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

Packages that use OntologyTerm

Package	Description
psidev.psi.mi.jami.bridges.fetcher
psidev.psi.mi.jami.bridges.fetcher.mock
psidev.psi.mi.jami.bridges.obo
psidev.psi.mi.jami.bridges.ols
psidev.psi.mi.jami.bridges.ontologymanager
psidev.psi.mi.jami.bridges.ontologymanager.impl
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.listener
psidev.psi.mi.jami.listener.impl
psidev.psi.mi.jami.model
psidev.psi.mi.jami.model.impl
psidev.psi.mi.jami.utils
psidev.psi.mi.jami.utils.clone

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

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

Modifier and Type	Method	Description
Set<OntologyTerm>	OntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	OntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.

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

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

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

Modifier and Type	Method	Description
Collection<OntologyTerm>	MockOntologyTermFetcher.fetchByIdentifiers(Collection<String> identifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<OntologyTerm>	MockOntologyTermFetcher.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<OntologyTerm>	MockOntologyTermFetcher.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<OntologyTerm>	MockOntologyTermFetcher.fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<OntologyTerm>	MockOntologyTermFetcher.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.
Set<OntologyTerm>	MockOntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	MockOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
Set<OntologyTerm>	OntologyTermCompositeFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	OntologyTermCompositeFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.

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

Modifier and Type	Method	Description
void	MockOntologyTermFetcher.addOntologyTerm(String identifier, OntologyTerm ontologyTerm)	addOntologyTerm.

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

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

Modifier and Type	Method	Description
protected OntologyTerm	OntologyOboLoader.instantiateNewTerm(String name, Xref identity)	instantiateNewTerm.

Methods in psidev.psi.mi.jami.bridges.obo that return types with arguments of type OntologyTerm

Modifier and Type	Method	Description
Set<OntologyTerm>	OboOntologyTermFetcher.fetchRootTerms(String database)	fetchRootTerms.
Set<OntologyTerm>	OboOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.

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

Modifier and Type	Method	Description
protected void	OntologyOboLoader.createDefinitionFor(String def, OntologyTerm term)	createDefinitionFor.
protected void	OntologyOboLoader.processAnnotations(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	Process the annotations of a term
protected void	OntologyOboLoader.processDefinition(String definition, OntologyTerm ontologyTerm)	Process the definition String
protected void	OntologyOboLoader.processDefinition(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	Process the definition of a term
protected void	OntologyOboLoader.processInfoInDescription(String definition, String otherInfoString, OntologyTerm ontologyTerm)	Process the other information in the description
protected void	OntologyOboLoader.processShortLabel(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	processShortLabel.
protected void	OntologyOboLoader.processSynonyms(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	processSynonyms.
protected void	OntologyOboLoader.processXref(String db, String accession, OntologyTerm ontologyTerm)	processXref.
protected String	OntologyOboLoader.processXrefDefinition(String xref, String database, String accession, String pubmedPrimary, OntologyTerm ontologyTerm)	processXrefDefinition.
protected void	OntologyOboLoader.processXrefs(uk.ac.ebi.ols.model.interfaces.Term term, OntologyTerm ontologyTerm)	processXrefs.

Method parameters in psidev.psi.mi.jami.bridges.obo with type arguments of type OntologyTerm

Modifier and Type	Method	Description
protected void	OntologyOboLoader.addLinkToTerm(String parentId, String childId, Map<String,OntologyTerm> id2Terms)	addLinkToTerm.
void	OntologyOboLoader.buildOntology(Map<String,OntologyTerm> id2Terms, Map<String,OntologyTerm> name2Terms)	buildOntology.
protected void	OntologyOboLoader.buildTermRelationships(Map<String,OntologyTerm> id2Terms)	buildTermRelationships.

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

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

Modifier and Type	Class	Description
class	LazyOntologyTerm	A lazy ontology term, which only checks for parents of children when required.

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

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

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

Modifier and Type	Method	Description
Set<OntologyTerm>	CachedOlsOntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	CachedOlsOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
Set<OntologyTerm>	OlsOntologyTermFetcher.fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	OlsOntologyTermFetcher.fetchRootTerms(CvTerm database)	fetchRootTerms.
Collection<OntologyTerm>	LazyOntologyTerm.getChildren()	Getter for the field children.
Collection<OntologyTerm>	LazyOntologyTerm.getParents()	Getter for the field parents.

Uses of OntologyTerm in psidev.psi.mi.jami.bridges.ontologymanager

Methods in psidev.psi.mi.jami.bridges.ontologymanager that return OntologyTerm

Modifier and Type	Method	Description
OntologyTerm	MIOntologyTermI.getDelegate()	getDelegate.

Uses of OntologyTerm in psidev.psi.mi.jami.bridges.ontologymanager.impl

Methods in psidev.psi.mi.jami.bridges.ontologymanager.impl that return OntologyTerm

Modifier and Type	Method	Description
OntologyTerm	OntologyTermWrapper.getDelegate()	Getter for the field delegate.

Constructors in psidev.psi.mi.jami.bridges.ontologymanager.impl with parameters of type OntologyTerm

Constructor	Description
OntologyTermWrapper(OntologyTerm cv)	Constructor for OntologyTermWrapper.

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

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

Constructor	Description
FullOntologyTermEnricher(FullCvTermEnricher<OntologyTerm> cvEnricher)	Constructor for FullOntologyTermEnricher.
FullOntologyTermUpdater(FullCvTermUpdater<OntologyTerm> cvTermEnricher)	Constructor for FullOntologyTermUpdater.

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

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

Modifier and Type	Method	Description
OntologyTerm	MinimalOntologyTermEnricher.find(OntologyTerm objectToEnrich)	find.

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

Modifier and Type	Method	Description
protected MinimalCvTermEnricher<OntologyTerm>	MinimalOntologyTermEnricher.getCvEnricher()	Getter for the field cvEnricher.
CvTermEnricherListener<OntologyTerm>	MinimalOntologyTermEnricher.getCvTermEnricherListener()	getCvTermEnricherListener.
CvTermFetcher<OntologyTerm>	MinimalOntologyTermEnricher.getCvTermFetcher()	getCvTermFetcher.

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

Modifier and Type	Method	Description
void	MinimalOntologyTermEnricher.enrich(OntologyTerm objectToEnrich)	enrich.
void	MinimalOntologyTermEnricher.enrich(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	enrich.
protected void	MinimalOntologyTermEnricher.enrichChild(OntologyTerm objectToEnrich)	enrichChild.
OntologyTerm	MinimalOntologyTermEnricher.find(OntologyTerm objectToEnrich)	find.
protected void	MinimalOntologyTermEnricher.mergeOntologyTerms(OntologyTerm termToEnrich, Collection<OntologyTerm> toEnrichTerms, Collection<OntologyTerm> fetchedTerms, boolean remove)	Takes two lists of ontology terms and produces a list of those to add and those to remove.
protected void	MinimalOntologyTermEnricher.onEnrichedVersionNotFound(OntologyTerm cvTermToEnrich)	onEnrichedVersionNotFound.
protected void	MinimalOntologyTermEnricher.processChildren(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	processChildren.
protected void	MinimalOntologyTermUpdater.processChildren(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	processChildren.
protected void	MinimalOntologyTermEnricher.processDefinition(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	processDefinition.
protected void	MinimalOntologyTermUpdater.processDefinition(OntologyTerm cvTermToEnrich, OntologyTerm cvTermFetched)	processDefinition.
protected void	MinimalOntologyTermEnricher.processOntologyTerm(OntologyTerm cvTermToEnrich, OntologyTerm 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 OntologyTerm

Modifier and Type	Method	Description
protected void	MinimalOntologyTermEnricher.enrichRelatedTerms(Collection<OntologyTerm> cvTermToEnrich)	enrichRelatedTerms.
protected void	MinimalOntologyTermEnricher.mergeOntologyTerms(OntologyTerm termToEnrich, Collection<OntologyTerm> toEnrichTerms, Collection<OntologyTerm> fetchedTerms, boolean remove)	Takes two lists of ontology terms and produces a list of those to add and those to remove.
void	MinimalOntologyTermEnricher.setCvTermEnricherListener(CvTermEnricherListener<OntologyTerm> listener)	setCvTermEnricherListener.

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

Constructor	Description
MinimalOntologyTermEnricher(MinimalCvTermEnricher<OntologyTerm> cvEnricher)	Constructor for MinimalOntologyTermEnricher.
MinimalOntologyTermUpdater(MinimalCvTermEnricher<OntologyTerm> cvEnricher)	Constructor for MinimalOntologyTermUpdater.

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

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

Modifier and Type	Method	Description
void	OntologyTermEnricherListenerManager.onAddedChild(OntologyTerm o, OntologyTerm added)	Listen to the event where a child has been added to the object children.
void	OntologyTermEnricherListenerManager.onAddedParent(OntologyTerm o, OntologyTerm added)	Listen to the event where a parent has been added to the object parents.
void	OntologyTermEnricherListenerManager.onDefinitionUpdate(OntologyTerm cv, String oldDef)	Listen to the event where the definition of a cv term has been changed.
void	OntologyTermEnricherListenerManager.onRemovedChild(OntologyTerm o, OntologyTerm removed)	Listen to the event where a child has been removed from the object children.
void	OntologyTermEnricherListenerManager.onRemovedParent(OntologyTerm o, OntologyTerm removed)	Listen to the event where a parent has been removed from the object parents.

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

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

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

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

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

Modifier and Type	Method	Description
void	OntologyTermEnricherStatisticsWriter.onAddedChild(OntologyTerm o, OntologyTerm added)	Listen to the event where a child has been added to the object children.
void	OntologyTermEnricherStatisticsWriter.onAddedParent(OntologyTerm o, OntologyTerm added)	Listen to the event where a parent has been added to the object parents.
void	OntologyTermEnricherStatisticsWriter.onDefinitionUpdate(OntologyTerm cv, String oldDef)	Listen to the event where the definition of a cv term has been changed.
void	OntologyTermEnricherStatisticsWriter.onRemovedChild(OntologyTerm o, OntologyTerm removed)	Listen to the event where a child has been removed from the object children.
void	OntologyTermEnricherStatisticsWriter.onRemovedParent(OntologyTerm o, OntologyTerm removed)	Listen to the event where a parent has been removed from the object parents.

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

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

Modifier and Type	Method	Description
void	OntologyTermChangeListener.onAddedChild(OntologyTerm o, OntologyTerm added)	Listen to the event where a child has been added to the object children.
void	OntologyTermChangeListener.onAddedParent(OntologyTerm o, OntologyTerm added)	Listen to the event where a parent has been added to the object parents.
void	OntologyTermChangeListener.onDefinitionUpdate(OntologyTerm cv, String oldDef)	Listen to the event where the definition of a cv term has been changed.
void	OntologyTermChangeListener.onRemovedChild(OntologyTerm o, OntologyTerm removed)	Listen to the event where a child has been removed from the object children.
void	OntologyTermChangeListener.onRemovedParent(OntologyTerm o, OntologyTerm removed)	Listen to the event where a parent has been removed from the object parents.

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

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

Modifier and Type	Method	Description
void	OntologyTermChangeLogger.onAddedChild(OntologyTerm cv, OntologyTerm added)	Listen to the event where a child has been added to the object children.
void	OntologyTermChangeLogger.onAddedParent(OntologyTerm cv, OntologyTerm added)	Listen to the event where a parent has been added to the object parents.
void	OntologyTermChangeLogger.onDefinitionUpdate(OntologyTerm cv, String oldDef)	Listen to the event where the definition of a cv term has been changed.
void	OntologyTermChangeLogger.onRemovedChild(OntologyTerm cv, OntologyTerm removed)	Listen to the event where a child has been removed from the object children.
void	OntologyTermChangeLogger.onRemovedParent(OntologyTerm cv, OntologyTerm removed)	Listen to the event where a parent has been removed from the object parents.

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

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

Modifier and Type	Method	Description
<O extends OntologyTerm> Collection<O>	OntologyTerm.getChildren()	The children terms of this controlled vocabulary term.
<O extends OntologyTerm> Collection<O>	OntologyTerm.getParents()	The parent terms of this controlled vocabulary term.

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

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

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

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

Modifier and Type	Method	Description
Collection<OntologyTerm>	DefaultOntologyTerm.getChildren()	Getter for the field children.
Collection<OntologyTerm>	DefaultOntologyTerm.getParents()	Getter for the field parents.

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

Modifier and Type	Method	Description
protected void	DefaultOntologyTerm.initialiseChildrenWith(Collection<OntologyTerm> children)	initialiseChildrenWith
protected void	DefaultOntologyTerm.initialiseParentsWith(Collection<OntologyTerm> parents)	initialiseParentsWith

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

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

Modifier and Type	Method	Description
static boolean	OntologyTermUtils.isCvTermChildOf(OntologyTerm term, String mi, String name)	Method to check if a Cv term is a child of a term having the given mi and/or name

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

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

Modifier and Type	Method	Description
static void	CvTermCloner.copyAndOverrideOntologyTermProperties(OntologyTerm source, OntologyTerm target)	This method will copy basic properties and parent/children from a ontology term source to a ontology term target