org.broad.igv.bbfile
Class BigBedIterator

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

All Implemented Interfaces:

java.util.Iterator<BedFeature>

public class BigBedIterator
extends java.lang.Object
implements java.util.Iterator<BedFeature>

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

Constructor Summary

BigBedIterator()

BigBedIterator(net.sf.samtools.util.SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)
Constructor for a BigBed iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromomosme ID's for chromosome names chromDataTree - R+ chromosome data locations tree selectionRegion - chromosome region for selection of Bed feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for features endChromID - ID of end chromosome endBase - starting base position for features contained - specifies bed features must be contained by region, if true; else return any intersecting region features

Method Summary

net.sf.samtools.util.SeekableStream	getBBFis()
RPTree	getChromosomeDataTree()
BPTree	getChromosomeIDTree()
java.util.ArrayList<RPTreeLeafNodeItem>	getLeafItems()
RPChromosomeRegion	getSelectionRegion()
boolean	hasNext()
boolean	isContained()
BedFeature	next() Method returns the current bed feature and advances to the next bed record.
void	remove()
int	setSelectionRegion(RPChromosomeRegion selectionRegion, boolean contained)

Methods inherited from class java.lang.Object

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

Constructor Detail

BigBedIterator

public BigBedIterator(net.sf.samtools.util.SeekableStream fis,
                      BPTree chromIDTree,
                      RPTree chromDataTree,
                      RPChromosomeRegion selectionRegion,
                      boolean contained)

Constructor for a BigBed iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromomosme ID's for chromosome names chromDataTree - R+ chromosome data locations tree selectionRegion - chromosome region for selection of Bed feature extraction consists of: startChromID - ID of start chromosome startBase - starting base position for features endChromID - ID of end chromosome endBase - starting base position for features contained - specifies bed features must be contained by region, if true; else return any intersecting region features

BigBedIterator

public BigBedIterator()

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<BedFeature>

next

public BedFeature next()

Method returns the current bed feature and advances to the next bed record.

Returns: Bed feature for current BigBed data record.

Note: If "next" method is called when a "next item" does not exist, an UnsupportedOperationException will be thrown.

Specified by:

next in interface java.util.Iterator<BedFeature>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<BedFeature>

getSelectionRegion

public RPChromosomeRegion getSelectionRegion()

setSelectionRegion

public int setSelectionRegion(RPChromosomeRegion selectionRegion,
                              boolean contained)

isContained

public boolean isContained()

getBBFis

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

getChromosomeIDTree

public BPTree getChromosomeIDTree()

getChromosomeDataTree

public RPTree getChromosomeDataTree()

getLeafItems

public java.util.ArrayList<RPTreeLeafNodeItem> getLeafItems()