org.broad.igv.bbfile
Class ZoomLevelIterator

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

Direct Known Subclasses:

ZoomLevelIterator.EmptyIterator

public class ZoomLevelIterator
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

ZoomLevelIterator.EmptyIterator

Constructor Summary

ZoomLevelIterator()
Default constructor.

ZoomLevelIterator(net.sf.samtools.util.SeekableStream fis, BPTree chromIDTree, RPTree zoomDataTree, int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained)
Constructs a zoom level iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromId for chromosome name key zoomLevelTree - zoom level R+ chromosome index tree zoomLevel - zoom level represented by the R+ 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()
BPTree	getChromosomeIDTree()
RPChromosomeRegion	getSelectionRegion()
RPTree	getZoomDataTree()
int	getZoomLevel()
boolean	hasNext()
boolean	isContained()
ZoomDataRecord	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

ZoomLevelIterator

public ZoomLevelIterator()

Default constructor. This is provided to support return of a subclassed "empty" iterator

ZoomLevelIterator

public ZoomLevelIterator(net.sf.samtools.util.SeekableStream fis,
                         BPTree chromIDTree,
                         RPTree zoomDataTree,
                         int zoomLevel,
                         RPChromosomeRegion selectionRegion,
                         boolean contained)

Constructs a zoom level iterator over the specified chromosome region

Parameters: fis - file input stream handle chromIDTree - B+ index tree returns chromId for chromosome name key zoomLevelTree - zoom level R+ chromosome index tree zoomLevel - zoom level represented by the R+ 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 Detail

hasNext

public boolean hasNext()

next

public ZoomDataRecord 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.

remove

public void remove()

getZoomLevel

public int getZoomLevel()

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()

getZoomDataTree

public RPTree getZoomDataTree()