	PublicationChangeListener.`onSourceUpdated(Publication publication, Source oldSource)`	onSourceUpdated
`void`	PublicationChangeListener.`onTitleUpdated(Publication publication, String oldTitle)`	onTitleUpdated

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

Methods in psidev.psi.mi.jami.listener.impl with parameters of type Publication
Modifier and Type	Method	Description
`void`	PublicationChangeLogger.`onAddedAnnotation(Publication publication, Annotation added)`	Listen to the event where an annotation has been added to the object annotations.
`void`	PublicationChangeLogger.`onAddedIdentifier(Publication publication, Xref added)`	Listen to the event where an identifier has been added to the protein identifiers.
`void`	PublicationChangeLogger.`onAddedXref(Publication publication, Xref added)`	Listen to the event where a xref has been added to the protein xrefs.
`void`	PublicationChangeLogger.`onAuthorAdded(Publication publication, String addedAuthor)`	onAuthorAdded
`void`	PublicationChangeLogger.`onAuthorRemoved(Publication publication, String removedAuthor)`	onAuthorRemoved
`void`	PublicationChangeLogger.`onCurationDepthUpdate(Publication publication, CurationDepth oldDepth)`	onCurationDepthUpdate
`void`	PublicationChangeLogger.`onDoiUpdate(Publication publication, String oldId)`	onDoiUpdate
`void`	PublicationChangeLogger.`onImexIdentifierUpdate(Publication publication, Xref oldId)`	onImexIdentifierUpdate
`void`	PublicationChangeLogger.`onJournalUpdated(Publication publication, String oldJournal)`	onJournalUpdated
`void`	PublicationChangeLogger.`onPublicationDateUpdated(Publication publication, Date oldDate)`	onPublicationDateUpdated
`void`	ExperimentChangeLogger.`onPublicationUpdate(Experiment experiment, Publication oldPublication)`	onPublicationUpdate
`void`	SourceChangeLogger.`onPublicationUpdate(Source cv, Publication oldPublication)`	Listen to the event where the publication of a source has been changed.
`void`	PublicationChangeLogger.`onPubmedIdUpdate(Publication publication, String oldId)`	onPubmedIdUpdate
`void`	PublicationChangeLogger.`onReleaseDateUpdated(Publication publication, Date oldDate)`	onReleaseDateUpdated
`void`	PublicationChangeLogger.`onRemovedAnnotation(Publication publication, Annotation removed)`	Listen to the event where an annotation has been removed from the object annotations.
`void`	PublicationChangeLogger.`onRemovedIdentifier(Publication publication, Xref removed)`	Listen to the event where an identifier has been removed from the protein identifiers.
`void`	PublicationChangeLogger.`onRemovedXref(Publication publication, Xref removed)`	Listen to the event where a xref has been removed from the interactor xrefs.
`void`	PublicationChangeLogger.`onSourceUpdated(Publication publication, Source oldSource)`	onSourceUpdated
`void`	PublicationChangeLogger.`onTitleUpdated(Publication publication, String oldTitle)`	onTitleUpdated

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

Methods in psidev.psi.mi.jami.model that return Publication
Modifier and Type	Method	Description
`Publication`	CooperativityEvidence.`getPublication()`	The publication where the cooperativityEvidence has been described.
`Publication`	Experiment.`getPublication()`	The publication where the experiment has been described.
`Publication`	ModelledConfidence.`getPublication()`	The publication where this confidence has been reported if relevant, null otherwise.
`Publication`	ModelledParameter.`getPublication()`	The publication where this parameter has been reported if relevant, null otherwise.
`Publication`	Source.`getPublication()`	Bibliographical reference of the data source.

Methods in psidev.psi.mi.jami.model with parameters of type Publication
Modifier and Type	Method	Description
`void`	CooperativityEvidence.`setPublication(Publication publication)`	Set the publication where the cooperativityEvidence has been described.
`void`	Experiment.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	ModelledConfidence.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	ModelledParameter.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	Source.`setPublication(Publication ref)`	Set the bibliographical reference
`void`	Experiment.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

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

Classes in psidev.psi.mi.jami.model.impl that implement Publication
Modifier and Type	Class	Description
`class`	`DefaultPublication`	Default implementation for a Publication Notes: The equals and hashcode methods have NOT been overridden because the Publication object is a complex object.

Methods in psidev.psi.mi.jami.model.impl that return Publication
Modifier and Type	Method	Description
`Publication`	DefaultCooperativityEvidence.`getPublication()`	Getter for the field `publication`.
`Publication`	DefaultExperiment.`getPublication()`	Getter for the field `publication`.
`Publication`	DefaultModelledConfidence.`getPublication()`	Getter for the field `publication`.
`Publication`	DefaultModelledParameter.`getPublication()`	Getter for the field `publication`.
`Publication`	DefaultSource.`getPublication()`	getPublication

Methods in psidev.psi.mi.jami.model.impl with parameters of type Publication
Modifier and Type	Method	Description
`void`	DefaultCooperativityEvidence.`setPublication(Publication publication)`	Set the publication where the cooperativityEvidence has been described.
`void`	DefaultExperiment.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	DefaultModelledConfidence.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	DefaultModelledParameter.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	DefaultSource.`setPublication(Publication ref)`	Set the bibliographical reference
`void`	DefaultExperiment.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

Constructors in psidev.psi.mi.jami.model.impl with parameters of type Publication
Constructor	Description
`DefaultCooperativityEvidence(Publication publication)`	Constructor for DefaultCooperativityEvidence.
`DefaultExperiment(Publication publication)`	Constructor for DefaultExperiment.
`DefaultExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for DefaultExperiment.
`DefaultExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for DefaultExperiment.
`DefaultModelledConfidence(CvTerm type, String value, Publication publication)`	Constructor for DefaultModelledConfidence.
`DefaultNamedExperiment(Publication publication)`	Constructor for DefaultNamedExperiment.
`DefaultNamedExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for DefaultNamedExperiment.
`DefaultNamedExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for DefaultNamedExperiment.
`DefaultSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultSource.
`DefaultSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultSource.
`DefaultSource(String shortName, String url, String address, Publication bibRef)`	Constructor for DefaultSource.
`DefaultSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultSource.
`DefaultSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultSource.

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

Classes in psidev.psi.mi.jami.tab.extension that implement Publication
Modifier and Type	Class	Description
`class`	`MitabPublication`	Mitab extension of Publication.

Constructors in psidev.psi.mi.jami.tab.extension with parameters of type Publication
Constructor	Description
`MitabExperiment(Publication publication)`	Constructor for MitabExperiment.
`MitabExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for MitabExperiment.
`MitabExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for MitabExperiment.
`MitabSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for MitabSource.
`MitabSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for MitabSource.
`MitabSource(String shortName, String url, String address, Publication bibRef)`	Constructor for MitabSource.
`MitabSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for MitabSource.
`MitabSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for MitabSource.

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

Methods in psidev.psi.mi.jami.tab.io.writer.feeder with parameters of type Publication
Modifier and Type	Method	Description
`protected void`	MitabInteractionEvidenceFeeder.`writeInteractionAnnotationTagsFrom(Publication pub)`	writeInteractionAnnotationTagsFrom.
`protected void`	MitabInteractionEvidenceFeeder.`writePublicationImexId(Publication pub, boolean writeFieldSeparator)`	writePublicationImexId.

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

Methods in psidev.psi.mi.jami.utils that return Publication
Modifier and Type	Method	Description
`static Publication`	PublicationUtils.`createBasicPublicationForModelledInteractions()`	createBasicPublicationForModelledInteractions
`static Publication`	PublicationUtils.`createPublicationDoi(String doi)`	createPublicationDoi
`static Publication`	PublicationUtils.`createPublicationPubmed(String pubmed)`	createPublicationPubmed
`static Publication`	PublicationUtils.`createUnknownBasicPublication()`	createUnknownBasicPublication

Methods in psidev.psi.mi.jami.utils with parameters of type Publication
Modifier and Type	Method	Description
`static Xref`	PublicationUtils.`getDoiReference(Publication pub)`	getDoiReference
`static Xref`	PublicationUtils.`getPubmedReference(Publication pub)`	getPubmedReference

Uses of Publication in psidev.psi.mi.jami.utils.clone

Methods in psidev.psi.mi.jami.utils.clone with parameters of type Publication
Modifier and Type	Method	Description
`static void`	PublicationCloner.`copyAndOverridePublicationProperties(Publication source, Publication target)`	This method will copy properties of publication source in publication target and will override all the other properties of Target publication.
`static void`	PublicationCloner.`copyAndOverridePublicationPropertiesAndExperiments(Publication source, Publication target)`	copyAndOverridePublicationPropertiesAndExperiments

Uses of Publication in psidev.psi.mi.jami.utils.comparator.cooperativity

Methods in psidev.psi.mi.jami.utils.comparator.cooperativity that return types with arguments of type Publication
Modifier and Type	Method	Description
`Comparator<Publication>`	CooperativityEvidenceComparator.`getPublicationComparator()`	Getter for the field `publicationComparator`.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.cooperativity with type arguments of type Publication
Constructor	Description
`CooperativityEvidenceComparator(CollectionComparator<CvTerm> cvTermComparator, Comparator<Publication> publicationComparator)`	Constructor for CooperativityEvidenceComparator.

Uses of Publication in psidev.psi.mi.jami.utils.comparator.experiment

Methods in psidev.psi.mi.jami.utils.comparator.experiment that return types with arguments of type Publication
Modifier and Type	Method	Description
`Comparator<Publication>`	ExperimentComparator.`getPublicationComparator()`	Getter for the field `publicationComparator`.

Constructor parameters in psidev.psi.mi.jami.utils.comparator.experiment with type arguments of type Publication
Constructor	Description
`ExperimentComparator(Comparator<Publication> publicationComparator, OrganismComparator organismComparator)`	Creates a new ExperimentComparator.
`ExperimentComparator(Comparator<Publication> publicationComparator, OrganismComparator organismComparator, CollectionComparator<VariableParameter> variableParameter)`	Constructor for ExperimentComparator.

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

Methods in psidev.psi.mi.jami.utils.comparator.publication that return types with arguments of type Publication
Modifier and Type	Method	Description
`Comparator<Publication>`	CuratedPublicationComparator.`getPublicationComparator()`	Getter for the field `publicationComparator`.

Methods in psidev.psi.mi.jami.utils.comparator.publication with parameters of type Publication
Modifier and Type	Method	Description
`static boolean`	DefaultCuratedPublicationComparator.`areEquals(Publication publication1, Publication publication2)`	Use DefaultCuratedPublicationComparator to know if two publications are equals.
`static boolean`	DefaultPublicationComparator.`areEquals(Publication publication1, Publication publication2)`	Use DefaultPublicationComparator to know if two publications are equals.
`static boolean`	UnambiguousCuratedPublicationComparator.`areEquals(Publication pub1, Publication pub2)`	Use UnambiguousCuratedPublicationComparator to know if two publications are equals.
`static boolean`	UnambiguousPublicationComparator.`areEquals(Publication pub1, Publication pub2)`	Use UnambiguousPublicationComparator to know if two publications are equals.
`int`	CuratedPublicationComparator.`compare(Publication publication1, Publication publication2)`	It uses a AbstractPublicationComparator to compares the bibliographic details and then will compare first the curation depth, then the source and then the released date.
`int`	PublicationComparator.`compare(Publication publication1, Publication publication2)`	It will first compare IMEx identifiers (publication with IMEx will always come first).
`int`	UnambiguousCuratedPublicationComparator.`compare(Publication publication1, Publication publication2)`	It uses a AbstractPublicationComparator to compares the bibliographic details and then will compare first the curation depth, then the source and then the released date.
`static int`	UnambiguousCuratedPublicationComparator.`hashCode(Publication pub)`	hashCode
`static int`	UnambiguousPublicationComparator.`hashCode(Publication pub)`	hashCode

Constructor parameters in psidev.psi.mi.jami.utils.comparator.publication with type arguments of type Publication
Constructor	Description
`CuratedPublicationComparator(Comparator<Publication> pubComparator, Comparator<CvTerm> sourceComparator)`	Creates a new CuratedPublicationComparator.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements that return Publication
Modifier and Type	Method	Description
`Publication`	PsiXmlExperimentWriter.`getDefaultPublication()`	getDefaultPublication.

Methods in psidev.psi.mi.jami.xml.io.writer.elements with parameters of type Publication
Modifier and Type	Method	Description
`void`	PsiXmlExperimentWriter.`setDefaultPublication(Publication pub)`	Sets the default publication to write in case an experiment does not have a publication
`void`	PsiXmlPublicationWriter.`writeAllPublicationAttributes(Publication object)`	writeAllPublicationAttributes.
`void`	PsiXmlPublicationWriter.`writeAllPublicationAttributes(Publication object, Collection<Annotation> attributesToFilter)`	writeAllPublicationAttributes.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl that return types with arguments of type Publication
Modifier and Type	Method	Description
`PsiXmlElementWriter<Publication>`	AbstractXmlSourceWriter.`getPublicationWriter()`	Getter for the field `publicationWriter`.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl with type arguments of type Publication
Modifier and Type	Method	Description
`void`	AbstractXmlSourceWriter.`setPublicationWriter(PsiXmlElementWriter<Publication> publicationWriter)`	Setter for the field `publicationWriter`.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractXmlExperimentWriter.`getDefaultPublication()`	getDefaultPublication.
`protected Publication`	AbstractXmlInteractionWriter.`newPublication(String pubmed)`
`protected Publication`	AbstractXmlInteractionWriter.`newPublication(String title, String journal, Date publicationDate)`

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts with parameters of type Publication
Modifier and Type	Method	Description
`protected ExtendedPsiXmlExperiment`	AbstractXmlInteractionWriter.`newExperiment(Publication publication)`
`void`	AbstractXmlExperimentWriter.`setDefaultPublication(Publication pub)`	Sets the default publication to write in case an experiment does not have a publication
`void`	AbstractXmlPublicationWriter.`write(Publication object)`	write.
`void`	AbstractXmlPublicationWriter.`writeAllPublicationAttributes(Publication object)`	writeAllPublicationAttributes.
`void`	AbstractXmlPublicationWriter.`writeAllPublicationAttributes(Publication object, Collection<Annotation> attributesToFilter)`	writeAllPublicationAttributes.
`protected abstract void`	AbstractXmlPublicationWriter.`writeBibrefContent(Publication object)`	writeBibrefContent.
`protected void`	AbstractXmlPublicationWriter.`writePublicationPropertiesAsAttributes(Publication object, boolean hasTitle, boolean hasJournal, boolean hasPublicationDate, boolean hasCurationDepth, boolean hasAuthors)`	writePublicationPropertiesAsAttributes.
`protected void`	AbstractXmlPublicationWriter.`writeXrefFromPublicationIdentifiers(Publication object)`	writeXrefFromPublicationIdentifiers.
`protected void`	AbstractXmlPublicationWriter.`writeXrefFromPublicationXrefs(Publication object)`	writeXrefFromPublicationXrefs.

Uses of Publication in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25 with parameters of type Publication
Modifier and Type	Method	Description
`protected void`	XmlPublicationWriter.`writeBibrefContent(Publication object)`	writeBibrefContent.

Uses of Publication in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 that return types with arguments of type Publication
Modifier and Type	Method	Description
`PsiXmlElementWriter<Publication>`	XmlCooperativityEvidenceWriter.`getPublicationWriter()`	Getter for the field `publicationWriter`.

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 with parameters of type Publication
Modifier and Type	Method	Description
`protected void`	XmlPublicationWriter.`writeBibrefContent(Publication object)`	writeBibrefContent.

Method parameters in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 with type arguments of type Publication
Modifier and Type	Method	Description
`void`	XmlCooperativityEvidenceWriter.`setPublicationWriter(PsiXmlElementWriter<Publication> publicationWriter)`	Setter for the field `publicationWriter`.

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

Classes in psidev.psi.mi.jami.xml.model.extension.xml253 that implement Publication
Modifier and Type	Class	Description
`class`	`BibRef`	Xml implementation of a Publication

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractXmlExperiment.`getPublication()`	Getter for the field `publication`.
`Publication`	AbstractXmlSource.`getPublication()`	getPublication.
`Publication`	ExperimentXrefContainer.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlConfidenceWrapper.`getPublication()`	The publication where this confidence has been reported if relevant, null otherwise.
`Publication`	XmlCooperativityEvidence.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlModelledConfidence.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlModelledParameter.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlParameterWrapper.`getPublication()`	The publication where this parameter has been reported if relevant, null otherwise.

Methods in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Publication
Modifier and Type	Method	Description
`void`	AbstractXmlExperiment.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	AbstractXmlSource.`setPublication(Publication ref)`	Set the bibliographical reference
`void`	ExperimentXrefContainer.`setPublication(Publication publication)`	Setter for the field `publication`.
`void`	XmlConfidenceWrapper.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	XmlCooperativityEvidence.`setPublication(Publication publication)`	Set the publication where the cooperativityEvidence has been described.
`void`	XmlModelledConfidence.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	XmlModelledParameter.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	XmlParameterWrapper.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	AbstractXmlExperiment.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

Constructors in psidev.psi.mi.jami.xml.model.extension.xml253 with parameters of type Publication
Constructor	Description
`AbstractXmlExperiment(Publication publication)`	Constructor for AbstractXmlExperiment.
`AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for AbstractXmlExperiment.
`AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for AbstractXmlExperiment.
`AbstractXmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`DefaultXmlExperiment(Publication publication)`	Constructor for DefaultXmlExperiment.
`DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for DefaultXmlExperiment.
`DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for DefaultXmlExperiment.
`DefaultXmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`XmlExperiment(Publication publication)`	Constructor for XmlExperiment.
`XmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for XmlExperiment.
`XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for XmlExperiment.
`XmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for XmlSource.

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

Classes in psidev.psi.mi.jami.xml.model.extension.xml254 that implement Publication
Modifier and Type	Class	Description
`class`	`BibRef`	Xml implementation of a Publication

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractXmlExperiment.`getPublication()`	Getter for the field `publication`.
`Publication`	AbstractXmlSource.`getPublication()`	getPublication.
`Publication`	ExperimentXrefContainer.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlConfidenceWrapper.`getPublication()`	The publication where this confidence has been reported if relevant, null otherwise.
`Publication`	XmlCooperativityEvidence.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlModelledConfidence.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlModelledParameter.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlParameterWrapper.`getPublication()`	The publication where this parameter has been reported if relevant, null otherwise.

Methods in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Publication
Modifier and Type	Method	Description
`void`	AbstractXmlExperiment.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	AbstractXmlSource.`setPublication(Publication ref)`	Set the bibliographical reference
`void`	ExperimentXrefContainer.`setPublication(Publication publication)`	Setter for the field `publication`.
`void`	XmlConfidenceWrapper.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	XmlCooperativityEvidence.`setPublication(Publication publication)`	Set the publication where the cooperativityEvidence has been described.
`void`	XmlModelledConfidence.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	XmlModelledParameter.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	XmlParameterWrapper.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	AbstractXmlExperiment.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

Constructors in psidev.psi.mi.jami.xml.model.extension.xml254 with parameters of type Publication
Constructor	Description
`AbstractXmlExperiment(Publication publication)`	Constructor for AbstractXmlExperiment.
`AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for AbstractXmlExperiment.
`AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for AbstractXmlExperiment.
`AbstractXmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`DefaultXmlExperiment(Publication publication)`	Constructor for DefaultXmlExperiment.
`DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for DefaultXmlExperiment.
`DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for DefaultXmlExperiment.
`DefaultXmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`XmlExperiment(Publication publication)`	Constructor for XmlExperiment.
`XmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for XmlExperiment.
`XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for XmlExperiment.
`XmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for XmlSource.

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

Classes in psidev.psi.mi.jami.xml.model.extension.xml300 that implement Publication
Modifier and Type	Class	Description
`class`	`BibRef`	Xml implementation of a Publication

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractXmlExperiment.`getPublication()`	Getter for the field `publication`.
`Publication`	AbstractXmlSource.`getPublication()`	getPublication.
`Publication`	ExperimentXrefContainer.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlConfidenceWrapper.`getPublication()`	The publication where this confidence has been reported if relevant, null otherwise.
`Publication`	XmlCooperativityEvidence.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlModelledConfidence.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlModelledParameter.`getPublication()`	Getter for the field `publication`.
`Publication`	XmlParameterWrapper.`getPublication()`	The publication where this parameter has been reported if relevant, null otherwise.

Methods in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Publication
Modifier and Type	Method	Description
`void`	AbstractXmlExperiment.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	AbstractXmlSource.`setPublication(Publication ref)`	Set the bibliographical reference
`void`	ExperimentXrefContainer.`setPublication(Publication publication)`	Setter for the field `publication`.
`void`	XmlConfidenceWrapper.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	XmlCooperativityEvidence.`setPublication(Publication publication)`	Set the publication where the cooperativityEvidence has been described.
`void`	XmlModelledConfidence.`setPublication(Publication publication)`	Sets the publication of this confidence
`void`	XmlModelledParameter.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	XmlParameterWrapper.`setPublication(Publication publication)`	Sets the publication of this parameter
`void`	AbstractXmlExperiment.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

Constructors in psidev.psi.mi.jami.xml.model.extension.xml300 with parameters of type Publication
Constructor	Description
`AbstractXmlExperiment(Publication publication)`	Constructor for AbstractXmlExperiment.
`AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for AbstractXmlExperiment.
`AbstractXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for AbstractXmlExperiment.
`AbstractXmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`AbstractXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for AbstractXmlSource.
`DefaultXmlExperiment(Publication publication)`	Constructor for DefaultXmlExperiment.
`DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for DefaultXmlExperiment.
`DefaultXmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for DefaultXmlExperiment.
`DefaultXmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`DefaultXmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for DefaultXmlSource.
`XmlCooperativityEvidence(Publication pub)`	Constructor for XmlCooperativityEvidence.
`XmlExperiment(Publication publication)`	Constructor for XmlExperiment.
`XmlExperiment(Publication publication, CvTerm interactionDetectionMethod)`	Constructor for XmlExperiment.
`XmlExperiment(Publication publication, CvTerm interactionDetectionMethod, Organism organism)`	Constructor for XmlExperiment.
`XmlSource(String shortName, String fullName, String miId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String miId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, String fullName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for XmlSource.
`XmlSource(String shortName, Xref ontologyId, String url, String address, Publication bibRef)`	Constructor for XmlSource.

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

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractExperimentRef.`getPublication()`	getPublication.

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 with parameters of type Publication
Modifier and Type	Method	Description
`void`	AbstractExperimentRef.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	AbstractExperimentRef.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

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

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractExperimentRef.`getPublication()`	getPublication.

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 with parameters of type Publication
Modifier and Type	Method	Description
`void`	AbstractExperimentRef.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	AbstractExperimentRef.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

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

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 that return Publication
Modifier and Type	Method	Description
`Publication`	AbstractExperimentRef.`getPublication()`	getPublication.

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 with parameters of type Publication
Modifier and Type	Method	Description
`void`	AbstractExperimentRef.`setPublication(Publication publication)`	Set the publication where the experiment has been described.
`void`	AbstractExperimentRef.`setPublicationAndAddExperiment(Publication publication)`	Set the publication where the experiment has been described and add the experiment to the list of experiments for this publication If publication is null, it will remove this experiment from the previous publication attached to this experiment

Uses of Interfacepsidev.psi.mi.jami.model.Publication

Uses of Publication in psidev.psi.mi.jami.bridges.europubmedcentral

Uses of Publication in psidev.psi.mi.jami.bridges.fetcher

Uses of Publication in psidev.psi.mi.jami.bridges.fetcher.mock

Uses of Publication in psidev.psi.mi.jami.bridges.imex

Uses of Publication in psidev.psi.mi.jami.bridges.imex.extension

Uses of Publication in psidev.psi.mi.jami.bridges.imex.mock

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

Uses of Publication in psidev.psi.mi.jami.datasource

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

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

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

Uses of Publication in psidev.psi.mi.jami.enricher.listener.impl.log

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

Uses of Publication in psidev.psi.mi.jami.html

Uses of Publication in psidev.psi.mi.jami.imex

Uses of Publication in psidev.psi.mi.jami.imex.actions

Uses of Publication in psidev.psi.mi.jami.imex.actions.impl

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

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

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

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

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

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

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

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

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

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

Uses of Publication in psidev.psi.mi.jami.utils.clone

Uses of Publication in psidev.psi.mi.jami.utils.comparator.cooperativity

Uses of Publication in psidev.psi.mi.jami.utils.comparator.experiment

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

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

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

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

Uses of Publication in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25

Uses of Publication in psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30

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

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

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

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

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

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

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