htsjdk.samtools.cram.encoding.core

Class CanonicalHuffmanByteEncoding

java.lang.Object

htsjdk.samtools.cram.encoding.CRAMEncoding<java.lang.Byte>

htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding

public final class CanonicalHuffmanByteEncoding
extends CRAMEncoding<java.lang.Byte>

CRAMEncoding class for Huffman byte values.

Constructor Summary

Constructors

Constructor and Description
CanonicalHuffmanByteEncoding(byte[] symbols, int[] bitLengths)

Method Summary

Modifier and Type	Method and Description
CRAMCodec<java.lang.Byte>	buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams, SliceBlocksWriteStreams sliceBlocksWriteStreams) Instantiate the codec represented by this encoding by supplying it with the appropriate streams
static CanonicalHuffmanByteEncoding	fromSerializedEncodingParams(byte[] serializedParams) Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
byte[]	toSerializedEncodingParams() Serialize encoding parameters to an ITF8-encoded byte array.
java.lang.String	toString()

Methods inherited from class htsjdk.samtools.cram.encoding.CRAMEncoding

buildReadCodec, buildWriteCodec, id, toEncodingDescriptor

Methods inherited from class java.lang.Object

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

Constructor Detail

CanonicalHuffmanByteEncoding

public CanonicalHuffmanByteEncoding(byte[] symbols,
                                    int[] bitLengths)

Method Detail

fromSerializedEncodingParams

public static CanonicalHuffmanByteEncoding fromSerializedEncodingParams(byte[] serializedParams)

Create a new instance of this encoding using the (ITF8 encoded) serializedParams.

Parameters:

serializedParams -

Returns:

CanonicalHuffmanByteEncoding with parameters populated from serializedParams

toSerializedEncodingParams

public byte[] toSerializedEncodingParams()

Description copied from class: CRAMEncoding

Serialize encoding parameters to an ITF8-encoded byte array. By convention, each subclass should have a corresponding and symmetric "fromSerializedEncodingParams" that returns a new instance of that encoding populated with values from the serialized encoding params.

Specified by:

toSerializedEncodingParams in class CRAMEncoding<java.lang.Byte>

Returns:

a byte array containing the encoding's parameter values encoded as an ITF8 stream.

buildCodec

public CRAMCodec<java.lang.Byte> buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams,
                                            SliceBlocksWriteStreams sliceBlocksWriteStreams)

Description copied from class: CRAMEncoding

Instantiate the codec represented by this encoding by supplying it with the appropriate streams

Specified by:

buildCodec in class CRAMEncoding<java.lang.Byte>

Parameters:

sliceBlocksReadStreams - the core block bit stream a CoreCodec will read from

sliceBlocksWriteStreams - the core block bit stream a CoreCodec will write to

Returns:

a newly instantiated codec

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object