loci.common

Class CBZip2InputStream

java.lang.Object

java.io.InputStream

loci.common.CBZip2InputStream

All Implemented Interfaces:

Closeable, AutoCloseable

public class CBZip2InputStream
extends InputStream

An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.

The decompression requires large amounts of memory. Thus you should call the close() method as soon as possible, to force CBZip2InputStream to release the allocated memory. See CBZip2OutputStream for information about memory usage.

CBZip2InputStream reads bytes from the compressed source stream via the single byte read() method exclusively. Thus you should consider using a buffered source stream.

Instances of this class are not threadsafe.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	CBZip2InputStream.Data

Field Summary

Fields

Modifier and Type	Field and Description
private static int	BASE_BLOCK_SIZE
private boolean	blockRandomised
private int	blockSize100k always: in the range 0 ..
private int	bsBuff
private int	bsLive
private int	computedBlockCRC
private int	computedCombinedCRC
private CRC	crc
private int	currentChar
private int	currentState
private CBZip2InputStream.Data	data All memory intensive stuff.
private static int	EOF
private static int	G_SIZE
private InputStream	in
private int	last Index of the last char in the block, so the block size == last + 1.
private static org.slf4j.Logger	LOGGER
private static int	MAX_ALPHA_SIZE
private static int	MAX_CODE_LEN
private static int	MAX_SELECTORS
private static int	N_GROUPS
private int	nInUse
private static int	NO_RAND_PART_A_STATE
private static int	NO_RAND_PART_B_STATE
private static int	NO_RAND_PART_C_STATE
private int	origPtr INdex in zptr[] of original string after sorting.
private static int[]	R_NUMS
private static int	RAND_PART_A_STATE
private static int	RAND_PART_B_STATE
private static int	RAND_PART_C_STATE
private static int	RUNA
private static int	RUNB
private static int	START_BLOCK_STATE
private int	storedBlockCRC
private int	storedCombinedCRC
private int	suCh2
private int	suChPrev
private int	suCount
private int	suI2
private int	suJ2
private int	suRNToGo
private int	suRTPos
private int	suTPos
private char	suZ

Constructor Summary

Constructors

Constructor and Description
CBZip2InputStream(InputStream in) Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.

Method Summary

Methods

Modifier and Type	Method and Description
private boolean	bsGetBit()
private int	bsGetInt()
private char	bsGetUByte()
private int	bsR(int n)
void	close()
private void	complete()
private void	createHuffmanDecodingTables(int alphaSize, int nGroups) Called by recvDecodingTables() exclusively.
private void	endBlock()
private void	getAndMoveToFrontDecode()
private int	getAndMoveToFrontDecode0(int groupNo)
private static void	hbCreateDecodeTables(int[] limit, int[] base, int[] perm, char[] length, int minLen, int maxLen, int alphaSize) Called by createHuffmanDecodingTables() exclusively.
private void	init()
private void	initBlock()
private void	makeMaps()
int	read()
int	read(byte[] dest, int offs, int len)
private int	read0()
private void	recvDecodingTables()
private static void	reportCRCError()
private void	setupBlock()
private void	setupNoRandPartA()
private void	setupNoRandPartB()
private void	setupNoRandPartC()
private void	setupRandPartA()
private void	setupRandPartB()
private void	setupRandPartC()

Methods inherited from class java.io.InputStream

available, mark, markSupported, read, reset, skip

Methods inherited from class java.lang.Object

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

Field Detail

BASE_BLOCK_SIZE

private static final int BASE_BLOCK_SIZE

See Also:

Constant Field Values

MAX_ALPHA_SIZE

private static final int MAX_ALPHA_SIZE

See Also:

Constant Field Values

MAX_CODE_LEN

private static final int MAX_CODE_LEN

See Also:

Constant Field Values

RUNA

private static final int RUNA

See Also:

Constant Field Values

RUNB

private static final int RUNB

See Also:

Constant Field Values

N_GROUPS

private static final int N_GROUPS

See Also:

Constant Field Values

G_SIZE

private static final int G_SIZE

See Also:

Constant Field Values

MAX_SELECTORS

private static final int MAX_SELECTORS

See Also:

Constant Field Values

R_NUMS

private static final int[] R_NUMS

LOGGER

private static final org.slf4j.Logger LOGGER

last

private int last

Index of the last char in the block, so the block size == last + 1.

origPtr

private int origPtr

INdex in zptr[] of original string after sorting.

blockSize100k

private int blockSize100k

always: in the range 0 .. 9. The current block size is 100000 * this number.

blockRandomised

private boolean blockRandomised

bsBuff

private int bsBuff

bsLive

private int bsLive

crc

private final CRC crc

nInUse

private int nInUse

in

private InputStream in

currentChar

private int currentChar

EOF

private static final int EOF

See Also:

Constant Field Values

START_BLOCK_STATE

private static final int START_BLOCK_STATE

See Also:

Constant Field Values

RAND_PART_A_STATE

private static final int RAND_PART_A_STATE

See Also:

Constant Field Values

RAND_PART_B_STATE

private static final int RAND_PART_B_STATE

See Also:

Constant Field Values

RAND_PART_C_STATE

private static final int RAND_PART_C_STATE

See Also:

Constant Field Values

NO_RAND_PART_A_STATE

private static final int NO_RAND_PART_A_STATE

See Also:

Constant Field Values

NO_RAND_PART_B_STATE

private static final int NO_RAND_PART_B_STATE

See Also:

Constant Field Values

NO_RAND_PART_C_STATE

private static final int NO_RAND_PART_C_STATE

See Also:

Constant Field Values

currentState

private int currentState

storedBlockCRC

private int storedBlockCRC

storedCombinedCRC

private int storedCombinedCRC

computedBlockCRC

private int computedBlockCRC

computedCombinedCRC

private int computedCombinedCRC

suCount

private int suCount

suCh2

private int suCh2

suChPrev

private int suChPrev

suI2

private int suI2

suJ2

private int suJ2

suRNToGo

private int suRNToGo

suRTPos

private int suRTPos

suTPos

private int suTPos

suZ

private char suZ

data

private CBZip2InputStream.Data data

All memory intensive stuff. This field is initialized by initBlock();

Constructor Detail

CBZip2InputStream

public CBZip2InputStream(InputStream in)
                  throws IOException

Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.

Although BZip2 headers are marked with the magic "Bz" this constructor expects the next byte in the stream to be the first one after the magic. Thus callers have to skip the first two bytes. Otherwise this constructor will throw an exception.

Throws:

IOException - if the stream content is malformed or an I/O error occurs.

NullPointerException - if in == null

Method Detail

reportCRCError

private static void reportCRCError()

makeMaps

private void makeMaps()

read

public int read()
         throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

public int read(byte[] dest,
       int offs,
       int len)
         throws IOException

Overrides:

read in class InputStream

Throws:

IOException

read0

private int read0()
           throws IOException

Throws:

IOException

init

private void init()
           throws IOException

Throws:

IOException

initBlock

private void initBlock()
                throws IOException

Throws:

IOException

endBlock

private void endBlock()

complete

private void complete()
               throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class InputStream

Throws:

IOException

bsR

private int bsR(int n)
         throws IOException

Throws:

IOException

bsGetBit

private boolean bsGetBit()
                  throws IOException

Throws:

IOException

bsGetUByte

private char bsGetUByte()
                 throws IOException

Throws:

IOException

bsGetInt

private int bsGetInt()
              throws IOException

Throws:

IOException

hbCreateDecodeTables

private static void hbCreateDecodeTables(int[] limit,
                        int[] base,
                        int[] perm,
                        char[] length,
                        int minLen,
                        int maxLen,
                        int alphaSize)

Called by createHuffmanDecodingTables() exclusively.

recvDecodingTables

private void recvDecodingTables()
                         throws IOException

Throws:

IOException

createHuffmanDecodingTables

private void createHuffmanDecodingTables(int alphaSize,
                               int nGroups)

Called by recvDecodingTables() exclusively.

getAndMoveToFrontDecode

private void getAndMoveToFrontDecode()
                              throws IOException

Throws:

IOException

getAndMoveToFrontDecode0

private int getAndMoveToFrontDecode0(int groupNo)
                              throws IOException

Throws:

IOException

setupBlock

private void setupBlock()
                 throws IOException

Throws:

IOException

setupRandPartA

private void setupRandPartA()
                     throws IOException

Throws:

IOException

setupNoRandPartA

private void setupNoRandPartA()
                       throws IOException

Throws:

IOException

setupRandPartB

private void setupRandPartB()
                     throws IOException

Throws:

IOException

setupRandPartC

private void setupRandPartC()
                     throws IOException

Throws:

IOException

setupNoRandPartB

private void setupNoRandPartB()
                       throws IOException

Throws:

IOException

setupNoRandPartC

private void setupNoRandPartC()
                       throws IOException

Throws:

IOException