Package org.broad.igv.bbfile

Class BigWigIterator

java.lang.Object

org.broad.igv.bbfile.BigWigIterator

All Implemented Interfaces:

java.util.Iterator<WigItem>

public class BigWigIterator
extends java.lang.Object
implements java.util.Iterator<WigItem>

Created by IntelliJ IDEA. User: martind Date: Apr 13, 2010 Time: 12:34:16 PM To change this template use File | Settings | File Templates.

Constructor Summary

Constructors

Constructor	Description
BigWigIterator()	Constructor for an "empty" iterator
BigWigIterator(SeekableStream fis, BPTree chromIDTree, RPTree chromDataTree, RPChromosomeRegion selectionRegion, boolean contained)	Constructor for a BigWig iterator over the specified chromosome region

Method Summary

Modifier and Type	Method	Description
SeekableStream	getBBFis()
RPTree	getChromosomeDataTree()
BPTree	getChromosomeIDTree()
RPChromosomeRegion	getSelectionRegion()
boolean	hasNext()
boolean	isContained()
WigItem	next()	Method returns the current Wig item and advances to the next Wig 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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

BigWigIterator

public BigWigIterator(SeekableStream fis,
                      BPTree chromIDTree,
                      RPTree chromDataTree,
                      RPChromosomeRegion selectionRegion,
                      boolean contained)

Constructor for a BigWig iterator over the specified chromosome region

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

BigWigIterator

public BigWigIterator()

Constructor for an "empty" iterator

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<WigItem>

next

public WigItem next()

Method returns the current Wig item and advances to the next Wig record.

Returns: Wig item for current BigWig data record.

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

Specified by:

next in interface java.util.Iterator<WigItem>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<WigItem>

getSelectionRegion

public RPChromosomeRegion getSelectionRegion()

setSelectionRegion

public int setSelectionRegion(RPChromosomeRegion selectionRegion,
                              boolean contained)

isContained

public boolean isContained()

getBBFis

public SeekableStream getBBFis()

getChromosomeIDTree

public BPTree getChromosomeIDTree()

getChromosomeDataTree

public RPTree getChromosomeDataTree()