htsjdk.samtools

Class Bin

java.lang.Object

htsjdk.samtools.Bin

All Implemented Interfaces:

java.lang.Comparable<Bin>

public class Bin
extends java.lang.Object
implements java.lang.Comparable<Bin>

An individual bin in a BAM file.

Constructor Summary

Constructors

Constructor and Description
Bin(int referenceSequence, int binNumber)

Method Summary

Methods

Modifier and Type	Method and Description
void	addInitialChunk(Chunk newChunk) Adds the first chunk to the bin
int	compareTo(Bin other) Compare two bins to see what ordering they should appear in.
boolean	containsChunks() Returns whether the bin currently contains chunks.
boolean	equals(java.lang.Object other) See whether two bins are equal.
int	getBinNumber()
java.util.List<Chunk>	getChunkList() Gets the list of chunks associated with this bin.
Chunk	getLastChunk() Warning: Currently only valid during index building, not when reading existing index, (AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)
protected int	getReferenceSequence()
int	hashCode() Compute a unique hash code for the given reference sequence and bin number.
void	setChunkList(java.util.List<Chunk> list) Sets the chunks associated with this bin
void	setLastChunk(Chunk c) Optimization to keep lastChunk instead of iterating over all chunks repeatedly

Methods inherited from class java.lang.Object

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

Constructor Detail

Bin

public Bin(int referenceSequence,
   int binNumber)

Method Detail

getReferenceSequence

protected int getReferenceSequence()

getBinNumber

public int getBinNumber()

equals

public boolean equals(java.lang.Object other)

See whether two bins are equal. If the ref seq and the bin number are equal, assume equality of the chunk list.

Overrides:

equals in class java.lang.Object

Parameters:

other - The other Bin to which to compare this.

Returns:

True if the two bins are equal. False otherwise.

hashCode

public int hashCode()

Compute a unique hash code for the given reference sequence and bin number.

Overrides:

hashCode in class java.lang.Object

Returns:

A unique hash code.

containsChunks

public boolean containsChunks()

Returns whether the bin currently contains chunks.

Returns:

True if the bin has chunks, false otherwise.

compareTo

public int compareTo(Bin other)

Compare two bins to see what ordering they should appear in.

Specified by:

compareTo in interface java.lang.Comparable<Bin>

Parameters:

other - Other bin to which this bin should be compared.

Returns:

-1 if this < other, 0 if this == other, 1 if this > other.

addInitialChunk

public void addInitialChunk(Chunk newChunk)

Adds the first chunk to the bin

setChunkList

public void setChunkList(java.util.List<Chunk> list)

Sets the chunks associated with this bin

getChunkList

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

Gets the list of chunks associated with this bin.

Returns:

the chunks in this bin. If no chunks are associated, an empty list will be returned.

setLastChunk

public void setLastChunk(Chunk c)

Optimization to keep lastChunk instead of iterating over all chunks repeatedly

getLastChunk

public Chunk getLastChunk()

Warning: Currently only valid during index building, not when reading existing index, (AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)

Returns:

the last Chunk of the chunkList