org.broad.igv.bbfile
Class BigWigSection

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

public class BigWigSection
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

BigWigSection(byte[] sectionBuffer, java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap, boolean isLowToHigh, RPTreeLeafNodeItem leafHitItem)

Method Summary

int	getItemCount()
int	getSectionData(RPChromosomeRegion selectionRegion, boolean contained, java.util.ArrayList<WigItem> wigItemList)
int	getSectionDataSize()
BigWigSectionHeader	getSectionHeader()
boolean	isValidSectionType()
void	print()

Methods inherited from class java.lang.Object

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

Constructor Detail

BigWigSection

public BigWigSection(byte[] sectionBuffer,
                     java.util.HashMap<java.lang.Integer,java.lang.String> chromosomeMap,
                     boolean isLowToHigh,
                     RPTreeLeafNodeItem leafHitItem)

Method Detail

isValidSectionType

public boolean isValidSectionType()

getItemCount

public int getItemCount()

getSectionHeader

public BigWigSectionHeader getSectionHeader()

getSectionDataSize

public int getSectionDataSize()

getSectionData

public int getSectionData(RPChromosomeRegion selectionRegion,
                          boolean contained,
                          java.util.ArrayList<WigItem> wigItemList)

print

public void print()