Uses of Class
org.snpeff.geneOntology.GoTerm
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Packages that use GoTerm Package Description org.snpeff.geneOntology -
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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 listGoTerm
GoTerm. getFirstParent()
Return first parent in the listGoTerm
GoTerms. getGoTerm(java.lang.String goTermAcc)
GoTerm
GoTerm. rootNode()
Get the root nodeMethods 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 GOTermsjava.util.List<GoTerm>
GoTerms. listTopTerms(int numberToSelect)
Select a number of GOTermsjava.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 goTermint
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
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