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

Packages that use Source

Package	Description
psidev.psi.mi.jami.binary.impl
psidev.psi.mi.jami.bridges.fetcher.mock
psidev.psi.mi.jami.bridges.imex.extension
psidev.psi.mi.jami.bridges.obo
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.commons
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.log
psidev.psi.mi.jami.enricher.listener.impl.writer
psidev.psi.mi.jami.imex.actions.impl
psidev.psi.mi.jami.imex.listener
psidev.psi.mi.jami.imex.listener.impl
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.utils.clone
psidev.psi.mi.jami.xml.io.writer
psidev.psi.mi.jami.xml.io.writer.compact
psidev.psi.mi.jami.xml.io.writer.compact.extended
psidev.psi.mi.jami.xml.io.writer.elements.impl
psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25
psidev.psi.mi.jami.xml.io.writer.expanded
psidev.psi.mi.jami.xml.io.writer.expanded.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.xml253
psidev.psi.mi.jami.xml.model.reference.xml254
psidev.psi.mi.jami.xml.model.reference.xml300

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

Methods in psidev.psi.mi.jami.binary.impl that return Source

Modifier and Type	Method	Description
Source	DefaultModelledBinaryInteraction.getSource()	Getter for the field source.
Source	ModelledBinaryInteractionWrapper.getSource()	getSource

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

Modifier and Type	Method	Description
void	DefaultModelledBinaryInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	ModelledBinaryInteractionWrapper.setSource(Source source)	Sets the source reporting the interaction.

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

Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return Source

Modifier and Type	Method	Description
Source	MockSourceFetcher.fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
Source	MockSourceFetcher.fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Source	MockSourceFetcher.fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.

Methods in psidev.psi.mi.jami.bridges.fetcher.mock that return types with arguments of type Source

Modifier and Type	Method	Description
Collection<Source>	MockSourceFetcher.fetchByIdentifiers(Collection<String> identifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<Source>	MockSourceFetcher.fetchByIdentifiers(Collection<String> identifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<Source>	MockSourceFetcher.fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<Source>	MockSourceFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<Source>	MockSourceFetcher.fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.

Methods in psidev.psi.mi.jami.bridges.fetcher.mock with parameters of type Source

Modifier and Type	Method	Description
void	MockSourceFetcher.addOntologyTerm(String identifier, Source source)	addOntologyTerm.

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

Methods in psidev.psi.mi.jami.bridges.imex.extension that return Source

Modifier and Type	Method	Description
Source	ImexPublication.getSource()	Getter for the field source.

Methods in psidev.psi.mi.jami.bridges.imex.extension that return types with arguments of type Source

Modifier and Type	Method	Description
List<Source>	ImexPublication.getSources()	Getter for the field sources.

Methods in psidev.psi.mi.jami.bridges.imex.extension with parameters of type Source

Modifier and Type	Method	Description
void	ImexPublication.setSource(Source source)	Sets the source who curated the publication.

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

Methods in psidev.psi.mi.jami.bridges.obo that return Source

Modifier and Type	Method	Description
protected Source	SourceOboLoader.instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.

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

Modifier and Type	Method	Description
protected void	SourceOboLoader.createDefinitionFor(String def, Source term)	createDefinitionFor.

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

Classes in psidev.psi.mi.jami.bridges.ols that implement Source

Modifier and Type	Class	Description
class	LazySource	A lazy cvTerm which will only fetch metadata when required.

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

Modifier and Type	Method	Description
protected Source	OlsSourceFetcher.instantiateCvTerm(String termName, Xref identity, String ontologyName)	instantiateCvTerm.

Uses of Source in psidev.psi.mi.jami.commons

Methods in psidev.psi.mi.jami.commons with parameters of type Source

Modifier and Type	Method	Description
Map<String,Object>	MIWriterOptionFactory.getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, PsiXmlVersion version)	Create the options for the compact PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getCompactXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)	Create the options for the compact PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, PsiXmlVersion version)	Create the options for the expanded PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getExpandedXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlObjectCache elementCache, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)	Create the options for the compact PSI-XML InteractionWriter.
Map<String,Object>	MIWriterOptionFactory.getXmlOptions(Object output, InteractionCategory objectCategory, ComplexType complexType, PsiXmlType xmlType, PsiXmlObjectCache elementCache, Set<Experiment> experimentSet, Set<Interactor> interactorSet, Set<String> availabilitySet, Set<Interaction> interactionSet, Source defaultSource, XMLGregorianCalendar defaultReleaseDate, Collection<Annotation> defaultEntryAnnotations, boolean writeComplexAsInteractors, boolean extended, PsiXmlVersion version)	Create the options for the PSI-XML InteractionWriter.

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

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

Constructor	Description
CsvInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for CsvInteractionEvidence.
CsvInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for CsvInteractionEvidence.

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

Constructor parameters in psidev.psi.mi.jami.enricher.impl.full with type arguments of type Source

Constructor	Description
FullSourceUpdater(FullCvTermUpdater<Source> cvTermUpdater)	Constructor for FullSourceUpdater.

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

Methods in psidev.psi.mi.jami.enricher.impl.minimal that return Source

Modifier and Type	Method	Description
Source	MinimalSourceEnricher.find(Source objectToEnrich)	find.

Methods in psidev.psi.mi.jami.enricher.impl.minimal that return types with arguments of type Source

Modifier and Type	Method	Description
CvTermEnricherListener<Source>	MinimalSourceEnricher.getCvTermEnricherListener()	getCvTermEnricherListener.
CvTermFetcher<Source>	MinimalSourceEnricher.getCvTermFetcher()	getCvTermFetcher.
protected MinimalCvTermEnricher<Source>	MinimalSourceEnricher.getDelegate()	Getter for the field delegate.

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

Modifier and Type	Method	Description
void	MinimalSourceEnricher.enrich(Source cvTermToEnrich, Source cvTermFetched)	enrich.
Source	MinimalSourceEnricher.find(Source objectToEnrich)	find.
protected void	MinimalSourceEnricher.onEnrichedVersionNotFound(Source objectToEnrich)	onEnrichedVersionNotFound.
protected void	MinimalSourceEnricher.processPublication(Source cvTermToEnrich, Source cvTermFetched)	processPublication.
protected void	MinimalSourceUpdater.processPublication(Source cvTermToEnrich, Source cvTermFetched)	processPublication.
protected void	MinimalSourceEnricher.processSource(Source cvTermToEnrich, Source cvTermFetched)	A method that can be overridden to add to or change the behaviour of enrichment without effecting fetching.

Method parameters in psidev.psi.mi.jami.enricher.impl.minimal with type arguments of type Source

Modifier and Type	Method	Description
void	MinimalSourceEnricher.setCvTermEnricherListener(CvTermEnricherListener<Source> listener)	setCvTermEnricherListener.

Constructor parameters in psidev.psi.mi.jami.enricher.impl.minimal with type arguments of type Source

Constructor	Description
MinimalSourceEnricher(MinimalCvTermEnricher<Source> cvEnricher)	Constructor for MinimalSourceEnricher.
MinimalSourceUpdater(MinimalCvTermEnricher<Source> cvEnricher)	Constructor for MinimalSourceUpdater.

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

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

Modifier and Type	Method	Description
void	SourceEnricherListenerManager.onPostalAddressUpdate(Source cv, String oldPostalAddress)	Listen to the event where the postal address of a source has been changed.
void	SourceEnricherListenerManager.onPublicationUpdate(Source cv, Publication oldPublication)	Listen to the event where the publication of a source has been changed.
void	ModelledInteractionEnricherListenerManager.onSourceUpdate(I interaction, Source oldSource)	onSourceUpdate
void	PublicationEnricherListenerManager.onSourceUpdated(Publication publication, Source oldSource)	onSourceUpdated
void	SourceEnricherListenerManager.onUrlUpdate(Source cv, String oldUrl)	Listen to the event where the URL of a source has been changed.

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

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

Modifier and Type	Method	Description
void	SourceEnricherLogger.onEnrichmentComplete(Source cvTerm, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	SourceEnricherLogger.onEnrichmentError(Source object, String message, Exception e)	onEnrichmentError.

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

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

Modifier and Type	Method	Description
void	SourceEnricherStatisticsWriter.onPostalAddressUpdate(Source cv, String oldPostalAddress)	Listen to the event where the postal address of a source has been changed.
void	SourceEnricherStatisticsWriter.onPublicationUpdate(Source cv, Publication oldPublication)	Listen to the event where the publication of a source has been changed.
void	ModelledInteractionEnricherStatisticsWriter.onSourceUpdate(I interaction, Source oldSource)	onSourceUpdate
void	PublicationEnricherStatisticsWriter.onSourceUpdated(Publication publication, Source oldSource)	onSourceUpdated
void	SourceEnricherStatisticsWriter.onUrlUpdate(Source cv, String oldUrl)	Listen to the event where the URL of a source has been changed.

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

Methods in psidev.psi.mi.jami.imex.actions.impl that return Source

Modifier and Type	Method	Description
protected Source	PublicationAdminGroupSynchronizerImpl.getImexPublicationOwnerGroup(List<Source> adminGroupList, Set<String> imexPartners)	checks any of the sources is a imex partner.

Methods in psidev.psi.mi.jami.imex.actions.impl with parameters of type Source

Modifier and Type	Method	Description
protected boolean	PublicationAdminGroupSynchronizerImpl.containsAdminGroup(List<Source> adminGroupList, Source group)	containsAdminGroup.

Method parameters in psidev.psi.mi.jami.imex.actions.impl with type arguments of type Source

Modifier and Type	Method	Description
protected boolean	PublicationAdminGroupSynchronizerImpl.containsAdminGroup(List<Source> adminGroupList, Source group)	containsAdminGroup.
protected Source	PublicationAdminGroupSynchronizerImpl.getImexPublicationOwnerGroup(List<Source> adminGroupList, Set<String> imexPartners)	checks any of the sources is a imex partner.

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

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

Modifier and Type	Method	Description
void	PublicationImexEnricherListener.onImexAdminGroupUpdated(Publication publication, Source oldSource)	onImexAdminGroupUpdated.

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

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

Modifier and Type	Method	Description
void	PublicationImexEnricherListenerManager.onImexAdminGroupUpdated(Publication publication, Source oldSource)	onImexAdminGroupUpdated.
void	PublicationImexEnricherLogger.onImexAdminGroupUpdated(Publication publication, Source oldSource)	onImexAdminGroupUpdated.
void	PublicationImexEnricherStatisticsWriter.onImexAdminGroupUpdated(Publication publication, Source oldSource)	onImexAdminGroupUpdated.

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

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

Modifier and Type	Method	Description
void	SourceChangeListener.onPostalAddressUpdate(Source cv, String oldPostalAddress)	Listen to the event where the postal address of a source has been changed.
void	SourceChangeListener.onPublicationUpdate(Source cv, Publication oldPublication)	Listen to the event where the publication of a source has been changed.
void	ModelledInteractionChangeListener.onSourceUpdate(I interaction, Source oldSource)	onSourceUpdate
void	PublicationChangeListener.onSourceUpdated(Publication publication, Source oldSource)	onSourceUpdated
void	SourceChangeListener.onUrlUpdate(Source cv, String oldUrl)	Listen to the event where the URL of a source has been changed.

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

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

Modifier and Type	Method	Description
void	SourceChangeLogger.onPostalAddressUpdate(Source cv, String oldPostalAddress)	Listen to the event where the postal address of a source has been changed.
void	SourceChangeLogger.onPublicationUpdate(Source cv, Publication oldPublication)	Listen to the event where the publication of a source has been changed.
void	ComplexChangeLogger.onSourceUpdate(Complex interaction, Source oldSource)	onSourceUpdate
void	ModelledInteractionChangeLogger.onSourceUpdate(I interaction, Source oldSource)	onSourceUpdate
void	PublicationChangeLogger.onSourceUpdated(Publication publication, Source oldSource)	onSourceUpdated
void	SourceChangeLogger.onUrlUpdate(Source cv, String oldUrl)	Listen to the event where the URL of a source has been changed.

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

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

Modifier and Type	Method	Description
Source	ModelledInteraction.getSource()	The source which reported this modelled interaction.
Source	Publication.getSource()	The source which curated this publication.

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

Modifier and Type	Method	Description
void	ModelledInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	Publication.setSource(Source source)	Sets the source who curated the publication.

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

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

Modifier and Type	Class	Description
class	DefaultSource	Default implementation for Source Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparator

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

Modifier and Type	Method	Description
Source	DefaultComplex.getSource()	Getter for the field source.
Source	DefaultModelledInteraction.getSource()	Getter for the field source.
Source	DefaultPublication.getSource()	Getter for the field source.

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

Modifier and Type	Method	Description
void	DefaultComplex.setSource(Source source)	Sets the source reporting the interaction.
void	DefaultModelledInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	DefaultPublication.setSource(Source source)	Sets the source who curated the publication.

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

Constructor	Description
DefaultInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for DefaultInteractionEvidence.
DefaultInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultInteractionEvidence.
DefaultModelledInteraction(String shortName, Source source)	Constructor for DefaultModelledInteraction.
DefaultModelledInteraction(String shortName, Source source, CvTerm type)	Constructor for DefaultModelledInteraction.
DefaultNamedInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for DefaultNamedInteractionEvidence.
DefaultNamedModelledInteraction(String shortName, Source source)	Constructor for DefaultNamedModelledInteraction.
DefaultNamedModelledInteraction(String shortName, Source source, CvTerm type)	Constructor for DefaultNamedModelledInteraction.
DefaultPublication(String title, String journal, Date publicationDate, String imexId, Source source)	Constructor for DefaultPublication.
DefaultPublication(String title, String journal, Date publicationDate, CurationDepth curationDepth, Source source)	Constructor for DefaultPublication.
DefaultPublication(String pubmed, String imexId, Source source)	Constructor for DefaultPublication.
DefaultPublication(String pubmed, CurationDepth curationDepth, Source source)	Constructor for DefaultPublication.
DefaultPublication(Xref identifier, String imexId, Source source)	Constructor for DefaultPublication.
DefaultPublication(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for DefaultPublication.

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

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

Modifier and Type	Class	Description
class	MitabSource	Mitab extension of DefaultMitabSource It contains a FileSourceLocator

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

Constructor	Description
MitabInteractionEvidence(String shortName, Source source, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Source source)	Constructor for MitabInteractionEvidence.
MitabInteractionEvidence(Experiment experiment, String shortName, Source source, Xref imexId)	Constructor for MitabInteractionEvidence.
MitabModelledInteraction(String shortName, Source source)	Constructor for MitabModelledInteraction.
MitabModelledInteraction(String shortName, Source source, CvTerm type)	Constructor for MitabModelledInteraction.
MitabPublication(String title, String journal, Date publicationDate, String imexId, Source source)	Constructor for MitabPublication.
MitabPublication(String title, String journal, Date publicationDate, CurationDepth curationDepth, Source source)	Constructor for MitabPublication.
MitabPublication(String pubmed, String imexId, Source source)	Constructor for MitabPublication.
MitabPublication(String pubmed, CurationDepth curationDepth, Source source)	Constructor for MitabPublication.
MitabPublication(Xref identifier, String imexId, Source source)	Constructor for MitabPublication.
MitabPublication(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for MitabPublication.

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

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

Modifier and Type	Method	Description
static void	CvTermCloner.copyAndOverrideSourceProperties(Source source, Source target)	This method will copy basic properties and source specific properties from a source to a target

Uses of Source in psidev.psi.mi.jami.xml.io.writer

Methods in psidev.psi.mi.jami.xml.io.writer that return Source

Modifier and Type	Method	Description
protected Source	AbstractXmlWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	AbstractXmlWriter.getCurrentSource()	Getter for the field currentSource.

Methods in psidev.psi.mi.jami.xml.io.writer with parameters of type Source

Modifier and Type	Method	Description
protected void	AbstractXmlWriter.setCurrentSource(Source currentSource)	Setter for the field currentSource.
void	AbstractXmlWriter.setDefaultSource(Source defaultSource)	Setter for the field defaultSource.

Uses of Source in psidev.psi.mi.jami.xml.io.writer.compact

Methods in psidev.psi.mi.jami.xml.io.writer.compact that return Source

Modifier and Type	Method	Description
protected Source	CompactXmlBinaryEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlComplexWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlModelledBinaryWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlModelledWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlNamedBinaryEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlNamedEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlNamedModelledBinaryWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlNamedModelledWriter.extractSourceFromInteraction()	extractSourceFromInteraction.

Methods in psidev.psi.mi.jami.xml.io.writer.compact with parameters of type Source

Modifier and Type	Method	Description
void	AbstractCompactXmlMixWriter.setDefaultSource(Source defaultSource)	Setter for the field defaultSource.

Uses of Source in psidev.psi.mi.jami.xml.io.writer.compact.extended

Methods in psidev.psi.mi.jami.xml.io.writer.compact.extended that return Source

Modifier and Type	Method	Description
protected Source	CompactXmlBinaryEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlComplexWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlModelledBinaryWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	CompactXmlModelledWriter.extractSourceFromInteraction()	extractSourceFromInteraction.

Uses of Source 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 Source

Modifier and Type	Method	Description
void	AbstractXmlSourceWriter.write(Source object)	write.
protected void	AbstractXmlSourceWriter.writeAttributes(Source object)	writeAttributes.
protected void	AbstractXmlSourceWriter.writeBibRef(Source object)	writeBibRef.
protected void	AbstractXmlSourceWriter.writeNames(Source object)	writeNames.
protected void	AbstractXmlSourceWriter.writeReleaseAttributes(Source object)	writeReleaseAttributes.
protected void	AbstractXmlSourceWriter.writeXref(Source object)	writeXref.
protected void	AbstractXmlSourceWriter.writeXrefFromSourceIdentifiers(Source object)	writeXrefFromSourceIdentifiers.
protected void	AbstractXmlSourceWriter.writeXrefFromSourceXrefs(Source object)	writeXrefFromSourceXrefs.

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

Methods in psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25 with parameters of type Source

Modifier and Type	Method	Description
protected void	XmlSourceWriter.writeReleaseAttributes(Source object)	writeReleaseAttributes.

Uses of Source in psidev.psi.mi.jami.xml.io.writer.expanded

Methods in psidev.psi.mi.jami.xml.io.writer.expanded that return Source

Modifier and Type	Method	Description
protected Source	ExpandedXmlBinaryEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlComplexWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlModelledBinaryWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlModelledWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlNamedBinaryEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlNamedEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlNamedModelledBinaryWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlNamedModelledWriter.extractSourceFromInteraction()	extractSourceFromInteraction.

Methods in psidev.psi.mi.jami.xml.io.writer.expanded with parameters of type Source

Modifier and Type	Method	Description
void	AbstractExpandedXmlMixWriter.setDefaultSource(Source defaultSource)	Setter for the field defaultSource.

Uses of Source in psidev.psi.mi.jami.xml.io.writer.expanded.extended

Methods in psidev.psi.mi.jami.xml.io.writer.expanded.extended that return Source

Modifier and Type	Method	Description
protected Source	ExpandedXmlBinaryEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlComplexWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlEvidenceWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlModelledBinaryWriter.extractSourceFromInteraction()	extractSourceFromInteraction.
protected Source	ExpandedXmlModelledWriter.extractSourceFromInteraction()	extractSourceFromInteraction.

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

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

Modifier and Type	Interface	Description
interface	ExtendedPsiXmlSource	Extended source for PSI-XML standards

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

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

Modifier and Type	Method	Description
Source	XmlModelledBinaryInteraction.getSource()	Getter for the field source.
Source	XmlModelledBinaryInteractionWrapper.getSource()	The source which reported this modelled interaction.

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

Modifier and Type	Method	Description
void	XmlModelledBinaryInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	XmlModelledBinaryInteractionWrapper.setSource(Source source)	Sets the source reporting the interaction.

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

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

Modifier and Type	Method	Description
Source	XmlModelledBinaryInteraction.getSource()	Getter for the field source.
Source	XmlModelledBinaryInteractionWrapper.getSource()	The source which reported this modelled interaction.

Methods in psidev.psi.mi.jami.xml.model.extension.binary.xml30 with parameters of type Source

Modifier and Type	Method	Description
void	XmlModelledBinaryInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	XmlModelledBinaryInteractionWrapper.setSource(Source source)	Sets the source reporting the interaction.

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

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

Modifier and Type	Class	Description
class	AbstractXmlSource	Desciption of the source of the entry, usually an organisation
class	DefaultXmlSource	Desciption of the source of the entry, usually an organisation
class	XmlSource	Desciption of the source of the entry, usually an organisation

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

Modifier and Type	Method	Description
Source	AbstractXmlModelledInteraction.getSource()	Getter for the field source.
Source	BibRef.getSource()	Getter for the field source.
Source	XmlBasicInteractionComplexWrapper.getSource()	Getter for the field source.
Source	XmlInteractionEvidenceComplexWrapper.getSource()	getSource.
Source	XmlModelledInteractionComplexWrapper.getSource()	getSource.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	BibRef.setSource(Source source)	Sets the source who curated the publication.
void	XmlBasicInteractionComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.
void	XmlInteractionEvidenceComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.
void	XmlModelledInteractionComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.

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

Constructor	Description
BibRef(String title, String journal, Date publicationDate, String imexId, Source source)	Constructor for BibRef.
BibRef(String title, String journal, Date publicationDate, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(String pubmed, String imexId, Source source)	Constructor for BibRef.
BibRef(String pubmed, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.

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

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

Modifier and Type	Class	Description
class	AbstractXmlSource	Desciption of the source of the entry, usually an organisation
class	DefaultXmlSource	Desciption of the source of the entry, usually an organisation
class	XmlSource	Desciption of the source of the entry, usually an organisation

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

Modifier and Type	Method	Description
Source	AbstractXmlModelledInteraction.getSource()	Getter for the field source.
Source	BibRef.getSource()	Getter for the field source.
Source	XmlBasicInteractionComplexWrapper.getSource()	Getter for the field source.
Source	XmlInteractionEvidenceComplexWrapper.getSource()	getSource.
Source	XmlModelledInteractionComplexWrapper.getSource()	getSource.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	BibRef.setSource(Source source)	Sets the source who curated the publication.
void	XmlBasicInteractionComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.
void	XmlInteractionEvidenceComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.
void	XmlModelledInteractionComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.

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

Constructor	Description
BibRef(String title, String journal, Date publicationDate, String imexId, Source source)	Constructor for BibRef.
BibRef(String title, String journal, Date publicationDate, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(String pubmed, String imexId, Source source)	Constructor for BibRef.
BibRef(String pubmed, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.

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

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

Modifier and Type	Class	Description
class	AbstractXmlSource	Desciption of the source of the entry, usually an organisation
class	DefaultXmlSource	Desciption of the source of the entry, usually an organisation
class	XmlSource	Desciption of the source of the entry, usually an organisation

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

Modifier and Type	Method	Description
Source	AbstractXmlModelledInteraction.getSource()	Getter for the field source.
Source	BibRef.getSource()	Getter for the field source.
Source	XmlBasicInteractionComplexWrapper.getSource()	Getter for the field source.
Source	XmlInteractionEvidenceComplexWrapper.getSource()	getSource.
Source	XmlModelledInteraction.getSource()	Getter for the field source.
Source	XmlModelledInteractionComplexWrapper.getSource()	getSource.

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

Modifier and Type	Method	Description
void	AbstractXmlModelledInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	BibRef.setSource(Source source)	Sets the source who curated the publication.
void	XmlBasicInteractionComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.
void	XmlInteractionEvidenceComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.
void	XmlModelledInteraction.setSource(Source source)	Sets the source reporting the interaction.
void	XmlModelledInteractionComplexWrapper.setSource(Source source)	Sets the source reporting the interaction.

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

Constructor	Description
BibRef(String title, String journal, Date publicationDate, String imexId, Source source)	Constructor for BibRef.
BibRef(String title, String journal, Date publicationDate, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(String pubmed, String imexId, Source source)	Constructor for BibRef.
BibRef(String pubmed, CurationDepth curationDepth, Source source)	Constructor for BibRef.
BibRef(Xref identifier, String imexId, Source source)	Constructor for BibRef.
BibRef(Xref identifier, CurationDepth curationDepth, Source source)	Constructor for BibRef.

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

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

Modifier and Type	Method	Description
Source	AbstractComplexRef.getSource()	getSource.

Methods in psidev.psi.mi.jami.xml.model.reference.xml253 with parameters of type Source

Modifier and Type	Method	Description
void	AbstractComplexRef.setSource(Source source)	Sets the source reporting the interaction.

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

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

Modifier and Type	Method	Description
Source	AbstractComplexRef.getSource()	getSource.

Methods in psidev.psi.mi.jami.xml.model.reference.xml254 with parameters of type Source

Modifier and Type	Method	Description
void	AbstractComplexRef.setSource(Source source)	Sets the source reporting the interaction.

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

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

Modifier and Type	Method	Description
Source	AbstractComplexRef.getSource()	getSource.

Methods in psidev.psi.mi.jami.xml.model.reference.xml300 with parameters of type Source

Modifier and Type	Method	Description
void	AbstractComplexRef.setSource(Source source)	Sets the source reporting the interaction.