Uses of Class
trans.anno.Region

Packages that use Region

trans.anno

For associating intervals, binding regions, and binding peaks with GFF annotation.

Uses of Region in trans.anno

Methods in trans.anno that return Region

static Region[]	Region.loadWriteBinaryRegions(java.io.File regionsFile) Looks for a binary version of the file xxx.corr, if found loads binary, otherwise it parses the txt file and then writes the binary for future use.
static Region[]	Region.loadBinaryCoordinates(java.io.File file) Reads binary chrom start stop file into Region[]
static Region[]	Region.parseRegions(java.io.File file) Parses a file for a tab delimited list of at minimum, chrom, start, stop, (optional) notes into a GenomicRegion[].
static Region[]	RandomRegions.loadWriteBinaryCoordinates(java.io.File regionsFile) Looks for a binary version of the file xxx.corr, if found loads binary, otherwise it parses the txt file and then writes the binary for future use.
static Region[]	RandomRegions.loadBinaryCoordinatesAsRegionArray(java.io.File file) Reads binary chrom start stop file into Region[]
Region	RandomRegions.findRandomRegion(int minimumLength) Attempt to find a random Region of the appropriate minimum length.

Methods in trans.anno with parameters of type Region

static void	Region.writeBinaryCoordinates(java.io.File file, Region[] r) Writes the chrom start stop of a Region[] as a binary file.
static java.util.HashMap	Region.splitByChromosome(Region[] sorted) Given a chromosome SORTED array of Regions returns a HashMap containing chromosome: sorted chromo specific Region[]
int	Region.bpIntersectionSameChromosome(Region other) Assumes regions are on the same chromosome, and the end base is included, not interbase numbering.
static void	RandomRegions.saveRegionsAsCoordinatesArray(java.io.File file, Region[] r) Writes the chrom start stop of a Region[] as a binary file.
int[]	RandomRegions.findRandomSegment(Region region, int length) Returns a random segment of the appropriate length within the region.
boolean[][]	RandomRegions.fetchGCContent(Region[] r) Converts the Region[] sequences into boolean[]s, everything not g or c are recorded as false.
int	RandomRegions.countLengths(Region[] rs)
void	IntersectKeyWithRegions.calculateAndPrintStats(Region[] r)
int	IntersectKeyWithRegions.intersectsKey(Region region) Returns 1 if bpInt <= maxGap and the particular key hasn't been hit, 0 not in key, -1 hits a key that has already been counted.