Uses of Interface
org.forester.go.GoTerm

Packages that use GoTerm

Package	Description
org.forester.go
org.forester.ws.seqdb

Uses of GoTerm in org.forester.go

Classes in org.forester.go that implement GoTerm

Modifier and Type	Class	Description
class	BasicGoTerm

Methods in org.forester.go that return GoTerm

Modifier and Type	Method	Description
static GoTerm	GoUtils.getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
static GoTerm	GoUtils.getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)

Methods in org.forester.go that return types with arguments of type GoTerm

Modifier and Type	Method	Description
static java.util.Map<GoId,GoTerm>	GoUtils.createGoIdToGoTermMap(java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
java.util.List<GoTerm>	OBOparser.parse()

Methods in org.forester.go with parameters of type GoTerm

Modifier and Type	Method	Description
int	BasicGoTerm.compareTo(GoTerm go_term)	Compares based on GO id.
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
static GoTerm	GoUtils.getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
static GoTerm	GoUtils.getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)

Method parameters in org.forester.go with type arguments of type GoTerm

Modifier and Type	Method	Description
static java.util.LinkedHashMap<GoId,java.lang.Integer>	GoUtils.countCategories(java.util.List<GoTerm> categories, java.util.List<GoTerm> experiment_set, java.util.Map<GoId,GoTerm> all_go_terms)	This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.
static java.util.LinkedHashMap<GoId,java.lang.Integer>	GoUtils.countCategories(java.util.List<GoTerm> categories, java.util.List<GoTerm> experiment_set, java.util.Map<GoId,GoTerm> all_go_terms)	This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.
static java.util.LinkedHashMap<GoId,java.lang.Integer>	GoUtils.countCategoriesId(java.util.List<GoId> categories, java.util.List<GoId> experiment_set, java.util.Map<GoId,GoTerm> all_go_terms)
static java.util.Map<GoId,GoTerm>	GoUtils.createGoIdToGoTermMap(java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoId>	GoUtils.getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>	GoUtils.getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
static GoTerm	GoUtils.getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
static GoTerm	GoUtils.getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)

Uses of GoTerm in org.forester.ws.seqdb

Methods in org.forester.ws.seqdb that return types with arguments of type GoTerm

Modifier and Type	Method	Description
java.util.SortedSet<GoTerm>	EbiDbEntry.getGoTerms()
java.util.SortedSet<GoTerm>	SequenceDatabaseEntry.getGoTerms()
java.util.SortedSet<GoTerm>	UniProtEntry.getGoTerms()