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

Packages that use Protein

Package	Description
psidev.psi.mi.jami.bridges.fetcher.mock
psidev.psi.mi.jami.bridges.mapper
psidev.psi.mi.jami.bridges.mapper.listener
psidev.psi.mi.jami.bridges.mapper.mock
psidev.psi.mi.jami.bridges.uniprot
psidev.psi.mi.jami.crosslink.extension
psidev.psi.mi.jami.enricher.impl.full
psidev.psi.mi.jami.enricher.impl.minimal
psidev.psi.mi.jami.factory
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.tab.extension
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.comparator.interactor
psidev.psi.mi.jami.xml.model.extension.factory
psidev.psi.mi.jami.xml.model.extension.xml253
psidev.psi.mi.jami.xml.model.extension.xml254
psidev.psi.mi.jami.xml.model.extension.xml300

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

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

Modifier and Type	Method	Description
Collection<Protein>	FailingProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Protein>	MockProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Protein>	FailingProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Protein>	MockProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
protected Collection<Protein>	FailingProteinFetcher.getEntry(String identifier)	getEntry.
protected Collection<Protein>	MockProteinFetcher.getEntry(String identifier)	getEntry.

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

Modifier and Type	Method	Description
void	FailingProteinFetcher.addEntry(String identifier, Protein protein)	addEntry.

Uses of Protein in psidev.psi.mi.jami.bridges.mapper

Methods in psidev.psi.mi.jami.bridges.mapper with parameters of type Protein

Modifier and Type	Method	Description
void	ProteinMapper.map(Protein p)	Will remap the protein using the settings provided.
void	ProteinMapperListener.onFailedMapping(Protein p, Collection<String> report)	onFailedMapping.
void	ProteinMapperListener.onSuccessfulMapping(Protein p, Collection<String> report)	A stacked report listing the exit case first, followed by any errors, the approaches used and the strategy.
void	ProteinMapperListener.onToBeReviewedMapping(Protein p, Collection<String> report)	onToBeReviewedMapping.

Uses of Protein in psidev.psi.mi.jami.bridges.mapper.listener

Methods in psidev.psi.mi.jami.bridges.mapper.listener with parameters of type Protein

Modifier and Type	Method	Description
void	ProteinMappingLogger.onFailedMapping(Protein p, Collection<String> report)	onFailedMapping.
void	ProteinMappingStatisticsWriter.onFailedMapping(Protein p, Collection<String> report)	onFailedMapping.
void	ProteinMappingLogger.onSuccessfulMapping(Protein p, Collection<String> report)	A stacked report listing the exit case first, followed by any errors, the approaches used and the strategy.
void	ProteinMappingStatisticsWriter.onSuccessfulMapping(Protein p, Collection<String> report)	A stacked report listing the exit case first, followed by any errors, the approaches used and the strategy.
void	ProteinMappingLogger.onToBeReviewedMapping(Protein p, Collection<String> report)	onToBeReviewedMapping.
void	ProteinMappingStatisticsWriter.onToBeReviewedMapping(Protein p, Collection<String> report)	onToBeReviewedMapping.

Uses of Protein in psidev.psi.mi.jami.bridges.mapper.mock

Methods in psidev.psi.mi.jami.bridges.mapper.mock with parameters of type Protein

Modifier and Type	Method	Description
void	MockProteinMapper.map(Protein p)	Will remap the protein using the settings provided.

Uses of Protein in psidev.psi.mi.jami.bridges.uniprot

Methods in psidev.psi.mi.jami.bridges.uniprot that return types with arguments of type Protein

Modifier and Type	Method	Description
Collection<Protein>	CachedUniprotProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Protein>	UniprotProteinFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Protein>	CachedUniprotProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Protein>	UniprotProteinFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.

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

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

Modifier and Type	Class	Description
class	CsvProtein	Crosslink CSV extension of Protein.

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

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

Modifier and Type	Method	Description
void	FullFeatureEvidenceEnricher.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FullFeatureEvidenceUpdater.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FullFeatureUpdater.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	FullFeatureEvidenceEnricher.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FullFeatureEvidenceUpdater.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FullFeatureUpdater.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	FullFeatureEvidenceEnricher.onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	FullFeatureEvidenceUpdater.onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	FullFeatureUpdater.onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	FullFeatureEvidenceEnricher.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FullFeatureEvidenceUpdater.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FullFeatureUpdater.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	FullFeatureEvidenceEnricher.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FullFeatureEvidenceUpdater.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FullFeatureUpdater.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	FullFeatureEvidenceEnricher.onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	FullFeatureEvidenceUpdater.onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	FullFeatureUpdater.onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	FullFeatureEvidenceEnricher.onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	FullFeatureEvidenceUpdater.onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	FullFeatureUpdater.onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	FullFeatureEvidenceEnricher.onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
void	FullFeatureEvidenceUpdater.onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
void	FullFeatureUpdater.onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
void	FullFeatureEvidenceEnricher.onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
void	FullFeatureEvidenceUpdater.onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
void	FullFeatureUpdater.onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
void	FullFeatureEvidenceEnricher.onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
void	FullFeatureEvidenceUpdater.onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
void	FullFeatureUpdater.onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
void	FullFeatureEvidenceEnricher.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FullFeatureEvidenceUpdater.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FullFeatureUpdater.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	FullFeatureEvidenceEnricher.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FullFeatureEvidenceUpdater.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FullFeatureUpdater.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	FullFeatureEvidenceEnricher.onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	FullFeatureEvidenceUpdater.onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	FullFeatureUpdater.onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	FullFeatureEvidenceEnricher.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FullFeatureEvidenceUpdater.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FullFeatureUpdater.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	FullFeatureEvidenceEnricher.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FullFeatureEvidenceUpdater.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FullFeatureUpdater.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	FullFeatureEvidenceEnricher.onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	FullFeatureEvidenceUpdater.onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	FullFeatureUpdater.onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	FullFeatureEvidenceEnricher.onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
void	FullFeatureEvidenceUpdater.onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
void	FullFeatureUpdater.onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
protected void	FullProteinEnricher.processOtherProperties(Protein proteinToEnrich, Protein fetched)	processOtherProperties.
protected void	FullProteinUpdater.processOtherProperties(Protein proteinToEnrich, Protein fetched)	processOtherProperties.

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

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

Modifier and Type	Method	Description
Protein	MinimalProteinEnricher.find(Protein proteinToEnrich)	find.
Protein	MinimalProteinUpdater.find(Protein objectToEnrich)	find.

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

Modifier and Type	Method	Description
protected boolean	MinimalProteinEnricher.canEnrichInteractor(Protein entityToEnrich, Protein fetchedEntity)	canEnrichInteractor.
Protein	MinimalProteinEnricher.find(Protein proteinToEnrich)	find.
Protein	MinimalProteinUpdater.find(Protein objectToEnrich)	find.
void	MinimalFeatureEnricher.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	MinimalFeatureEvidenceUpdater.onAddedAlias(Protein o, Alias added)	Listen to the event where an alias has been added to the object aliases.
void	MinimalFeatureEnricher.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	MinimalFeatureEvidenceUpdater.onAddedAnnotation(Protein o, Annotation added)	Listen to the event where an annotation has been added to the object annotations.
void	MinimalFeatureEnricher.onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	MinimalFeatureEvidenceUpdater.onAddedChecksum(Protein interactor, Checksum added)	Listen to the event where a checksum has been added to the interactor checksums.
void	MinimalFeatureEnricher.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	MinimalFeatureEvidenceUpdater.onAddedIdentifier(Protein o, Xref added)	Listen to the event where an identifier has been added to the protein identifiers.
void	MinimalFeatureEnricher.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
void	MinimalFeatureEvidenceUpdater.onAddedXref(Protein o, Xref added)	Listen to the event where a xref has been added to the protein xrefs.
protected void	MinimalProteinEnricher.onCompletedEnrichment(Protein objectToEnrich)	onCompletedEnrichment.
protected void	MinimalProteinEnricher.onEnrichedVersionNotFound(Protein objectToEnrich)	onEnrichedVersionNotFound.
void	MinimalFeatureEnricher.onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	MinimalFeatureEvidenceUpdater.onEnrichmentComplete(Protein object, EnrichmentStatus status, String message)	onEnrichmentComplete.
void	MinimalFeatureEnricher.onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	MinimalFeatureEvidenceUpdater.onEnrichmentError(Protein object, String message, Exception e)	onEnrichmentError.
void	MinimalFeatureEnricher.onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
void	MinimalFeatureEvidenceUpdater.onFullNameUpdate(Protein interactor, String oldFullName)	Listens for the event where the fullName has been changed.
protected void	MinimalProteinEnricher.onInteractorCheckFailure(Protein objectToEnrich, Protein fetchedObject)	onInteractorCheckFailure.
void	MinimalFeatureEnricher.onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
void	MinimalFeatureEvidenceUpdater.onInteractorTypeUpdate(Protein interactor, CvTerm old)	Listen to the event where the interactor type has been initialised.
void	MinimalFeatureEnricher.onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
void	MinimalFeatureEvidenceUpdater.onOrganismUpdate(Protein interactor, Organism o)	Listen to the event where the organism of a interactor has been initialised.
void	MinimalFeatureEnricher.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	MinimalFeatureEvidenceUpdater.onRemovedAlias(Protein o, Alias removed)	Listen to the event where an alias has been removed from the object aliases.
void	MinimalFeatureEnricher.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	MinimalFeatureEvidenceUpdater.onRemovedAnnotation(Protein o, Annotation removed)	Listen to the event where an annotation has been removed from the object annotations.
void	MinimalFeatureEnricher.onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	MinimalFeatureEvidenceUpdater.onRemovedChecksum(Protein interactor, Checksum removed)	Listen to the event where a checksum has been removed from the interactor checksums.
void	MinimalFeatureEnricher.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	MinimalFeatureEvidenceUpdater.onRemovedIdentifier(Protein o, Xref removed)	Listen to the event where an identifier has been removed from the protein identifiers.
void	MinimalFeatureEnricher.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	MinimalFeatureEvidenceUpdater.onRemovedXref(Protein o, Xref removed)	Listen to the event where a xref has been removed from the interactor xrefs.
void	MinimalFeatureEnricher.onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	MinimalFeatureEvidenceUpdater.onSequenceUpdate(Protein protein, String oldSequence)	Listen to the event where the sequence of a protein has been changed.
void	MinimalFeatureEnricher.onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
void	MinimalFeatureEvidenceUpdater.onShortNameUpdate(Protein interactor, String oldShortName)	Listens for the event where the shortName has been changed.
protected void	MinimalProteinEnricher.processDeadUniprotIdentity(Protein proteinToEnrich, Xref uniprotIdentity)	processDeadUniprotIdentity.
protected void	MinimalProteinUpdater.processDeadUniprotIdentity(Protein proteinToEnrich, String oldUniprot)	processDeadUniprotIdentity.
protected boolean	MinimalProteinEnricher.remapProtein(Protein proteinToEnrich)	Attempts to remap the protein using the provided proteinRemapper.

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

Methods in psidev.psi.mi.jami.factory that return Protein

Modifier and Type	Method	Description
Protein	DefaultInteractorFactory.createProtein(String name, CvTerm type)	Creates a new Protein with the name and interactor type
Protein	InteractorFactory.createProtein(String name, CvTerm type)	Creates a new Protein with the name and interactor type

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

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

Modifier and Type	Class	Description
class	DefaultProtein	Default implementation for proteins and peptides Notes: The equals and hashcode methods have NOT been overridden because the Protein object is a complex object.

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

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

Modifier and Type	Class	Description
class	MitabProtein	Mitab extension of Protein.

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

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

Modifier and Type	Method	Description
static Protein	InteractorUtils.createProteinGeneName(String name, String geneName)	createProteinGeneName
static Protein	InteractorUtils.createProteinRefseq(String name, String refseq)	createProteinRefseq
static Protein	InteractorUtils.createProteinRogid(String name, String rogid)	createProteinRogid
static Protein	InteractorUtils.createProteinUniprot(String name, String uniprot)	createProteinUniprot

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

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

Modifier and Type	Method	Description
Comparator<Protein>	InteractorComparator.getProteinComparator()	Getter for the field proteinComparator.

Methods in psidev.psi.mi.jami.utils.comparator.interactor with parameters of type Protein

Modifier and Type	Method	Description
static boolean	DefaultExactProteinComparator.areEquals(Protein protein1, Protein protein2)	Use DefaultExactProteinComparator to know if two proteins are equals.
static boolean	DefaultProteinComparator.areEquals(Protein protein1, Protein protein2)	Use DefaultProteinComparator to know if two proteins are equals.
static boolean	UnambiguousExactProteinComparator.areEquals(Protein protein1, Protein protein2)	Use DefaultExactProteinComparator to know if two proteins are equals.
static boolean	UnambiguousProteinComparator.areEquals(Protein protein1, Protein protein2)	Use UnambiguousProteinComparator to know if two proteins are equals.
int	ProteinComparator.compare(Protein protein1, Protein protein2)	It will first use UnambiguousPolymerComparator to compare the basic interactor properties If the basic interactor properties are the same, It will look for uniprotkb identifier (The interactor with non null uniprot id will always come first).
int	UnambiguousExactProteinComparator.compare(Protein protein1, Protein protein2)

Uses of Protein in psidev.psi.mi.jami.xml.model.extension.factory

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

Modifier and Type	Method	Description
Protein	XmlInteractorFactory.createProtein(String name, CvTerm type)	Creates a new Protein with the name and interactor type

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

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

Modifier and Type	Class	Description
class	XmlProtein	Xml implementation of protein

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

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

Modifier and Type	Class	Description
class	XmlProtein	Xml implementation of protein

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

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

Modifier and Type	Class	Description
class	XmlProtein	Xml implementation of protein