htsjdk.samtools.cram.io

Class DefaultBitOutputStream

java.lang.Object

java.io.OutputStream

htsjdk.samtools.cram.io.DefaultBitOutputStream

All Implemented Interfaces:

BitOutputStream, java.io.Closeable, java.io.Flushable, java.lang.AutoCloseable

public class DefaultBitOutputStream
extends java.io.OutputStream
implements BitOutputStream

Constructor Summary

Constructors

Constructor and Description
DefaultBitOutputStream(java.io.OutputStream delegate)

Method Summary

Modifier and Type	Method and Description
void	close()
void	flush()
java.lang.String	toString()
void	write(boolean bit) Write a single bit specified in the boolean argument.
void	write(boolean bit, long repeat) Write a single bit specified in the boolean argument repeatedly.
void	write(byte b)
void	write(byte[] b)
void	write(byte[] b, int off, int length)
void	write(byte bitContainer, int nofBits) Write specified number of bits supplied in the byte value.
void	write(int value)
void	write(int bitContainer, int nofBits) Write specified number of bits supplied in the integer value.
void	write(long bitContainer, int nofBits) Write specified number of bits supplied in the long value.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultBitOutputStream

public DefaultBitOutputStream(java.io.OutputStream delegate)

Method Detail

write

public void write(byte b)
           throws java.io.IOException

Throws:

java.io.IOException

write

public void write(int value)
           throws java.io.IOException

Specified by:

write in class java.io.OutputStream

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

write

public void write(long bitContainer,
                  int nofBits)
           throws java.io.IOException

Description copied from interface: BitOutputStream

Write specified number of bits supplied in the long value. The method is naturally limited to 64 bits max.

Specified by:

write in interface BitOutputStream

Parameters:

bitContainer - an integer containing the bits to be written out

nofBits - the number of bits to written out, minimum 0, maximum 64.

Throws:

java.io.IOException - as per streaming contract in java.

write

public void write(int bitContainer,
                  int nofBits)
           throws java.io.IOException

Description copied from interface: BitOutputStream

Write specified number of bits supplied in the integer value. The method is naturally limited to 32 bits max.

Specified by:

write in interface BitOutputStream

Parameters:

bitContainer - an integer containing the bits to be written out

nofBits - the number of bits to written out, minimum 0, maximum 32.

Throws:

java.io.IOException - as per streaming contract in java.

write

public void write(byte bitContainer,
                  int nofBits)
           throws java.io.IOException

Description copied from interface: BitOutputStream

Write specified number of bits supplied in the byte value. The method is naturally limited to 8 bits max.

Specified by:

write in interface BitOutputStream

Parameters:

bitContainer - an integer containing the bits to be written out

nofBits - the number of bits to written out, minimum 0, maximum 8.

Throws:

java.io.IOException - as per streaming contract in java.

write

public void write(boolean bit)
           throws java.io.IOException

Description copied from interface: BitOutputStream

Write a single bit specified in the boolean argument.

Specified by:

write in interface BitOutputStream

Parameters:

bit - emit 1 if true, 0 otherwise.

Throws:

java.io.IOException - as per streaming contract in java.

write

public void write(boolean bit,
                  long repeat)
           throws java.io.IOException

Description copied from interface: BitOutputStream

Write a single bit specified in the boolean argument repeatedly.

Specified by:

write in interface BitOutputStream

Parameters:

bit - emit 1 if true, 0 otherwise.

repeat - the number of bits to emit.

Throws:

java.io.IOException - as per streaming contract in java.

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.OutputStream

Throws:

java.io.IOException

flush

public void flush()
           throws java.io.IOException

Specified by:

flush in interface java.io.Flushable

Overrides:

flush in class java.io.OutputStream

Throws:

java.io.IOException

write

public void write(byte[] b)
           throws java.io.IOException

Overrides:

write in class java.io.OutputStream

Throws:

java.io.IOException

write

public void write(byte[] b,
                  int off,
                  int length)
           throws java.io.IOException

Overrides:

write in class java.io.OutputStream

Throws:

java.io.IOException