htsjdk.samtools

Class BinList

java.lang.Object

htsjdk.samtools.BinList

All Implemented Interfaces:

java.lang.Iterable<Bin>

public class BinList
extends java.lang.Object
implements java.lang.Iterable<Bin>

Provides a list of all bins which could exist in the BAM file. Allows the user to iterate over all bins, selecting ones of interest for later inspection.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	BinList(int referenceSequence, java.util.BitSet bins) Create a new BinList over sequenceCount sequences, consisting of the given bins.

Method Summary

Methods

Modifier and Type	Method and Description
protected java.util.BitSet	getBins() Retrieves the bins stored in this list.
protected int	getReferenceSequence() Get the reference sequence to which this bin belongs.
java.util.Iterator<Bin>	iterator() Gets an iterator over all selected bins.

Methods inherited from class java.lang.Object

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

Constructor Detail

BinList

protected BinList(int referenceSequence,
       java.util.BitSet bins)

Create a new BinList over sequenceCount sequences, consisting of the given bins.

Parameters:

referenceSequence - Reference sequence to which these bins are relevant.

bins - The given bins to include.

Method Detail

iterator

public java.util.Iterator<Bin> iterator()

Gets an iterator over all selected bins.

Specified by:

iterator in interface java.lang.Iterable<Bin>

Returns:

An iterator over all selected bins.

getReferenceSequence

protected int getReferenceSequence()

Get the reference sequence to which this bin belongs.

Returns:

Integer representing the reference sequence.

getBins

protected java.util.BitSet getBins()

Retrieves the bins stored in this list.

Returns:

A bitset where a bin is present in the list if the bit is true.