org.broad.igv.bbfile
Class BBFileHeader

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

public class BBFileHeader
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	BBFILE_HEADER_SIZE
static int	BIGBED_MAGIC_HTL
static int	BIGBED_MAGIC_LTH
static int	BIGWIG_MAGIC_HTL
static int	BIGWIG_MAGIC_LTH

Constructor Summary

BBFileHeader(int magic, short version, short zoomLevels, long chromTreeOffset, long fullDataOffset, long fullIndexOffset, short fieldCount, short definedFieldCount, long autoSqlOffset, long totalSummaryOffset, int uncompressBuffSize, long reserved)

BBFileHeader(net.sf.samtools.util.SeekableStream fis, long fileOffset)

Method Summary

long	getAutoSqlOffset()
long	getChromosomeTreeOffset()
short	getDefinedFieldCount()
short	getFieldCount()
int	getFileHeaderSize()
long	getFullDataOffset()
long	getFullIndexOffset()
int	getMagic()
long	getTotalSummaryOffset()
int	getUncompressBuffSize()
short	getVersion()
short	getZoomLevels()
boolean	isBigBed()
boolean	isBigWig()
boolean	isHeaderOK()
boolean	isLowToHigh()

Methods inherited from class java.lang.Object

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

Field Detail

BBFILE_HEADER_SIZE

public static final int BBFILE_HEADER_SIZE

See Also:

Constant Field Values

BIGWIG_MAGIC_LTH

public static final int BIGWIG_MAGIC_LTH

See Also:

Constant Field Values

BIGWIG_MAGIC_HTL

public static final int BIGWIG_MAGIC_HTL

See Also:

Constant Field Values

BIGBED_MAGIC_LTH

public static final int BIGBED_MAGIC_LTH

See Also:

Constant Field Values

BIGBED_MAGIC_HTL

public static final int BIGBED_MAGIC_HTL

See Also:

Constant Field Values

Constructor Detail

BBFileHeader

public BBFileHeader(net.sf.samtools.util.SeekableStream fis,
                    long fileOffset)

BBFileHeader

public BBFileHeader(int magic,
                    short version,
                    short zoomLevels,
                    long chromTreeOffset,
                    long fullDataOffset,
                    long fullIndexOffset,
                    short fieldCount,
                    short definedFieldCount,
                    long autoSqlOffset,
                    long totalSummaryOffset,
                    int uncompressBuffSize,
                    long reserved)

Method Detail

isHeaderOK

public boolean isHeaderOK()

isLowToHigh

public boolean isLowToHigh()

isBigBed

public boolean isBigBed()

isBigWig

public boolean isBigWig()

getFileHeaderSize

public int getFileHeaderSize()

getMagic

public int getMagic()

getVersion

public short getVersion()

getZoomLevels

public short getZoomLevels()

getChromosomeTreeOffset

public long getChromosomeTreeOffset()

getFullDataOffset

public long getFullDataOffset()

getFullIndexOffset

public long getFullIndexOffset()

getFieldCount

public short getFieldCount()

getDefinedFieldCount

public short getDefinedFieldCount()

getAutoSqlOffset

public long getAutoSqlOffset()

getTotalSummaryOffset

public long getTotalSummaryOffset()

getUncompressBuffSize

public int getUncompressBuffSize()