Package 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

Created by IntelliJ IDEA. User: martind Date: Apr 16, 2010 Time: 4:19:29 PM To change this template use File | Settings | File Templates.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ZoomLevelIterator.EmptyIterator

Constructor Summary

Constructors

Constructor	Description
ZoomLevelIterator()	Default constructor.
ZoomLevelIterator(SeekableStream fis, BPTree chromIDTree, RPTree zoomDataTree, int zoomLevel, RPChromosomeRegion selectionRegion, boolean contained)	Constructs a zoom level iterator over the specified chromosome region

Method Summary

Modifier and Type	Method	Description
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(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 SeekableStream getBBFis()

getChromosomeIDTree

public BPTree getChromosomeIDTree()

getZoomDataTree

public RPTree getZoomDataTree()