htsjdk.samtools.cram.encoding

Class SubexpIntegerCodec

java.lang.Object

htsjdk.samtools.cram.encoding.AbstractBitCodec<java.lang.Integer>

htsjdk.samtools.cram.encoding.SubexpIntegerCodec

All Implemented Interfaces:

BitCodec<java.lang.Integer>

public class SubexpIntegerCodec
extends AbstractBitCodec<java.lang.Integer>

Constructor Summary

Constructors

Constructor and Description
SubexpIntegerCodec(int k)
SubexpIntegerCodec(int offset, int k)
SubexpIntegerCodec(int offset, int k, boolean unaryBit)

Method Summary

Methods

Modifier and Type	Method and Description
int	getK()
int	getOffset()
boolean	isUnaryBit()
long	numberOfBits(java.lang.Integer value)
java.lang.Integer	read(BitInputStream bis)
java.lang.Integer	read(BitInputStream bis, int len)
void	setK(int k)
void	setOffset(int offset)
void	setUnaryBit(boolean unaryBit)
long	write(BitOutputStream bos, java.lang.Integer value)

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

SubexpIntegerCodec

public SubexpIntegerCodec(int offset,
                  int k)

SubexpIntegerCodec

public SubexpIntegerCodec(int offset,
                  int k,
                  boolean unaryBit)

SubexpIntegerCodec

public SubexpIntegerCodec(int k)

Method Detail

read

public final java.lang.Integer read(BitInputStream bis)
                             throws java.io.IOException

Specified by:

read in interface BitCodec<java.lang.Integer>

Specified by:

read in class AbstractBitCodec<java.lang.Integer>

Throws:

java.io.IOException

write

public final long write(BitOutputStream bos,
         java.lang.Integer value)
                 throws java.io.IOException

Specified by:

write in interface BitCodec<java.lang.Integer>

Specified by:

write in class AbstractBitCodec<java.lang.Integer>

Throws:

java.io.IOException

numberOfBits

public final long numberOfBits(java.lang.Integer value)

Specified by:

numberOfBits in interface BitCodec<java.lang.Integer>

Specified by:

numberOfBits in class AbstractBitCodec<java.lang.Integer>

getOffset

public int getOffset()

setOffset

public void setOffset(int offset)

getK

public int getK()

setK

public void setK(int k)

isUnaryBit

public boolean isUnaryBit()

setUnaryBit

public void setUnaryBit(boolean unaryBit)

read

public java.lang.Integer read(BitInputStream bis,
                     int len)
                       throws java.io.IOException

Specified by:

read in interface BitCodec<java.lang.Integer>

Specified by:

read in class AbstractBitCodec<java.lang.Integer>

Throws:

java.io.IOException