htsjdk.samtools.cram.encoding

Class AbstractBitCodec<T>

java.lang.Object

htsjdk.samtools.cram.encoding.AbstractBitCodec<T>

All Implemented Interfaces:

BitCodec<T>

Direct Known Subclasses:

ArithCodec, ArithCodec1, BetaIntegerCodec, ByteArrayStopEncoding.ByteArrayStopCodec, CanonicalHuffmanByteCodec, CanonicalHuffmanByteCodec2, CanonicalHuffmanIntegerCodec, CanonicalHuffmanIntegerCodec2, ExternalByteArrayCodec, ExternalByteCodec, ExternalIntegerCodec, ExternalLongCodec, GammaIntegerCodec, GolombIntegerCodec, GolombLongCodec, GolombRiceIntegerCodec, NullCodec, SubexpIntegerCodec, UnaryIntegerCodec

public abstract class AbstractBitCodec<T>
extends java.lang.Object
implements BitCodec<T>

Constructor Summary

Constructors

Constructor and Description
AbstractBitCodec()

Method Summary

Methods

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

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractBitCodec

public AbstractBitCodec()

Method Detail

read

public abstract T read(BitInputStream bis)
                throws java.io.IOException

Specified by:

read in interface BitCodec<T>

Throws:

java.io.IOException

read

public abstract T read(BitInputStream bis,
     int valueLen)
                throws java.io.IOException

Specified by:

read in interface BitCodec<T>

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<T>

Throws:

java.io.IOException

skip

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

Specified by:

skip in interface BitCodec<T>

Throws:

java.io.IOException

skip

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

Specified by:

skip in interface BitCodec<T>

Throws:

java.io.IOException

write

public abstract long write(BitOutputStream bos,
         T object)
                    throws java.io.IOException

Specified by:

write in interface BitCodec<T>

Throws:

java.io.IOException

numberOfBits

public abstract long numberOfBits(T object)

Specified by:

numberOfBits in interface BitCodec<T>