Uses of Class
org.snpeff.geneSets.GeneSet
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Packages that use GeneSet Package Description org.snpeff.geneSets -
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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 GeneSetsjava.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 tojava.util.HashMap<java.lang.String,GeneSet>
GeneSets. getGeneSetsByName()
java.util.Iterator<GeneSet>
GeneSets. iterator()
Iterate through each GeneSet in this GeneSetsjava.util.Iterator<GeneSet>
GeneSets. iteratorSorted()
Iterate through each GeneSet in this GeneSetsjava.util.List<GeneSet>
GeneSets. listTopTerms(int numberToSelect)
Select a number of GeneSetsjava.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 setvoid
GeneSets. add(GeneSet geneSet)
Add a gene setint
GeneSet. compareTo(GeneSet geneSet)
Comparable interface (to order terms)int
GeneSet. countOverlap(GeneSet gs)
COunt how many genes are in both GeneSetsvoid
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 pvaluevoid
GeneSets. setGeneSetByName(java.util.HashMap<java.lang.String,GeneSet> geneSets)
void
Result. setGeneSets(java.util.List<GeneSet> newGeneSets)
Assign geneSetsConstructors 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 listResult(java.util.List<GeneSet> list, double pValue)
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