htsjdk.samtools.cram.encoding

Class ByteArrayStopEncoding.ByteArrayStopCodec

java.lang.Object

htsjdk.samtools.cram.encoding.AbstractBitCodec<byte[]>

htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec

All Implemented Interfaces:

BitCodec<byte[]>

Enclosing class:

ByteArrayStopEncoding

public static class ByteArrayStopEncoding.ByteArrayStopCodec
extends AbstractBitCodec<byte[]>

Constructor Summary

Constructors

Constructor and Description
ByteArrayStopCodec(byte stopByte, java.io.InputStream inputStream, java.io.OutputStream outputStream)

Method Summary

Modifier and Type	Method and Description
long	numberOfBits(byte[] object) Calculate the number of bits that the object would take in bit serialized form.
byte[]	read(BitInputStream bitInputStream) Read a single object from the bit stream.
byte[]	read(BitInputStream bitInputStream, int length) Read a array of specified length from the bit stream.
long	write(BitOutputStream bitOutputStream, byte[] object) Write an object into the bit stream

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

readInto, skip, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

ByteArrayStopCodec

public ByteArrayStopCodec(byte stopByte,
                          java.io.InputStream inputStream,
                          java.io.OutputStream outputStream)

Method Detail

read

public byte[] read(BitInputStream bitInputStream)
            throws java.io.IOException

Description copied from interface: BitCodec

Read a single object from the bit stream.

Specified by:

read in interface BitCodec<byte[]>

Specified by:

read in class AbstractBitCodec<byte[]>

Parameters:

bitInputStream - the bit input stream to rad from

Returns:

an object from the stream

Throws:

java.io.IOException - as per java IO contract

read

public byte[] read(BitInputStream bitInputStream,
                   int length)
            throws java.io.IOException

Description copied from interface: BitCodec

Read a array of specified length from the bit stream.

Specified by:

read in interface BitCodec<byte[]>

Specified by:

read in class AbstractBitCodec<byte[]>

Parameters:

bitInputStream - the bit input stream to rad from param valueLen the number of elements to read

Returns:

an object from the stream

Throws:

java.io.IOException - as per java IO contract

write

public long write(BitOutputStream bitOutputStream,
                  byte[] object)
           throws java.io.IOException

Description copied from interface: BitCodec

Write an object into the bit stream

Specified by:

write in interface BitCodec<byte[]>

Specified by:

write in class AbstractBitCodec<byte[]>

Parameters:

bitOutputStream - the output bit stream to write to

object - the object to write

Returns:

the number of bits written out

Throws:

java.io.IOException - as per java IO contract

numberOfBits

public long numberOfBits(byte[] object)

Description copied from interface: BitCodec

Calculate the number of bits that the object would take in bit serialized form.

Specified by:

numberOfBits in interface BitCodec<byte[]>

Specified by:

numberOfBits in class AbstractBitCodec<byte[]>

Parameters:

object - an object

Returns:

the number of bits