htsjdk.samtools

Class BinningIndexContent

java.lang.Object

htsjdk.samtools.BinningIndexContent

public class BinningIndexContent
extends java.lang.Object

In-memory representation of the binning index for a single reference. BAM and Tabix are both binning indices with slightly different disk formats but identical in-memory representations.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BinningIndexContent.BinList This class is used to encapsulate the list of Bins store in the BAMIndexContent While it is currently represented as an array, we may decide to change it to an ArrayList or other structure

Constructor Summary

Constructors

Constructor and Description
BinningIndexContent(int referenceSequence, BinningIndexContent.BinList binList, LinearIndex linearIndex)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	containsBin(Bin bin) Does this content have anything in this bin?
boolean	equals(java.lang.Object o)
java.util.List<Chunk>	getAllChunks()
BinningIndexContent.BinList	getBins()
java.util.List<Chunk>	getChunksOverlapping(int startPos, int endPos)
LinearIndex	getLinearIndex()
int	getReferenceSequence() Reference for this Content
int	hashCode()

Methods inherited from class java.lang.Object

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

Constructor Detail

BinningIndexContent

public BinningIndexContent(int referenceSequence,
                   BinningIndexContent.BinList binList,
                   LinearIndex linearIndex)

Parameters:

referenceSequence - Content corresponds to this reference.

binList - Array of bins represented by this content, possibly sparse

linearIndex - Additional index used to optimize queries

Method Detail

getReferenceSequence

public int getReferenceSequence()

Reference for this Content

containsBin

public boolean containsBin(Bin bin)

Does this content have anything in this bin?

getBins

public BinningIndexContent.BinList getBins()

Returns:

iterable list of bins represented by this content

getAllChunks

public java.util.List<Chunk> getAllChunks()

Returns:

all chunks associated with all bins in this content

getLinearIndex

public LinearIndex getLinearIndex()

Returns:

the linear index represented by this content

getChunksOverlapping

public java.util.List<Chunk> getChunksOverlapping(int startPos,
                                         int endPos)

Parameters:

startPos - 1-based, inclusive

endPos - 1-based, inclusive

Returns:

List of Chunks overlapping the given region. May return null if there are none.

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object