htsjdk.samtools.cram.encoding

Class ExternalByteArrayCodec

java.lang.Object

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

htsjdk.samtools.cram.encoding.ExternalByteArrayCodec

All Implemented Interfaces:

BitCodec<byte[]>

public class ExternalByteArrayCodec
extends AbstractBitCodec<byte[]>

Constructor Summary

Constructors

Constructor and Description
ExternalByteArrayCodec(java.io.OutputStream os, java.io.InputStream is)

Method Summary

Methods

Modifier and Type	Method and Description
long	numberOfBits(byte[] object)
byte[]	read(BitInputStream bis)
byte[]	read(BitInputStream bis, int len)
void	readInto(BitInputStream bis, byte[] array, int offset, int valueLen)
void	skip(BitInputStream bis)
void	skip(BitInputStream bis, int len)
long	write(BitOutputStream bos, byte[] object)

Methods inherited from class java.lang.Object

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

Constructor Detail

ExternalByteArrayCodec

public ExternalByteArrayCodec(java.io.OutputStream os,
                      java.io.InputStream is)

Method Detail

read

public byte[] read(BitInputStream bis,
          int len)
            throws java.io.IOException

Specified by:

read in interface BitCodec<byte[]>

Specified by:

read in class AbstractBitCodec<byte[]>

Throws:

java.io.IOException

readInto

public void readInto(BitInputStream bis,
            byte[] array,
            int offset,
            int valueLen)
              throws java.io.IOException

Specified by:

readInto in interface BitCodec<byte[]>

Overrides:

readInto in class AbstractBitCodec<byte[]>

Throws:

java.io.IOException

skip

public void skip(BitInputStream bis)
          throws java.io.IOException

Specified by:

skip in interface BitCodec<byte[]>

Overrides:

skip in class AbstractBitCodec<byte[]>

Throws:

java.io.IOException

skip

public void skip(BitInputStream bis,
        int len)
          throws java.io.IOException

Specified by:

skip in interface BitCodec<byte[]>

Overrides:

skip in class AbstractBitCodec<byte[]>

Throws:

java.io.IOException

write

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

Specified by:

write in interface BitCodec<byte[]>

Specified by:

write in class AbstractBitCodec<byte[]>

Throws:

java.io.IOException

numberOfBits

public long numberOfBits(byte[] object)

Specified by:

numberOfBits in interface BitCodec<byte[]>

Specified by:

numberOfBits in class AbstractBitCodec<byte[]>

read

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

Specified by:

read in interface BitCodec<byte[]>

Specified by:

read in class AbstractBitCodec<byte[]>

Throws:

java.io.IOException