Uses of Class
org.snpeff.geneOntology.GoTerm

Packages that use GoTerm

Package	Description
org.snpeff.geneOntology

Uses of GoTerm in org.snpeff.geneOntology

Methods in org.snpeff.geneOntology that return GoTerm

Modifier and Type	Method	Description
GoTerm	GoTerms.add(GoTerm goTerm)	Add a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds.
GoTerm	GoTerms.disjointSet(java.util.List<GoTerm> goTermList, int activeSets)	Produce a GOTerm based on a list of GOTerms and a 'mask'
GoTerm	GoTerm.getFirstChild()	Return first child in the list
GoTerm	GoTerm.getFirstParent()	Return first parent in the list
GoTerm	GoTerms.getGoTerm(java.lang.String goTermAcc)
GoTerm	GoTerm.rootNode()	Get the root node

Methods in org.snpeff.geneOntology that return types with arguments of type GoTerm

Modifier and Type	Method	Description
java.util.HashSet<GoTerm>	GoTerm.getChilds()
java.util.HashMap<java.lang.String,GoTerm>	GoTerms.getGoTermsByGoTermAcc()
java.util.HashMap<java.lang.String,java.util.Set<GoTerm>>	GoTerms.getGoTermsBySymbolId()
java.util.Set<GoTerm>	GoTerms.getGoTermsBySymbolId(java.lang.String symbolId)
java.util.HashSet<GoTerm>	GoTerm.getParents()
java.util.Iterator<GoTerm>	GoTerms.iterator()	Iterate through each GOterm in this GOTerms
java.util.List<GoTerm>	GoTerms.listTopTerms(int numberToSelect)	Select a number of GOTerms
java.util.Set<GoTerm>	GoTerms.rootNodes()
java.util.Collection<GoTerm>	GoTerms.values()

Methods in org.snpeff.geneOntology with parameters of type GoTerm

Modifier and Type	Method	Description
GoTerm	GoTerms.add(GoTerm goTerm)	Add a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds.
void	GoTerm.addChild(GoTerm childGoTerm)	Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'
boolean	GoTerms.addSymbolId(GoTerm goTerm, java.lang.String symbolId)	Add a symbolId (as well as all needed mappings)
void	GoTerm.addSymbolsFromChilds(GoTerm goTerm)	Add all symbols from childs to goTerm
int	GoTerm.compareTo(GoTerm goTerm)
void	GoTerm.intersection(GoTerm goTerm)	Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').
void	GoTerm.setMinus(GoTerm goTerm)	Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').
void	GoTerm.union(GoTerm goTerm)	Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').

Method parameters in org.snpeff.geneOntology with type arguments of type GoTerm

Modifier and Type	Method	Description
GoTerm	GoTerms.disjointSet(java.util.List<GoTerm> goTermList, int activeSets)	Produce a GOTerm based on a list of GOTerms and a 'mask'
void	GoTerm.setChilds(java.util.HashSet<GoTerm> childs)
void	GoTerm.setParents(java.util.HashSet<GoTerm> parents)

Constructor parameters in org.snpeff.geneOntology with type arguments of type GoTerm

Constructor	Description
GoTerm(java.util.List<GoTerm> goTermList, GoTerms goTerms)	Create a new GOTerm by joining all GOTerms in the list