Uses of Class
trans.graphics.GenomicRegion

Packages that use GenomicRegion

trans.graphics

For graphically representing '.cel' files and intervals.

Uses of GenomicRegion in trans.graphics

Methods in trans.graphics that return GenomicRegion

GenomicRegion	RankedSetDrawPanel.findRegion(GenomicRegion[] regions, java.awt.geom.Point2D point) Scans an array of GenomicRegions Rectangles to see if the Point is present, ie they clicked it.
static GenomicRegion[]	RankedSetAnalysis.parseGenomicRegionsFile(java.io.File f) Parses a regions file.
GenomicRegion[]	RankedSetAnalysis.getRegionsOne()
GenomicRegion[]	RankedSetAnalysis.getRegionsTwo()

Methods in trans.graphics with parameters of type GenomicRegion

java.lang.String	RankedSetDrawPanel.formattedInfo(GenomicRegion g)
GenomicRegion	RankedSetDrawPanel.findRegion(GenomicRegion[] regions, java.awt.geom.Point2D point) Scans an array of GenomicRegions Rectangles to see if the Point is present, ie they clicked it.
static int[]	RankedSetAnalysis.rankedIntersection(GenomicRegion[] r) Calculates the number of hits in the ranked matched list.
static boolean	RankedSetAnalysis.containsMatchedRankIntersect(GenomicRegion r, int testRank) Checks to see if among the hits to a particular GenomicRegion they have an equal or smaller rank.
double	RankedSetAnalysis.fractionTotalIntersection(GenomicRegion[] r) Returns the total fraction of intersection.
void	RankedSetAnalysis.printRankedIntersectionAll(GenomicRegion[] r) Rank analysis where each regions is check against the entire other list.
boolean	GenomicRegion.overlap(GenomicRegion other, int maxGap) checks to see if regions overlap by the minimum maxGap, can set maxGap negative to require an overlap.
static int	GenomicRegion.findBiggestGenomicRegion(GenomicRegion[] gr) Returns the length of the biggest GenomicRegion