Uses of Class
trans.anno.BindingRegion

Packages that use BindingRegion

trans.anno	For associating intervals, binding regions, and binding peaks with GFF annotation.
util.bio.parsers	Parsers and extractors, fasta, quality, text, gff....

Uses of BindingRegion in trans.anno

Methods in trans.anno that return BindingRegion

static BindingRegion[]	IntersectRegions.fetchChromosomeSpecificBRs(BindingRegion[] sortedBRs, java.lang.String chromosome) Given a sorted array of BindingRegion and a chromosome, returns the appropriate BindingRegions.
static BindingRegion[]	IntersectRegions.makeBindingRegions(int[][] regions, java.lang.String chromosome) Given an array of start stops and a chromosome, makes BindingRegions.
static BindingRegion[]	IntersectRegions.parseRegionsFile(java.io.File picksFile)
static BindingRegion[]	IntersectRegions.parseIntervalFile(java.io.File intervalFile)
BindingRegion	BindingRegion.getClosestBindingRegion()
static BindingRegion[]	AnnotateRegionsWithGeneList.makeRandomBindingRegions(BindingRegion[] br, java.util.HashMap chromLengths, int sizeNeighborhood) For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.
static BindingRegion[]	AnnotateRegionsWithGeneList.parsePicksFile(java.io.File picksFile, int sizeNeighborhood)
static BindingRegion[]	AnnotateRegionsWithGeneList.parseIntervalFile(java.io.File intervalFile, int sizeNeighborhood) Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.
static BindingRegion[]	AnnotateRegions.makeRandomBindingRegions(BindingRegion[] br, java.util.HashMap chromLengths, int sizeNeighborhood) For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.
static BindingRegion[]	AnnotateRegions.parsePicksFile(java.io.File picksFile, int sizeNeighborhood)
static BindingRegion[]	AnnotateRegions.parseIntervalFile(java.io.File intervalFile, int sizeNeighborhood) Attempts to fetch a serialized array of Interval[], then sorts/ ranks the intervals by the median ratio of the sub window.

Methods in trans.anno with parameters of type BindingRegion

static BindingRegion[]	IntersectRegions.fetchChromosomeSpecificBRs(BindingRegion[] sortedBRs, java.lang.String chromosome) Given a sorted array of BindingRegion and a chromosome, returns the appropriate BindingRegions.
static boolean	IntersectRegions.writeBindingRegions(BindingRegion[] brs, java.io.File file)
void	IntersectRegions.intersectRandomBindingRegions(BindingRegion[] allTrialsOfSingleBR, BindingRegion[] chrOne) Assumes the same chromosome
static boolean	IntersectRegions.containedWithin(BindingRegion one, BindingRegion two) Returns true if two entirely contains one.
static double[]	IntersectRegions.statBindingRegionArray(BindingRegion[] brs)
static int	IntersectRegions.numberBases(BindingRegion[] brs)
static void	IntersectBindingPeaks.findClosestPeak(BindingRegion[] one, BindingRegion[] two)
boolean	BindingRegion.intersects(BindingRegion other)
int	BindingRegion.intersectReturnGap(BindingRegion other) Returns -1 if on diff chromosomes, 0 if they overlap, or the # of bases between the two.
int	BindingRegion.bpIntersectionSameChromosome(BindingRegion other) Assumes regions are on the same chromosome, and the end base is included, not interbase numbering.
int	BindingRegion.intersectReturnBP(BindingRegion other) Returns -1 for no overlap or the # bases of intersection.
int	BindingRegion.overlap(BindingRegion other) Returns -1 for no overlap, 0 for complete overlap, or a positive int for the # bases of overlap.
void	BindingRegion.setClosestBindingRegion(BindingRegion closestBindingRegion)
static BindingRegion[]	AnnotateRegionsWithGeneList.makeRandomBindingRegions(BindingRegion[] br, java.util.HashMap chromLengths, int sizeNeighborhood) For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.
void	AnnotateRegionsWithGeneList.printDistToClosestATGAndTranscript(BindingRegion[] br) Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.
int	AnnotateRegionsWithGeneList.findDistToClosestATG(BindingRegion br) Finds the distance to the closest ATG translation start site.
int	AnnotateRegionsWithGeneList.findDistToClosestATG(BindingRegion br, java.util.ArrayList geneGroups)
int	AnnotateRegionsWithGeneList.findDistToClosestTranscript(BindingRegion br) Finds the distance to the closest ATG translation start site.
int	AnnotateRegionsWithGeneList.findDistToClosestTranscript(BindingRegion br, java.util.ArrayList geneGroups)
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 int	AnnotateRegionsWithGeneList.countNumberNeighbors(BindingRegion[] br)
static int	AnnotateRegionsWithGeneList.countNumberBindingRegionsWithNeighbors(BindingRegion[] br)
static int[]	AnnotateRegionsWithGeneList.countGenes(BindingRegion[] br) Returns: the number of genes with one or more binding regions within the neighborhood.
static void	AnnotateRegionsWithGeneList.compareBindingRegionsVsGeneGrps(GeneGroup[] geneGroups, BindingRegion[] bindingRegions) Does a complete scan, could be optimized.
static BindingRegion[]	AnnotateRegions.makeRandomBindingRegions(BindingRegion[] br, java.util.HashMap chromLengths, int sizeNeighborhood) For each binding region this will make another binding region from the same chromosome with the same length, yet at a random location.
void	AnnotateRegions.printDistToClosestATGAndTranscript(BindingRegion[] br) Prints rank, chrom, start, stop, distance to closest ATG, to closest transcript start.
int	AnnotateRegions.findDistToClosestATG(BindingRegion br) Finds the distance to the closest ATG translation start site.
int	AnnotateRegions.findDistToClosestATG(BindingRegion br, java.util.ArrayList geneGroups)
int	AnnotateRegions.findDistToClosestTranscript(BindingRegion br) Finds the distance to the closest ATG translation start site.
int	AnnotateRegions.findDistToClosestTranscript(BindingRegion br, java.util.ArrayList geneGroups)
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 int	AnnotateRegions.countNumberNeighbors(BindingRegion[] br)
static int	AnnotateRegions.countNumberBindingRegionsWithNeighbors(BindingRegion[] br)
static int[]	AnnotateRegions.countGenes(BindingRegion[] br) Returns the number of genes where the binding region is on the 5' end and the number of genes where the binding region is on the 3' end of the respective gene, the number of genes that overlap a binding region on their 5' end and 3' end, lastly the number of regions entirely contained by a gene, the number of binding regions with neighbors, the number of regions with no neighbors as defined by the neighborhood, the number of regions in non coding DNA, the number of regions in coding DNA, the number of regions that overlap coding and nonCoding DNA
static void	AnnotateRegions.compareBindingRegionsVsGeneGrps(GeneGroup[] geneGroups, BindingRegion[] bindingRegions) Does a complete scan, could be optimized.

Uses of BindingRegion in util.bio.parsers

Methods in util.bio.parsers with parameters of type BindingRegion

static double[]	FetchGenomicSequences.statBindingRegionArray(BindingRegion[] brs)
static int	FetchGenomicSequences.numberBases(BindingRegion[] brs)