Uses of Interface
org.forester.go.GoTerm
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Packages that use GoTerm Package Description org.forester.go org.forester.ws.seqdb -
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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)
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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()
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