Uses of Class
org.snpeff.geneOntology.GoTerm
Packages that use GoTerm
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Uses of GoTerm in org.snpeff.geneOntology
Methods in org.snpeff.geneOntology that return GoTermModifier and TypeMethodDescriptionAdd a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds.GoTerms.disjointSet
(List<GoTerm> goTermList, int activeSets) Produce a GOTerm based on a list of GOTerms and a 'mask'GoTerm.getFirstChild()
Return first child in the listGoTerm.getFirstParent()
Return first parent in the listGoTerm.rootNode()
Get the root nodeMethods in org.snpeff.geneOntology that return types with arguments of type GoTermModifier and TypeMethodDescriptionGoTerm.getChilds()
GoTerms.getGoTermsByGoTermAcc()
GoTerms.getGoTermsBySymbolId()
GoTerms.getGoTermsBySymbolId
(String symbolId) GoTerm.getParents()
GoTerms.iterator()
Iterate through each GOterm in this GOTermsGoTerms.listTopTerms
(int numberToSelect) Select a number of GOTermsGoTerms.rootNodes()
GoTerms.values()
Methods in org.snpeff.geneOntology with parameters of type GoTermModifier and TypeMethodDescriptionAdd a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds.void
Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'boolean
GoTerms.addSymbolId
(GoTerm goTerm, String symbolId) Add a symbolId (as well as all needed mappings)void
GoTerm.addSymbolsFromChilds
(GoTerm goTerm) Add all symbols from childs to goTermint
void
GoTerm.intersection
(GoTerm goTerm) Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').void
Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').void
Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').Method parameters in org.snpeff.geneOntology with type arguments of type GoTermModifier and TypeMethodDescriptionGoTerms.disjointSet
(List<GoTerm> goTermList, int activeSets) Produce a GOTerm based on a list of GOTerms and a 'mask'void
void
GoTerm.setParents
(HashSet<GoTerm> parents) Constructor parameters in org.snpeff.geneOntology with type arguments of type GoTerm