org.broad.igv.bbfile
Class BigBedDataBlock

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

public class BigBedDataBlock
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

BigBedDataBlock(net.sf.samtools.util.SeekableStream fis, RPTreeLeafNodeItem leafHitItem, java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap, boolean isLowToHigh, int uncompressBufSize)

Method Summary

java.util.ArrayList<BedFeature>	getBedData(RPChromosomeRegion selectionRegion, boolean contained)
void	print()

Methods inherited from class java.lang.Object

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

Constructor Detail

BigBedDataBlock

public BigBedDataBlock(net.sf.samtools.util.SeekableStream fis,
                       RPTreeLeafNodeItem leafHitItem,
                       java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap,
                       boolean isLowToHigh,
                       int uncompressBufSize)

Method Detail

getBedData

public java.util.ArrayList<BedFeature> getBedData(RPChromosomeRegion selectionRegion,
                                                  boolean contained)

print

public void print()