htsjdk.samtools.cram.compression

Class ExternalCompressor

java.lang.Object

htsjdk.samtools.cram.compression.ExternalCompressor

Direct Known Subclasses:

BZIP2ExternalCompressor, GZIPExternalCompressor, LZMAExternalCompressor, RANSExternalCompressor, RAWExternalCompressor

public abstract class ExternalCompressor
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static int	NO_COMPRESSION_ARG

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ExternalCompressor(BlockCompressionMethod method)

Method Summary

Modifier and Type	Method and Description
abstract byte[]	compress(byte[] data)
boolean	equals(java.lang.Object o)
static ExternalCompressor	getCompressorForMethod(BlockCompressionMethod compressionMethod, int compressorSpecificArg) Return an ExternalCompressor subclass based on the BlockCompressionMethod.
BlockCompressionMethod	getMethod()
int	hashCode()
java.lang.String	toString()
abstract byte[]	uncompress(byte[] data)

Methods inherited from class java.lang.Object

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

Field Detail

NO_COMPRESSION_ARG

public static final int NO_COMPRESSION_ARG

See Also:

Constant Field Values

Constructor Detail

ExternalCompressor

protected ExternalCompressor(BlockCompressionMethod method)

Method Detail

compress

public abstract byte[] compress(byte[] data)

uncompress

public abstract byte[] uncompress(byte[] data)

getMethod

public BlockCompressionMethod getMethod()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

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

getCompressorForMethod

public static ExternalCompressor getCompressorForMethod(BlockCompressionMethod compressionMethod,
                                                        int compressorSpecificArg)

Return an ExternalCompressor subclass based on the BlockCompressionMethod. Compressor-specific arguments must be populated by the caller.

Parameters:

compressionMethod - the type of compressor required (BlockCompressionMethod)

compressorSpecificArg - the required order for RANS compressors; or the desired write compression level for GZIP

Returns:

an ExternalCompressor of the requested type, populated with an compressor-specific args