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## Uses of Class
baseCode.bio.geneset.GeneAnnotations

Packages that use GeneAnnotations
baseCode.bio.geneset |

Uses of GeneAnnotations in baseCode.bio.geneset

Methods in baseCode.bio.geneset with parameters of type GeneAnnotations
`static double` | `GeneSetMapTools.meanGeneSetSize(GeneAnnotations ga, boolean countEmpty)`
`static double` | `GeneSetMapTools.meanSetsPerGene(GeneAnnotations ga, boolean countEmpty)`
`static hep.aida.IHistogram1D` | `GeneSetMapTools.geneSetSizeDistribution(GeneAnnotations ga, int numBins, int minSize, int maxSize)`
`static void` | `GeneSetMapTools.removeAspect(GeneAnnotations ga, GONames gon, StatusViewer messenger, java.lang.String aspect)`
`static void` | `GeneSetMapTools.removeBySize(GeneAnnotations ga, StatusViewer messenger, int minClassSize, int maxClassSize)` Remove gene sets that don't meet certain criteria.
`static void` | `GeneSetMapTools.ignoreSimilar(double fractionSameThreshold, GeneAnnotations ga, StatusViewer messenger, int maxClassSize, int minClassSize, double bigClassPenalty)` Remove classes which are too similar to some other class.
`static void` | `GeneSetMapTools.collapseGeneSets(GeneAnnotations geneData, StatusViewer messenger)` Identify classes which are absoluely identical to others.

Constructors in baseCode.bio.geneset with parameters of type GeneAnnotations
`GeneAnnotations(GeneAnnotations geneData, java.util.Set activeProbes)` This is for creating GeneAnnotations by pruning a copy.

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