org.broad.igv.bbfile
Class BigWigSectionHeader

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

public class BigWigSectionHeader
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

Nested Class Summary

static class

BigWigSectionHeader.WigItemType

Field Summary

static int	BEDGRAPH_ITEM_SIZE
static int	FIXEDSTEP_ITEM_SIZE
static int	SECTION_HEADER_SIZE
static int	VARSTEP_ITEM_SIZE

Constructor Summary

BigWigSectionHeader(java.io.DataInputStream bdis)

BigWigSectionHeader(LittleEndianInputStream lbdis)

Method Summary

int	getChromID()
int	getChromosomeEnd()
int	getChromosomeStart()
short	getItemCount()
int	getItemSpan()
int	getItemStep()
BigWigSectionHeader.WigItemType	getItemType()
byte	getReserved()
boolean	IsValidType()
void	print()

Methods inherited from class java.lang.Object

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

Field Detail

SECTION_HEADER_SIZE

public static final int SECTION_HEADER_SIZE

See Also:

Constant Field Values

FIXEDSTEP_ITEM_SIZE

public static final int FIXEDSTEP_ITEM_SIZE

See Also:

Constant Field Values

VARSTEP_ITEM_SIZE

public static final int VARSTEP_ITEM_SIZE

See Also:

Constant Field Values

BEDGRAPH_ITEM_SIZE

public static final int BEDGRAPH_ITEM_SIZE

See Also:

Constant Field Values

Constructor Detail

BigWigSectionHeader

public BigWigSectionHeader(LittleEndianInputStream lbdis)

BigWigSectionHeader

public BigWigSectionHeader(java.io.DataInputStream bdis)

Method Detail

getChromID

public int getChromID()

getChromosomeStart

public int getChromosomeStart()

getChromosomeEnd

public int getChromosomeEnd()

getItemStep

public int getItemStep()

getItemSpan

public int getItemSpan()

getItemType

public BigWigSectionHeader.WigItemType getItemType()

IsValidType

public boolean IsValidType()

getItemCount

public short getItemCount()

getReserved

public byte getReserved()

print

public void print()