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

Packages that use Gene

Package	Description
psidev.psi.mi.jami.bridges.fetcher
psidev.psi.mi.jami.bridges.fetcher.mock
psidev.psi.mi.jami.bridges.uniprot
psidev.psi.mi.jami.enricher.impl
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 Gene in psidev.psi.mi.jami.bridges.fetcher

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

Modifier and Type	Method	Description
Collection<Gene>	GeneFetcher.fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
Collection<Gene>	GeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)	fetchByIdentifiers.

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

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

Modifier and Type	Method	Description
Collection<Gene>	FailingGeneFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifier(String identifier, int taxID)
Collection<Gene>	MockGeneFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	MockGeneFetcher.fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	FailingGeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)
Collection<Gene>	MockGeneFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	MockGeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)
protected Collection<Gene>	FailingGeneFetcher.getEntry(String identifier)	getEntry.
protected Collection<Gene>	MockGeneFetcher.getEntry(String identifier)	getEntry.

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

Modifier and Type	Method	Description
void	FailingGeneFetcher.addEntry(String identifier, Gene gene)	addEntry.

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

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

Modifier and Type	Method	Description
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	UniprotGeneFetcher.fetchByIdentifiers(Collection<String> identifiers, int taxID)	fetchByIdentifiers.
Collection<Gene>	CachedUniprotGeneFetcher.getByIdentifier(String identifier)	getByIdentifier.
Collection<Gene>	CachedUniprotGeneFetcher.getByIdentifier(String identifier, int taxID)	getByIdentifier.

Uses of Gene in psidev.psi.mi.jami.enricher.impl

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

Modifier and Type	Method	Description
InteractorEnricher<Gene>	CompositeInteractorEnricher.getGeneEnricher()	Getter for the field geneEnricher.

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

Modifier and Type	Method	Description
void	CompositeInteractorEnricher.setGeneEnricher(InteractorEnricher<Gene> geneEnricher)	Setter for the field geneEnricher.

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

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

Modifier and Type	Method	Description
Gene	MinimalGeneEnricher.find(Gene geneToEnrich)	find.

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

Modifier and Type	Method	Description
protected boolean	MinimalGeneEnricher.canEnrichInteractor(Gene entityToEnrich, Gene fetchedEntity)	canEnrichInteractor.
Gene	MinimalGeneEnricher.find(Gene geneToEnrich)	find.
protected void	MinimalGeneEnricher.onCompletedEnrichment(Gene objectToEnrich)	onCompletedEnrichment.
protected void	MinimalGeneEnricher.onEnrichedVersionNotFound(Gene objectToEnrich)	onEnrichedVersionNotFound.
protected void	MinimalGeneEnricher.onInteractorCheckFailure(Gene objectToEnrich, Gene fetchedObject)	onInteractorCheckFailure.

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

Constructor	Description
MinimalGeneUpdater(AbstractInteractorEnricher<Gene> interactorEnricher)	Constructor for MinimalGeneUpdater.

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

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

Modifier and Type	Method	Description
Gene	DefaultInteractorFactory.createGene(String name)	Creates a new Gene with the name
Gene	InteractorFactory.createGene(String name)	Creates a new Gene with the name

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

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

Modifier and Type	Class	Description
class	DefaultGene	Default implementation for gene Notes: The equals and hashcode methods have NOT been overridden because the Gene object is a complex object.

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

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

Modifier and Type	Class	Description
class	MitabGene	Mitab extension for Gene.

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

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

Modifier and Type	Method	Description
static Gene	InteractorUtils.createGeneEnsembl(String name, String identity)	createGeneEnsembl
static Gene	InteractorUtils.createGeneEnsemblGenomes(String name, String identity)	createGeneEnsemblGenomes
static Gene	InteractorUtils.createGeneEntrezGene(String name, String identity)	createGeneEntrezGene
static Gene	InteractorUtils.createGeneRefseq(String name, String identity)	createGeneRefseq

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

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

Modifier and Type	Method	Description
Comparator<Gene>	InteractorComparator.getGeneComparator()	Getter for the field geneComparator.

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

Modifier and Type	Method	Description
static boolean	DefaultExactGeneComparator.areEquals(Gene gene1, Gene gene2)	Use DefaultGeneComparator to know if two genes are equals.
static boolean	DefaultGeneComparator.areEquals(Gene gene1, Gene gene2)	Use DefaultGeneComparator to know if two genes are equals.
static boolean	UnambiguousExactGeneComparator.areEquals(Gene gene1, Gene gene2)	Use DefaultGeneComparator to know if two genes are equals.
static boolean	UnambiguousGeneComparator.areEquals(Gene gene1, Gene gene2)	Use UnambiguousGeneComparator to know if two genes are equals.
int	GeneComparator.compare(Gene gene1, Gene gene2)	It will first use UnambiguousInteractorBaseComparator to compare the basic interactor properties If the basic interactor properties are the same, It will look at ensembl identifier (the interactor with non null ensembl identifier will always come first).
int	UnambiguousExactGeneComparator.compare(Gene gene1, Gene gene2)	It will first use UnambiguousExactInteractorBaseComparator to compare the basic interactor properties If the basic interactor properties are the same, It will look at ensembl identifier if both are set.

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

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

Modifier and Type	Method	Description
Gene	XmlInteractorFactory.createGene(String name)	Creates a new Gene with the name

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

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

Modifier and Type	Class	Description
class	XmlGene	Xml implementation of a Gene

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

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

Modifier and Type	Class	Description
class	XmlGene	Xml implementation of a Gene

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

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

Modifier and Type	Class	Description
class	XmlGene	Xml implementation of a Gene