trans.anno
Class Region

java.lang.Object
  trans.anno.Region

All Implemented Interfaces:

java.io.Serializable

public class Region

extends java.lang.Object

implements java.io.Serializable

Represents a genomic region. See Coordinates for a more simple class.

See Also:

Serialized Form

Constructor Summary

Region(java.lang.String chromosome, int start, int end, java.lang.String notes)

Method Summary

int	bpIntersectionSameChromosome(Region other) Assumes regions are on the same chromosome, and the end base is included, not interbase numbering.
double	calculateGCContent() Returns the fraction of GC provided the Region.gcContent[] is loaded.
java.lang.String	getChromosome()
int	getEnd()
boolean[]	getGcContent()
java.util.HashSet	getHits()
int	getLength() Returns end - start +1, thus last base is included, not interbase numbering!
java.lang.String	getNotes()
int	getStart()
boolean	intersect(Interval interval)
boolean	intersect(TPMapLine line)
boolean	intersect(Window window, int sizeOligo, double fractionAcceptibleCoverage) Returns true only if region contains or is contained or is covered by >= fractionAcceptibleCoverage by a window.
static Region[]	loadBinaryCoordinates(java.io.File file) Reads binary chrom start stop file into Region[]
static 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.
int	overlap(Interval interval) Returns -1 for no overlap, or a positive int for the # bases of overlap.
static 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[].
void	setChromosome(java.lang.String chromosome)
void	setEnd(int end)
void	setGcContent(boolean[] gcContent)
void	setHits(java.util.HashSet hits)
void	setNotes(java.lang.String notes)
void	setStart(int start)
static java.util.HashMap	splitByChromosome(Region[] sorted) Given a chromosome SORTED array of Regions returns a HashMap containing chromosome: sorted chromo specific Region[]
java.lang.String	toString()
static void	writeBinaryCoordinates(java.io.File file, Region[] r) Writes the chrom start stop of a Region[] as a binary file.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Region

public Region(java.lang.String chromosome,
              int start,
              int end,
              java.lang.String notes)

Method Detail

getLength

public int getLength()

Returns end - start +1, thus last base is included, not interbase numbering!

loadWriteBinaryRegions

public static 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.

loadBinaryCoordinates

public static Region[] loadBinaryCoordinates(java.io.File file)

Reads binary chrom start stop file into Region[]

writeBinaryCoordinates

public static void writeBinaryCoordinates(java.io.File file,
                                          Region[] r)

Writes the chrom start stop of a Region[] as a binary file.

splitByChromosome

public static java.util.HashMap splitByChromosome(Region[] sorted)

Given a chromosome SORTED array of Regions returns a HashMap containing chromosome: sorted chromo specific Region[]

toString

public java.lang.String toString()

calculateGCContent

public double calculateGCContent()

Returns the fraction of GC provided the Region.gcContent[] is loaded. Otherwise returns zero.

intersect

public boolean intersect(Interval interval)

intersect

public boolean intersect(TPMapLine line)

intersect

public boolean intersect(Window window,
                         int sizeOligo,
                         double fractionAcceptibleCoverage)

Returns true only if region contains or is contained or is covered by >= fractionAcceptibleCoverage by a window. ie 0.5 for 50% or region covered by a window.

bpIntersectionSameChromosome

public int bpIntersectionSameChromosome(Region other)

Assumes regions are on the same chromosome, and the end base is included, not interbase numbering. Returns 0 if the regions abut, positive ints for each base in the gap (ie 1= 1bp between an end of 12 and a start of 14), negative ints for each base of intersection (ie -1= 1bp overlap), max negative int is the length of the smaller region (ie end - start +1).

overlap

public int overlap(Interval interval)

Returns -1 for no overlap, or a positive int for the # bases of overlap. Doesn't check chromosome!

parseRegions

public static 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[].

getChromosome

public java.lang.String getChromosome()

setChromosome

public void setChromosome(java.lang.String chromosome)

getEnd

public int getEnd()

setEnd

public void setEnd(int end)

getHits

public java.util.HashSet getHits()

setHits

public void setHits(java.util.HashSet hits)

getNotes

public java.lang.String getNotes()

setNotes

public void setNotes(java.lang.String notes)

getStart

public int getStart()

setStart

public void setStart(int start)

getGcContent

public boolean[] getGcContent()

setGcContent

public void setGcContent(boolean[] gcContent)