trans.graphics
Class GenomicRegion

java.lang.Object
  trans.graphics.GenomicRegion

public class GenomicRegion

extends java.lang.Object

Constructor Summary

GenomicRegion(java.lang.String line, int rank)

Method Summary

static int	findBiggestGenomicRegion(GenomicRegion[] gr) Returns the length of the biggest GenomicRegion
java.lang.String	getChromosome()
GenomicRegionGlyph	getGlyph()
java.util.ArrayList	getIntersectingRegions()
java.lang.String	getNotes()
int	getRank()
double	getScore()
int	getStart()
int	getStop()
boolean	overlap(GenomicRegion other, int maxGap) checks to see if regions overlap by the minimum maxGap, can set maxGap negative to require an overlap.
void	setGlyph(GenomicRegionGlyph glyph)
void	setRank(int rank)
java.lang.String	toString() Returns tab delimited rank+1, chrom, st, stp, scr, notes.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomicRegion

public GenomicRegion(java.lang.String line,
                     int rank)

Method Detail

toString

public java.lang.String toString()

Returns tab delimited rank+1, chrom, st, stp, scr, notes.

overlap

public boolean overlap(GenomicRegion other,
                       int maxGap)

checks to see if regions overlap by the minimum maxGap, can set maxGap negative to require an overlap.

findBiggestGenomicRegion

public static int findBiggestGenomicRegion(GenomicRegion[] gr)

Returns the length of the biggest GenomicRegion

getChromosome

public java.lang.String getChromosome()

getIntersectingRegions

public java.util.ArrayList getIntersectingRegions()

getNotes

public java.lang.String getNotes()

getScore

public double getScore()

getStart

public int getStart()

getStop

public int getStop()

getGlyph

public GenomicRegionGlyph getGlyph()

setGlyph

public void setGlyph(GenomicRegionGlyph glyph)

getRank

public int getRank()

setRank

public void setRank(int rank)