Uses of Class
org.snpeff.geneSets.GeneSet

Packages that use GeneSet

Package	Description
org.snpeff.geneSets

Uses of GeneSet in org.snpeff.geneSets

Methods in org.snpeff.geneSets that return GeneSet

Modifier and Type	Method	Description
GeneSet	GeneSets.disjointSet(java.util.List<GeneSet> geneSetList, int activeSets)	Produce a GeneSet based on a list of GeneSets and a 'mask'
GeneSet	GeneSets.getGeneSet(java.lang.String geneSetName)	Get a gene set named 'geneSetName'
GeneSet	Result.getLatestGeneSet()

Methods in org.snpeff.geneSets that return types with arguments of type GeneSet

Modifier and Type	Method	Description
java.util.List<GeneSet>	GeneSets.geneSetsSorted()	Iterate through each GeneSet in this GeneSets
java.util.List<GeneSet>	GeneSets.geneSetsSortedSize(boolean reverse)	Gene sets sorted by size (if same size, sort by name).
java.util.List<GeneSet>	Result.getGeneSets()
java.util.HashSet<GeneSet>	GeneSets.getGeneSetsByGene(java.lang.String gene)	All gene sets that this gene belongs to
java.util.HashMap<java.lang.String,GeneSet>	GeneSets.getGeneSetsByName()
java.util.Iterator<GeneSet>	GeneSets.iterator()	Iterate through each GeneSet in this GeneSets
java.util.Iterator<GeneSet>	GeneSets.iteratorSorted()	Iterate through each GeneSet in this GeneSets
java.util.List<GeneSet>	GeneSets.listTopTerms(int numberToSelect)	Select a number of GeneSets
java.util.Collection<GeneSet>	GeneSets.values()

Methods in org.snpeff.geneSets with parameters of type GeneSet

Modifier and Type	Method	Description
boolean	GeneSets.add(java.lang.String gene, GeneSet geneSet)	Add a gene and it's corresponding gene set
void	GeneSets.add(GeneSet geneSet)	Add a gene set
int	GeneSet.compareTo(GeneSet geneSet)	Comparable interface (to order terms)
int	GeneSet.countOverlap(GeneSet gs)	COunt how many genes are in both GeneSets
void	GeneSet.intersection(GeneSet geneSet)	Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').
protected boolean	GeneSets.isUsed(GeneSet gs)	Is this gene set used? I.e.
protected boolean	GeneSetsRanked.isUsed(GeneSet gs)	Is this gene set used? I.e.
void	GeneSets.remove(GeneSet geneSet)
void	GeneSet.setMinus(GeneSet geneSet)	Perform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').
void	GeneSet.union(GeneSet geneSet)	Union this term with 'geneSet' (union for 'geneSet' and 'interestingGeneSet').

Method parameters in org.snpeff.geneSets with type arguments of type GeneSet

Modifier and Type	Method	Description
GeneSet	GeneSets.disjointSet(java.util.List<GeneSet> geneSetList, int activeSets)	Produce a GeneSet based on a list of GeneSets and a 'mask'
void	Result.set(java.util.List<GeneSet> geneSets, org.apfloat.Apfloat pValue)	Ser a new list and pvalue
void	GeneSets.setGeneSetByName(java.util.HashMap<java.lang.String,GeneSet> geneSets)
void	Result.setGeneSets(java.util.List<GeneSet> newGeneSets)	Assign geneSets

Constructors in org.snpeff.geneSets with parameters of type GeneSet

Constructor	Description
Result(GeneSet geneSet, org.apfloat.Apfloat pValue, int geneSetCount)

Constructor parameters in org.snpeff.geneSets with type arguments of type GeneSet

Constructor	Description
GeneSet(java.util.List<GeneSet> geneSetList, GeneSets geneSets)	Create a new GeneSet by joining all GeneSets in the list
Result(java.util.List<GeneSet> list, double pValue)