org.broad.igv.bbfile
Class BPTree

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

public class BPTree
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

static int	BPTREE_NODE_FORMAT_SIZE
static int	BPTREE_NODE_ITEM_SIZE

Constructor Summary

BPTree(net.sf.samtools.util.SeekableStream fis, long fileOffset, boolean isLowToHigh)

Method Summary

void	findAllChromosomeNames(BPTreeNode thisNode, java.util.ArrayList<java.lang.String> chromosomeList)
int	getBlockSize()
long	getBPTreeOffset()
int	getChromosomeID(java.lang.String chromKey)
java.util.HashMap<java.lang.Integer,java.lang.String>	getChromosomeIDMap(int startChromID, int endChromID)
java.lang.String	getChromosomeKey(java.lang.String chromosome)
java.lang.String	getChromosomeName(int chromID)
java.util.ArrayList<java.lang.String>	getChromosomeNames()
net.sf.samtools.util.SeekableStream	getFis()
long	getItemCount()
int	getKeySize()
long	getNodeCount()
BPTreeNode	getRootNode()
BPTreeHeader	getTreeHeader()
int	getValueSize()
void	print()

Methods inherited from class java.lang.Object

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

Field Detail

BPTREE_NODE_FORMAT_SIZE

public static final int BPTREE_NODE_FORMAT_SIZE

See Also:

Constant Field Values

BPTREE_NODE_ITEM_SIZE

public static final int BPTREE_NODE_ITEM_SIZE

See Also:

Constant Field Values

Constructor Detail

BPTree

public BPTree(net.sf.samtools.util.SeekableStream fis,
              long fileOffset,
              boolean isLowToHigh)

Method Detail

getFis

public net.sf.samtools.util.SeekableStream getFis()

getBPTreeOffset

public long getBPTreeOffset()

getTreeHeader

public BPTreeHeader getTreeHeader()

getBlockSize

public int getBlockSize()

getKeySize

public int getKeySize()

getValueSize

public int getValueSize()

getItemCount

public long getItemCount()

getNodeCount

public long getNodeCount()

getRootNode

public BPTreeNode getRootNode()

getChromosomeKey

public java.lang.String getChromosomeKey(java.lang.String chromosome)

getChromosomeID

public int getChromosomeID(java.lang.String chromKey)

getChromosomeName

public java.lang.String getChromosomeName(int chromID)

getChromosomeNames

public java.util.ArrayList<java.lang.String> getChromosomeNames()

getChromosomeIDMap

public java.util.HashMap<java.lang.Integer,java.lang.String> getChromosomeIDMap(int startChromID,
                                                                                int endChromID)

print

public void print()

findAllChromosomeNames

public void findAllChromosomeNames(BPTreeNode thisNode,
                                   java.util.ArrayList<java.lang.String> chromosomeList)