org.broad.igv.bbfile
Class BBFileReader

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

public class BBFileReader
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 long

BBFILE_HEADER_OFFSET

Constructor Summary

BBFileReader(Locator path, net.sf.samtools.util.SeekableStream stream)

BBFileReader(java.lang.String path)

Method Summary

BBFileHeader	getBBFileHeader()
net.sf.samtools.util.SeekableStream	getBBFis()
BigBedIterator	getBigBedIterator() Returns an iterator for BigBed features for all chromosome regions.
BigBedIterator	getBigBedIterator(java.lang.String startChromosome, int startBase, java.lang.String endChromosome, int endBase, boolean contained) Returns an iterator for BigBed features which occupy a chromosome selection region.
BigWigIterator	getBigWigIterator() Returns an iterator for BigWig values for all chromosome regions.
BigWigIterator	getBigWigIterator(java.lang.String startChromosome, int startBase, java.lang.String endChromosome, int endBase, boolean contained) Returns an iterator for BigWig values which occupy the specified startChromosome region.
RPChromosomeRegion	getChromosomeBounds()
RPChromosomeRegion	getChromosomeBounds(int startChromID, int endChromID)
RPTree	getChromosomeDataTree()
int	getChromosomeID(java.lang.String chromosomeKey)
BPTree	getChromosomeIDTree()
java.lang.String	getChromosomeName(int chromID)
long	getChromosomeNameCount()
java.util.ArrayList<java.lang.String>	getChromosomeNames()
long	getChromosomeRegionCount()
java.util.ArrayList<RPChromosomeRegion>	getChromosomeRegions()
int	getDataCount()
int	getDecompressionBufSize()
Locator	getLocator()
BBTotalSummaryBlock	getTotalSummaryBlock()
RPChromosomeRegion	getZoomLevelBounds(int zoomLevel)
RPChromosomeRegion	getZoomLevelBounds(int zoomLevel, int startChromID, int endChromID)
int	getZoomLevelCount()
ZoomLevelIterator	getZoomLevelIterator(int zoomLevel) Returns an iterator for zoom level records for all chromosome regions.
ZoomLevelIterator	getZoomLevelIterator(int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained) Returns an iterator for zoom level records for the chromosome selection region.
ZoomLevelIterator	getZoomLevelIterator(int zoomLevel, java.lang.String startChromosome, int startBase, java.lang.String endChromosome, int endBase, boolean contained) Returns an iterator for zoom level records for the chromosome selection region.
int	getZoomLevelRecordCount(int zoomLevel)
java.util.ArrayList<RPChromosomeRegion>	getZoomLevelRegions(int zoomLevel)
BBZoomLevels	getZoomLevels()
boolean	isBigBedFile()
boolean	isBigWigFile()
boolean	isLowToHigh()

Methods inherited from class java.lang.Object

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

Field Detail

BBFILE_HEADER_OFFSET

public static final long BBFILE_HEADER_OFFSET

See Also:

Constant Field Values

Constructor Detail

BBFileReader

public BBFileReader(java.lang.String path)
             throws java.io.IOException

Throws:

java.io.IOException

BBFileReader

public BBFileReader(Locator path,
                    net.sf.samtools.util.SeekableStream stream)

Method Detail

getBBFis

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

getBBFileHeader

public BBFileHeader getBBFileHeader()

isBigBedFile

public boolean isBigBedFile()

isBigWigFile

public boolean isBigWigFile()

getDataCount

public int getDataCount()

getChromosomeNameCount

public long getChromosomeNameCount()

getChromosomeRegionCount

public long getChromosomeRegionCount()

getDecompressionBufSize

public int getDecompressionBufSize()

isLowToHigh

public boolean isLowToHigh()

getTotalSummaryBlock

public BBTotalSummaryBlock getTotalSummaryBlock()

getChromosomeIDTree

public BPTree getChromosomeIDTree()

getChromosomeDataTree

public RPTree getChromosomeDataTree()

getZoomLevelCount

public int getZoomLevelCount()

getZoomLevels

public BBZoomLevels getZoomLevels()

getZoomLevelBounds

public RPChromosomeRegion getZoomLevelBounds(int zoomLevel,
                                             int startChromID,
                                             int endChromID)

getZoomLevelBounds

public RPChromosomeRegion getZoomLevelBounds(int zoomLevel)

getZoomLevelRecordCount

public int getZoomLevelRecordCount(int zoomLevel)

getChromosomeName

public java.lang.String getChromosomeName(int chromID)

getChromosomeNames

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

getChromosomeID

public int getChromosomeID(java.lang.String chromosomeKey)

getChromosomeBounds

public RPChromosomeRegion getChromosomeBounds(int startChromID,
                                              int endChromID)

getChromosomeBounds

public RPChromosomeRegion getChromosomeBounds()

getChromosomeRegions

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

getZoomLevelRegions

public java.util.ArrayList<RPChromosomeRegion> getZoomLevelRegions(int zoomLevel)

getBigBedIterator

public BigBedIterator getBigBedIterator(java.lang.String startChromosome,
                                        int startBase,
                                        java.lang.String endChromosome,
                                        int endBase,
                                        boolean contained)

Returns an iterator for BigBed features which occupy a chromosome selection region.

Note: the BBFile type should be BigBed; else a null iterator is returned.

Parameters: startChromosome - name of start chromosome startBase - starting base position for features endChromosome - name of end chromosome endBase - ending base position for feature contained - flag specifies bed features must be contained in the specified base region if true; else can intersect the region if false

Returns: Iterator to provide BedFeature(s) for the requested chromosome region. Error conditions: 1) An empty iterator is returned if region has no data available 2) A null object is returned if the file is not BigBed.(see isBigBedFile method)

getBigBedIterator

public BigBedIterator getBigBedIterator()

Returns an iterator for BigBed features for all chromosome regions.

Note: the BBFile type should be BigBed; else a null iterator is returned.

Returns: Iterator to provide BedFeature(s) for all chromosome regions. Error conditions: 1) An empty iterator is returned if region has no data available 2) A null object is returned if the file is not BigBed.(see isBigBedFile method)

getBigWigIterator

public BigWigIterator getBigWigIterator(java.lang.String startChromosome,
                                        int startBase,
                                        java.lang.String endChromosome,
                                        int endBase,
                                        boolean contained)

Returns an iterator for BigWig values which occupy the specified startChromosome region.

Note: the BBFile type should be BigWig; else a null iterator is returned.

Parameters: startChromosome - name of start chromosome startBase - starting base position for features endChromosome - name of end chromosome endBase - ending base position for feature contained - flag specifies bed features must be contained in the specified base region if true; else can intersect the region if false

Returns: Iterator to provide BedFeature(s) for the requested chromosome region. Error conditions: 1) An empty iterator is returned if region has no data available 2) A null object is returned if the file is not BigWig.(see isBigWigFile method)

getBigWigIterator

public BigWigIterator getBigWigIterator()

Returns an iterator for BigWig values for all chromosome regions.

Note: the BBFile type should be BigWig; else a null iterator is returned.

Returns: Iterator to provide BedFeature(s) for all chromosome regions. Error conditions: 1) An empty iterator is returned if region has no data available 2) A null object is returned if the file is not BigWig.(see isBigWigFile method)

getZoomLevelIterator

public ZoomLevelIterator getZoomLevelIterator(int zoomLevel,
                                              java.lang.String startChromosome,
                                              int startBase,
                                              java.lang.String endChromosome,
                                              int endBase,
                                              boolean contained)

Returns an iterator for zoom level records for the chromosome selection region.

Note: the BBFile can be BigBed or BigWig.

Parameters: zoomLevel - zoom level for data extraction; levels start at 1 startChromosome - start chromosome name startBase - staring base position for features endChromosome - end chromosome name endBase - ending base position for feature contained - flag specifies bed features must be contained in the specified base region if true; else can intersect the region if false

Returns: Iterator to provide BedFeature(s) for the requested chromosome region. Error conditions: 1) An empty iterator is returned if region has no data available

getZoomLevelIterator

public ZoomLevelIterator getZoomLevelIterator(int zoomLevel)

Returns an iterator for zoom level records for all chromosome regions.

Note: the BBFile can be BigBed or BigWig.

Parameters: zoomLevel - zoom level for data extraction; levels start at 1

Returns: Iterator to provide BedFeature(s) for the requested chromosome region. Error conditions: 1) An empty iterator is returned if region has no data available

getZoomLevelIterator

public ZoomLevelIterator getZoomLevelIterator(int zoomLevel,
                                              RPChromosomeRegion selectionRegion,
                                              boolean contained)

Returns an iterator for zoom level records for the chromosome selection region.

Note: the BBFile can be BigBed or BigWig.

Parameters: zoomLevel - zoom level for data extraction; levels start at 1 selectionRegion - chromosome selection region consists of: startChromID - ID of starting chromosome startBase - staring base position for features endChromID - ID of endind chromosome endBase - ending base position for feature contained - flag specifies bed features must be contained in the specified base region if true; else can intersect the region if false

Returns: Iterator to provide BedFeature(s) for the requested chromosome region. Error conditions: 1) An empty iterator is returned if region has no data available

getLocator

public Locator getLocator()