org.broad.igv.bbfile
Class RPChromosomeRegion

java.lang.Object
  org.broad.igv.bbfile.RPChromosomeRegion

Direct Known Subclasses:

RPTreeLeafNodeItem

public class RPChromosomeRegion
extends java.lang.Object

File retrieved from BigWig project at Google code on July 26, 2011, revision 36 http://code.google.com/p/bigwig/ This project provides java readers for the UCSC's BigWig and BigBed formats. It was originally developed by Martin Decautis and Jim Robinson for the Integrative Genomics Viewer (http://www.broadinstitute.org/igv). Thanks to Jim Kent and Ann Zweig and from UCSC for their assistance. Modification to work with GenomeView by Thomas Abeel.

Author:

Martin Decautis, Jim Robinson, Thomas Abeel

Constructor Summary

RPChromosomeRegion()

RPChromosomeRegion(int startChromID, int startBase, int endChromID, int endBase)

RPChromosomeRegion(RPChromosomeRegion region)

Method Summary

int	compareRegions(RPChromosomeRegion testRegion)
boolean	containedIn(RPChromosomeRegion testRegion)
boolean	disjointAbove(RPChromosomeRegion testRegion)
boolean	disjointBelow(RPChromosomeRegion testRegion)
boolean	equals(RPChromosomeRegion testRegion)
void	expand(RPChromosomeRegion testRegion)
int	getEndBase()
int	getEndChromID()
RPChromosomeRegion	getExtremes(RPChromosomeRegion testRegion)
int	getStartBase()
int	getStartChromID()
boolean	intersectsAbove(RPChromosomeRegion testRegion)
boolean	intersectsBelow(RPChromosomeRegion testRegion)
void	print()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RPChromosomeRegion

public RPChromosomeRegion(int startChromID,
                          int startBase,
                          int endChromID,
                          int endBase)

RPChromosomeRegion

public RPChromosomeRegion(RPChromosomeRegion region)

RPChromosomeRegion

public RPChromosomeRegion()

Method Detail

getStartChromID

public int getStartChromID()

getStartBase

public int getStartBase()

getEndChromID

public int getEndChromID()

getEndBase

public int getEndBase()

print

public void print()

compareRegions

public int compareRegions(RPChromosomeRegion testRegion)

equals

public boolean equals(RPChromosomeRegion testRegion)

containedIn

public boolean containedIn(RPChromosomeRegion testRegion)

intersectsBelow

public boolean intersectsBelow(RPChromosomeRegion testRegion)

intersectsAbove

public boolean intersectsAbove(RPChromosomeRegion testRegion)

disjointBelow

public boolean disjointBelow(RPChromosomeRegion testRegion)

disjointAbove

public boolean disjointAbove(RPChromosomeRegion testRegion)

getExtremes

public RPChromosomeRegion getExtremes(RPChromosomeRegion testRegion)

expand

public void expand(RPChromosomeRegion testRegion)