Package gov.nih.mipav.model.file

Class CBZip2OutputStream

java.lang.Object

java.io.OutputStream

gov.nih.mipav.model.file.CBZip2OutputStream

All Implemented Interfaces:

BZip2Constants, java.io.Closeable, java.io.Flushable, java.lang.AutoCloseable

public class CBZip2OutputStream
extends java.io.OutputStream
implements BZip2Constants

An output stream that compresses into the BZip2 format (without the file header chars) into another stream.

Author:

Keiron Liddle TODO: Update to BZip2 1.0.1

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private static class	CBZip2OutputStream.StackElem

Field Summary

Fields

Modifier and Type	Field	Description
private int	allowableBlockSize
private char[]	block
private int	blockCRC
(package private) boolean	blockRandomised
(package private) int	blockSize100k
(package private) int	bsBuff
(package private) int	bsLive
private java.io.OutputStream	bsStream
(package private) int	bytesOut
protected static int	CLEARMASK
(package private) boolean	closed
private int	combinedCRC
private int	currentChar
protected static int	DEPTH_THRESH
private boolean	firstAttempt
private int[]	ftab
protected static int	GREATER_ICOST
private int[]	incs
private boolean[]	inUse
(package private) int	last
protected static int	LESSER_ICOST
(package private) CRC	mCrc
private int[]	mtfFreq
private int	nBlocksRandomised
private int	nInUse
private int	nMTF
(package private) int	origPtr
protected static int	QSORT_STACK_SIZE
private int[]	quadrant
private int	runLength
private char[]	selector
private char[]	selectorMtf
private char[]	seqToUnseq
protected static int	SETMASK
protected static int	SMALL_THRESH
private short[]	szptr
private char[]	unseqToSeq
private int	workDone
private int	workFactor
private int	workLimit
private int[]	zptr

Fields inherited from interface gov.nih.mipav.model.file.BZip2Constants

baseBlockSize, G_SIZE, MAX_ALPHA_SIZE, MAX_CODE_LEN, MAX_SELECTORS, N_GROUPS, N_ITERS, NUM_OVERSHOOT_BYTES, rNums, RUNA, RUNB

Constructor Summary

Constructors

Constructor	Description
CBZip2OutputStream(java.io.OutputStream inStream)
CBZip2OutputStream(java.io.OutputStream inStream, int inBlockSize)

Method Summary

Modifier and Type	Method	Description
private void	allocateCompressStructures()
private void	bsFinishedWithStream()
private void	bsPutint(int u)
private void	bsPutIntVS(int numBits, int c)
private void	bsPutUChar(int c)
private void	bsSetStream(java.io.OutputStream f)
private void	bsW(int n, int v)
void	close()
private void	doReversibleTransformation()
private void	endBlock()
private void	endCompression()
protected void	finalize()
void	flush()
private boolean	fullGtU(int i1, int i2)
private void	generateMTFValues()
private void	hbAssignCodes(int[] code, char[] length, int minLen, int maxLen, int alphaSize)
protected static void	hbMakeCodeLengths(char[] len, int[] freq, int alphaSize, int maxLen)
private void	initBlock()
private void	initialize()
private void	mainSort()
private void	makeMaps()
private char	med3(char a, char b, char c)
private void	moveToFrontCodeAndSend()
private static void	panic()
private void	qSort3(int loSt, int hiSt, int dSt)
private void	randomiseBlock()
private void	sendMTFValues()
private void	simpleSort(int lo, int hi, int d)
private void	vswap(int p1, int p2, int n)
void	write(int bv)	modified by Oliver Merkel, 010128
private void	writeRun()

Methods inherited from class java.io.OutputStream

nullOutputStream, write, write

Methods inherited from class java.lang.Object

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

Field Detail

SETMASK

protected static final int SETMASK

See Also:

Constant Field Values

CLEARMASK

protected static final int CLEARMASK

See Also:

Constant Field Values

GREATER_ICOST

protected static final int GREATER_ICOST

See Also:

Constant Field Values

LESSER_ICOST

protected static final int LESSER_ICOST

See Also:

Constant Field Values

SMALL_THRESH

protected static final int SMALL_THRESH

See Also:

Constant Field Values

DEPTH_THRESH

protected static final int DEPTH_THRESH

See Also:

Constant Field Values

QSORT_STACK_SIZE

protected static final int QSORT_STACK_SIZE

See Also:

Constant Field Values

last

int last

origPtr

int origPtr

blockSize100k

int blockSize100k

blockRandomised

boolean blockRandomised

bytesOut

int bytesOut

bsBuff

int bsBuff

bsLive

int bsLive

mCrc

CRC mCrc

inUse

private boolean[] inUse

nInUse

private int nInUse

seqToUnseq

private char[] seqToUnseq

unseqToSeq

private char[] unseqToSeq

selector

private char[] selector

selectorMtf

private char[] selectorMtf

block

private char[] block

quadrant

private int[] quadrant

zptr

private int[] zptr

szptr

private short[] szptr

ftab

private int[] ftab

nMTF

private int nMTF

mtfFreq

private int[] mtfFreq

workFactor

private int workFactor

workDone

private int workDone

workLimit

private int workLimit

firstAttempt

private boolean firstAttempt

nBlocksRandomised

private int nBlocksRandomised

currentChar

private int currentChar

runLength

private int runLength

closed

boolean closed

blockCRC

private int blockCRC

combinedCRC

private int combinedCRC

allowableBlockSize

private int allowableBlockSize

bsStream

private java.io.OutputStream bsStream

incs

private int[] incs

Constructor Detail

CBZip2OutputStream

public CBZip2OutputStream(java.io.OutputStream inStream)
                   throws java.io.IOException

Throws:

java.io.IOException

CBZip2OutputStream

public CBZip2OutputStream(java.io.OutputStream inStream,
                          int inBlockSize)
                   throws java.io.IOException

Throws:

java.io.IOException

Method Detail

panic

private static void panic()

makeMaps

private void makeMaps()

hbMakeCodeLengths

protected static void hbMakeCodeLengths(char[] len,
                                        int[] freq,
                                        int alphaSize,
                                        int maxLen)

write

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

modified by Oliver Merkel, 010128

Specified by:

write in class java.io.OutputStream

Throws:

java.io.IOException

writeRun

private void writeRun()
               throws java.io.IOException

Throws:

java.io.IOException

finalize

protected void finalize()
                 throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

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

initialize

private void initialize()
                 throws java.io.IOException

Throws:

java.io.IOException

initBlock

private void initBlock()

endBlock

private void endBlock()
               throws java.io.IOException

Throws:

java.io.IOException

endCompression

private void endCompression()
                     throws java.io.IOException

Throws:

java.io.IOException

hbAssignCodes

private void hbAssignCodes(int[] code,
                           char[] length,
                           int minLen,
                           int maxLen,
                           int alphaSize)

bsSetStream

private void bsSetStream(java.io.OutputStream f)

bsFinishedWithStream

private void bsFinishedWithStream()
                           throws java.io.IOException

Throws:

java.io.IOException

bsW

private void bsW(int n,
                 int v)
          throws java.io.IOException

Throws:

java.io.IOException

bsPutUChar

private void bsPutUChar(int c)
                 throws java.io.IOException

Throws:

java.io.IOException

bsPutint

private void bsPutint(int u)
               throws java.io.IOException

Throws:

java.io.IOException

bsPutIntVS

private void bsPutIntVS(int numBits,
                        int c)
                 throws java.io.IOException

Throws:

java.io.IOException

sendMTFValues

private void sendMTFValues()
                    throws java.io.IOException

Throws:

java.io.IOException

moveToFrontCodeAndSend

private void moveToFrontCodeAndSend()
                             throws java.io.IOException

Throws:

java.io.IOException

simpleSort

private void simpleSort(int lo,
                        int hi,
                        int d)

vswap

private void vswap(int p1,
                   int p2,
                   int n)

med3

private char med3(char a,
                  char b,
                  char c)

qSort3

private void qSort3(int loSt,
                    int hiSt,
                    int dSt)

mainSort

private void mainSort()

randomiseBlock

private void randomiseBlock()

doReversibleTransformation

private void doReversibleTransformation()

fullGtU

private boolean fullGtU(int i1,
                        int i2)

allocateCompressStructures

private void allocateCompressStructures()

generateMTFValues

private void generateMTFValues()