Uses of Class
util.bio.annotation.GeneGroup

Packages that use GeneGroup

trans.anno	For associating intervals, binding regions, and binding peaks with GFF annotation.
trans.roc	For manipulating the BAC dmel spike in data and generating ROC curves.
util.bio.annotation	For representing gene annotation.
util.bio.parsers.gff	GFF2 and GFF3 parsers.

Uses of GeneGroup in trans.anno

Methods in trans.anno that return GeneGroup

GeneGroup	BindingRegion.getGeneGrp3Prime()
GeneGroup	BindingRegion.getGeneGrp5Prime()
static GeneGroup[]	AnnotateRegions.filterGeneGroups(GeneGroup[] genes, java.util.HashSet cgNames) Returns an array of GeneGroup whose names were found in the Hash

Methods in trans.anno with parameters of type GeneGroup

void	BindingRegion.compare(GeneGroup geneGrp) Compares a binding region to a gene grp looking for where it is in relation to the binding region, 5', 3', overlap, contained.
int	AnnotateRegionsWithGeneList.findDistanceToATG(BindingRegion br, GeneGroup gp) Finds the distance to conservative estimate of an ATG, returns 0 if overlaps.
int	AnnotateRegionsWithGeneList.findDistToClosestTranscript(BindingRegion br, GeneGroup gp) Finds the distance to conservative estimate of start of first exon, returns 0 if overlaps.
static void	AnnotateRegionsWithGeneList.compareBindingRegionsVsGeneGrps(GeneGroup[] geneGroups, BindingRegion[] bindingRegions) Does a complete scan, could be optimized.
int	AnnotateRegions.findDistanceToATG(BindingRegion br, GeneGroup gp) Finds the distance to conservative estimate of an ATG, returns 0 if overlaps.
int	AnnotateRegions.findDistToClosestTranscript(BindingRegion br, GeneGroup gp) Finds the distance to conservative estimate of start of first exon, returns 0 if overlaps.
static void	AnnotateRegions.compareBindingRegionsVsGeneGrps(GeneGroup[] geneGroups, BindingRegion[] bindingRegions) Does a complete scan, could be optimized.
static GeneGroup[]	AnnotateRegions.filterGeneGroups(GeneGroup[] genes, java.util.HashSet cgNames) Returns an array of GeneGroup whose names were found in the Hash

Uses of GeneGroup in trans.roc

Methods in trans.roc that return GeneGroup

static GeneGroup[]

ParsePatternedWindows.extractGeneGroups(java.util.HashMap geneGroups, java.lang.String[] geneList) Pulls out a sub set of GeneGroups with the names in the geneList.

Methods in trans.roc with parameters of type GeneGroup

static RocWindow[]

ParsePatternedWindows.fetchProximalWindows(GeneGroup[] geneGrps, RocWindow[] windows, int sizeUpstream)

Uses of GeneGroup in util.bio.annotation

Methods in util.bio.annotation that return GeneGroup

GeneGroup

GeneRep.getGeneGrp()

Constructors in util.bio.annotation with parameters of type GeneGroup

GeneRep(TransGroup[] transGrps, GeneGroup geneGrpRef)

Uses of GeneGroup in util.bio.parsers.gff

Methods in util.bio.parsers.gff that return GeneGroup

GeneGroup[]

DmelRel4Extractor.getGeneGroups() Final product from the extractor.