org.broad.igv.bbfile
Class RPTree

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

public class RPTree
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

Field Summary

int	RPTREE_NODE_CHILD_ITEM_SIZE
int	RPTREE_NODE_FORMAT_SIZE
int	RPTREE_NODE_LEAF_ITEM_SIZE

Constructor Summary

RPTree(int order)

RPTree(net.sf.samtools.util.SeekableStream fis, long fileOffset, boolean isLowToHigh, int uncompressBuffSize)

Method Summary

java.util.ArrayList<RPChromosomeRegion>	getAllChromosomeRegions()
RPChromosomeRegion	getChromosomeBounds()
java.util.ArrayList<RPTreeLeafNodeItem>	getChromosomeDataHits(RPChromosomeRegion selectionRegion, boolean contained)
RPChromosomeRegion	getChromosomeRegion(int startChromID, int endChromID)
long	getItemCount()
long	getNodeCount()
int	getOrder()
RPTreeHeader	getRPTreeHeader()
int	getUncompressBuffSize()
boolean	isIsLowToHigh()
void	print()

Methods inherited from class java.lang.Object

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

Field Detail

RPTREE_NODE_FORMAT_SIZE

public final int RPTREE_NODE_FORMAT_SIZE

See Also:

Constant Field Values

RPTREE_NODE_LEAF_ITEM_SIZE

public final int RPTREE_NODE_LEAF_ITEM_SIZE

See Also:

Constant Field Values

RPTREE_NODE_CHILD_ITEM_SIZE

public final int RPTREE_NODE_CHILD_ITEM_SIZE

See Also:

Constant Field Values

Constructor Detail

RPTree

public RPTree(net.sf.samtools.util.SeekableStream fis,
              long fileOffset,
              boolean isLowToHigh,
              int uncompressBuffSize)

RPTree

public RPTree(int order)

Method Detail

getUncompressBuffSize

public int getUncompressBuffSize()

isIsLowToHigh

public boolean isIsLowToHigh()

getOrder

public int getOrder()

getRPTreeHeader

public RPTreeHeader getRPTreeHeader()

getItemCount

public long getItemCount()

getChromosomeBounds

public RPChromosomeRegion getChromosomeBounds()

getNodeCount

public long getNodeCount()

getChromosomeRegion

public RPChromosomeRegion getChromosomeRegion(int startChromID,
                                              int endChromID)

getAllChromosomeRegions

public java.util.ArrayList<RPChromosomeRegion> getAllChromosomeRegions()

getChromosomeDataHits

public java.util.ArrayList<RPTreeLeafNodeItem> getChromosomeDataHits(RPChromosomeRegion selectionRegion,
                                                                     boolean contained)

print

public void print()