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Contains common I/O, date parsing, and XML processing classes.
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/*
* #%L
* Common package for I/O and related utilities
* %%
* Copyright (C) 2005 - 2016 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/*
* This package is based on the work done by Keiron Liddle, Aftex Software
* to whom the Ant project is very grateful for his
* great code.
*/
package loci.common;
import java.io.IOException;
import java.io.InputStream;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* 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 {@link #close() 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 {@link java.io.InputStream#read() read()}
* method exclusively. Thus you should consider using a buffered source stream.
*
*
* Instances of this class are not threadsafe.
*/
public class CBZip2InputStream extends InputStream {
// -- Constants --
private static final int BASE_BLOCK_SIZE = 100000;
private static final int MAX_ALPHA_SIZE = 258;
private static final int MAX_CODE_LEN = 23;
private static final int RUNA = 0;
private static final int RUNB = 1;
private static final int N_GROUPS = 6;
private static final int G_SIZE = 50;
private static final int MAX_SELECTORS = (2 + (900000 / G_SIZE));
private static final int[] R_NUMS = {
619, 720, 127, 481, 931, 816, 813, 233, 566, 247,
985, 724, 205, 454, 863, 491, 741, 242, 949, 214,
733, 859, 335, 708, 621, 574, 73, 654, 730, 472,
419, 436, 278, 496, 867, 210, 399, 680, 480, 51,
878, 465, 811, 169, 869, 675, 611, 697, 867, 561,
862, 687, 507, 283, 482, 129, 807, 591, 733, 623,
150, 238, 59, 379, 684, 877, 625, 169, 643, 105,
170, 607, 520, 932, 727, 476, 693, 425, 174, 647,
73, 122, 335, 530, 442, 853, 695, 249, 445, 515,
909, 545, 703, 919, 874, 474, 882, 500, 594, 612,
641, 801, 220, 162, 819, 984, 589, 513, 495, 799,
161, 604, 958, 533, 221, 400, 386, 867, 600, 782,
382, 596, 414, 171, 516, 375, 682, 485, 911, 276,
98, 553, 163, 354, 666, 933, 424, 341, 533, 870,
227, 730, 475, 186, 263, 647, 537, 686, 600, 224,
469, 68, 770, 919, 190, 373, 294, 822, 808, 206,
184, 943, 795, 384, 383, 461, 404, 758, 839, 887,
715, 67, 618, 276, 204, 918, 873, 777, 604, 560,
951, 160, 578, 722, 79, 804, 96, 409, 713, 940,
652, 934, 970, 447, 318, 353, 859, 672, 112, 785,
645, 863, 803, 350, 139, 93, 354, 99, 820, 908,
609, 772, 154, 274, 580, 184, 79, 626, 630, 742,
653, 282, 762, 623, 680, 81, 927, 626, 789, 125,
411, 521, 938, 300, 821, 78, 343, 175, 128, 250,
170, 774, 972, 275, 999, 639, 495, 78, 352, 126,
857, 956, 358, 619, 580, 124, 737, 594, 701, 612,
669, 112, 134, 694, 363, 992, 809, 743, 168, 974,
944, 375, 748, 52, 600, 747, 642, 182, 862, 81,
344, 805, 988, 739, 511, 655, 814, 334, 249, 515,
897, 955, 664, 981, 649, 113, 974, 459, 893, 228,
433, 837, 553, 268, 926, 240, 102, 654, 459, 51,
686, 754, 806, 760, 493, 403, 415, 394, 687, 700,
946, 670, 656, 610, 738, 392, 760, 799, 887, 653,
978, 321, 576, 617, 626, 502, 894, 679, 243, 440,
680, 879, 194, 572, 640, 724, 926, 56, 204, 700,
707, 151, 457, 449, 797, 195, 791, 558, 945, 679,
297, 59, 87, 824, 713, 663, 412, 693, 342, 606,
134, 108, 571, 364, 631, 212, 174, 643, 304, 329,
343, 97, 430, 751, 497, 314, 983, 374, 822, 928,
140, 206, 73, 263, 980, 736, 876, 478, 430, 305,
170, 514, 364, 692, 829, 82, 855, 953, 676, 246,
369, 970, 294, 750, 807, 827, 150, 790, 288, 923,
804, 378, 215, 828, 592, 281, 565, 555, 710, 82,
896, 831, 547, 261, 524, 462, 293, 465, 502, 56,
661, 821, 976, 991, 658, 869, 905, 758, 745, 193,
768, 550, 608, 933, 378, 286, 215, 979, 792, 961,
61, 688, 793, 644, 986, 403, 106, 366, 905, 644,
372, 567, 466, 434, 645, 210, 389, 550, 919, 135,
780, 773, 635, 389, 707, 100, 626, 958, 165, 504,
920, 176, 193, 713, 857, 265, 203, 50, 668, 108,
645, 990, 626, 197, 510, 357, 358, 850, 858, 364,
936, 638
};
private static final Logger LOGGER =
LoggerFactory.getLogger(CBZip2InputStream.class);
private static void reportCRCError() {
LOGGER.error("BZip2 CRC error");
}
private void makeMaps() {
final boolean[] inUse = this.data.inUse;
final byte[] seqToUnseq = this.data.seqToUnseq;
int nInUseShadow = 0;
for (int i=0; i<256; i++) {
if (inUse[i]) seqToUnseq[nInUseShadow++] = (byte) i;
}
this.nInUse = nInUseShadow;
}
/**
* Index of the last char in the block, so the block size == last + 1.
*/
private int last;
/**
* INdex in zptr[] of original string after sorting.
*/
private int origPtr;
/**
* always: in the range 0 .. 9.
* The current block size is 100000 * this number.
*/
private int blockSize100k;
private boolean blockRandomised;
private int bsBuff;
private int bsLive;
private final CRC crc = new CRC();
private int nInUse;
private InputStream in;
private int currentChar = -1;
private static final int EOF = 0;
private static final int START_BLOCK_STATE = 1;
private static final int RAND_PART_A_STATE = 2;
private static final int RAND_PART_B_STATE = 3;
private static final int RAND_PART_C_STATE = 4;
private static final int NO_RAND_PART_A_STATE = 5;
private static final int NO_RAND_PART_B_STATE = 6;
private static final int NO_RAND_PART_C_STATE = 7;
private int currentState = START_BLOCK_STATE;
private int storedBlockCRC, storedCombinedCRC;
private int computedBlockCRC, computedCombinedCRC;
// Variables used by setup* methods exclusively
private int suCount;
private int suCh2;
private int suChPrev;
private int suI2;
private int suJ2;
private int suRNToGo;
private int suRTPos;
private int suTPos;
private char suZ;
/**
* All memory intensive stuff.
* This field is initialized by initBlock();
*/
private CBZip2InputStream.Data data;
// -- Constructor --
/**
* 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.
*
* @param in stream from which to read BZip2 data; expected to be
* set to the first byte past the 2 byte magic marker
* @throws IOException
* if the stream content is malformed or an I/O error occurs.
* @throws NullPointerException
* if in == null
*/
public CBZip2InputStream(final InputStream in) throws IOException {
super();
this.in = in;
init();
}
// -- InputStream API --
@Override
public int read() throws IOException {
if (this.in != null) return read0();
throw new IOException("stream closed");
}
@Override
public int read(final byte[] dest, final int offs, final int len)
throws IOException
{
if (offs < 0) {
throw new IndexOutOfBoundsException("offs(" + offs + ") < 0.");
}
if (len < 0) {
throw new IndexOutOfBoundsException("len(" + len + ") < 0.");
}
if (offs + len > dest.length) {
throw new IndexOutOfBoundsException("offs(" + offs + ") + len(" +
len + ") > dest.length(" + dest.length + ").");
}
if (this.in == null) throw new IOException("stream closed");
final int hi = offs + len;
int destOffs = offs;
for (int b; (destOffs < hi) && ((b = read0()) >= 0);) {
dest[destOffs++] = (byte) b;
}
return (destOffs == offs) ? -1 : (destOffs - offs);
}
private int read0() throws IOException {
final int retChar = this.currentChar;
switch (this.currentState) {
case EOF:
return -1;
case START_BLOCK_STATE:
throw new IllegalStateException();
case RAND_PART_A_STATE:
throw new IllegalStateException();
case RAND_PART_B_STATE:
setupRandPartB();
break;
case RAND_PART_C_STATE:
setupRandPartC();
break;
case NO_RAND_PART_A_STATE:
throw new IllegalStateException();
case NO_RAND_PART_B_STATE:
setupNoRandPartB();
break;
case NO_RAND_PART_C_STATE:
setupNoRandPartC();
break;
default:
throw new IllegalStateException();
}
return retChar;
}
private void init() throws IOException {
int magic2 = this.in.read();
if (magic2 != 'h') {
throw new IOException("Stream is not BZip2 formatted: expected 'h'" +
" as first byte but got '" + (char) magic2 + "'");
}
int blockSize = this.in.read();
if ((blockSize < '1') || (blockSize > '9')) {
throw new IOException("Stream is not BZip2 formatted: illegal " +
"blocksize " + (char) blockSize);
}
this.blockSize100k = blockSize - '0';
initBlock();
setupBlock();
}
private void initBlock() throws IOException {
char magic0 = bsGetUByte();
char magic1 = bsGetUByte();
char magic2 = bsGetUByte();
char magic3 = bsGetUByte();
char magic4 = bsGetUByte();
char magic5 = bsGetUByte();
if (magic0 == 0x17 &&
magic1 == 0x72 &&
magic2 == 0x45 &&
magic3 == 0x38 &&
magic4 == 0x50 &&
magic5 == 0x90)
{
complete(); // end of file
}
else if (magic0 != 0x31 || // '1'
magic1 != 0x41 || // ')'
magic2 != 0x59 || // 'Y'
magic3 != 0x26 || // '&'
magic4 != 0x53 || // 'S'
magic5 != 0x59) // 'Y'
{
this.currentState = EOF;
throw new IOException("bad block header");
}
else {
this.storedBlockCRC = bsGetInt();
this.blockRandomised = bsR(1) == 1;
// Allocate data here instead in constructor, so we do not
// allocate it if the input file is empty.
if (this.data == null) {
this.data = new Data(this.blockSize100k);
}
// currBlockNo++;
getAndMoveToFrontDecode();
this.crc.initialiseCRC();
this.currentState = START_BLOCK_STATE;
}
}
private void endBlock() {
this.computedBlockCRC = this.crc.getFinalCRC();
// A bad CRC is considered a fatal error.
if (this.storedBlockCRC != this.computedBlockCRC) {
// make next blocks readable without error
// (repair feature, not yet documented, not tested)
this.computedCombinedCRC =
(this.storedCombinedCRC << 1) | (this.storedCombinedCRC >>> 31);
this.computedCombinedCRC ^= this.storedBlockCRC;
reportCRCError();
}
this.computedCombinedCRC =
(this.computedCombinedCRC << 1) | (this.computedCombinedCRC >>> 31);
this.computedCombinedCRC ^= this.computedBlockCRC;
}
private void complete() throws IOException {
this.storedCombinedCRC = bsGetInt();
this.currentState = EOF;
this.data = null;
if (this.storedCombinedCRC != this.computedCombinedCRC) {
reportCRCError();
}
}
@Override
public void close() throws IOException {
InputStream inShadow = this.in;
if (inShadow != null) {
try {
if (inShadow != System.in) inShadow.close();
}
finally {
this.data = null;
this.in = null;
}
}
}
private int bsR(final int n) throws IOException {
int bsLiveShadow = this.bsLive;
int bsBuffShadow = this.bsBuff;
if (bsLiveShadow < n) {
final InputStream inShadow = this.in;
do {
int thech = inShadow.read();
if (thech < 0) throw new IOException("unexpected end of stream");
bsBuffShadow = (bsBuffShadow << 8) | thech;
bsLiveShadow += 8;
}
while (bsLiveShadow < n);
this.bsBuff = bsBuffShadow;
}
this.bsLive = bsLiveShadow - n;
return (bsBuffShadow >> (bsLiveShadow - n)) & ((1 << n) - 1);
}
private boolean bsGetBit() throws IOException {
return bsR(1) != 0;
}
private char bsGetUByte() throws IOException {
return (char) bsR(8);
}
private int bsGetInt() throws IOException {
return (((((bsR(8) << 8) | bsR(8)) << 8) | bsR(8)) << 8) | bsR(8);
}
/** Called by createHuffmanDecodingTables() exclusively. */
private static void hbCreateDecodeTables(final int[] limit,
final int[] base, final int[] perm, final char[] length,
final int minLen, final int maxLen, final int alphaSize)
{
for (int i = minLen, pp = 0; i <= maxLen; i++) {
for (int j = 0; j < alphaSize; j++) {
if (length[j] == i) perm[pp++] = j;
}
}
for (int i = MAX_CODE_LEN; --i > 0;) {
base[i] = 0;
limit[i] = 0;
}
for (int i = 0; i < alphaSize; i++) {
base[length[i] + 1]++;
}
for (int i = 1, b = base[0]; i < MAX_CODE_LEN; i++) {
b += base[i];
base[i] = b;
}
for (int i = minLen, vec = 0, b = base[i]; i <= maxLen; i++) {
final int nb = base[i + 1];
vec += nb - b;
b = nb;
limit[i] = vec - 1;
vec <<= 1;
}
for (int i = minLen + 1; i <= maxLen; i++) {
base[i] = ((limit[i - 1] + 1) << 1) - base[i];
}
}
private void recvDecodingTables() throws IOException {
final Data dataShadow = this.data;
final boolean[] inUse = dataShadow.inUse;
final byte[] pos = dataShadow.recvDecodingTablesPos;
final byte[] selector = dataShadow.selector;
final byte[] selectorMtf = dataShadow.selectorMtf;
int inUse16 = 0;
// Receive the mapping table
for (int i = 0; i < 16; i++) {
if (bsGetBit()) {
inUse16 |= 1 << i;
}
}
for (int i = 256; --i >= 0;) inUse[i] = false;
for (int i = 0; i < 16; i++) {
if ((inUse16 & (1 << i)) != 0) {
final int i16 = i << 4;
for (int j = 0; j < 16; j++) {
if (bsGetBit()) inUse[i16 + j] = true;
}
}
}
makeMaps();
final int alphaSize = this.nInUse + 2;
// Now the selectors
final int nGroups = bsR(3);
final int nSelectors = bsR(15);
for (int i = 0; i < nSelectors; i++) {
int j = 0;
while (bsGetBit()) j++;
selectorMtf[i] = (byte) j;
}
// Undo the MTF values for the selectors.
for (int v = nGroups; --v >= 0;) pos[v] = (byte) v;
for (int i = 0; i < nSelectors; i++) {
int v = selectorMtf[i] & 0xff;
final byte tmp = pos[v];
while (v > 0) {
// nearly all times v is zero, 4 in most other cases
pos[v] = pos[v - 1];
v--;
}
pos[0] = tmp;
selector[i] = tmp;
}
final char[][] len = dataShadow.tempCharArray2d;
// Now the coding tables
for (int t = 0; t < nGroups; t++) {
int curr = bsR(5);
final char[] tLen = len[t];
for (int i = 0; i < alphaSize; i++) {
while (bsGetBit()) curr += bsGetBit() ? -1 : 1;
tLen[i] = (char) curr;
}
}
// finally create the Huffman tables
createHuffmanDecodingTables(alphaSize, nGroups);
}
/** Called by recvDecodingTables() exclusively. */
private void createHuffmanDecodingTables(final int alphaSize,
final int nGroups)
{
final Data dataShadow = this.data;
final char[][] len = dataShadow.tempCharArray2d;
final int[] minLens = dataShadow.minLens;
final int[][] limit = dataShadow.limit;
final int[][] base = dataShadow.base;
final int[][] perm = dataShadow.perm;
for (int t = 0; t < nGroups; t++) {
int minLen = 32;
int maxLen = 0;
final char[] tLen = len[t];
for (int i = alphaSize; --i >= 0;) {
final char lent = tLen[i];
if (lent > maxLen) maxLen = lent;
if (lent < minLen) minLen = lent;
}
hbCreateDecodeTables(limit[t], base[t], perm[t], len[t], minLen,
maxLen, alphaSize);
minLens[t] = minLen;
}
}
private void getAndMoveToFrontDecode() throws IOException {
this.origPtr = bsR(24);
recvDecodingTables();
final InputStream inShadow = this.in;
final Data dataShadow = this.data;
final byte[] ll8 = dataShadow.ll8;
final int[] unzftab = dataShadow.unzftab;
final byte[] selector = dataShadow.selector;
final byte[] seqToUnseq = dataShadow.seqToUnseq;
final char[] yy = dataShadow.getAndMoveToFrontDecodeYY;
final int[] minLens = dataShadow.minLens;
final int[][] limit = dataShadow.limit;
final int[][] base = dataShadow.base;
final int[][] perm = dataShadow.perm;
final int limitLast = this.blockSize100k * 100000;
// Setting up the unzftab entries here is not strictly
// necessary, but it does save having to do it later
// in a separate pass, and so saves a block's worth of
// cache misses.
for (int i = 256; --i >= 0;) {
yy[i] = (char) i;
unzftab[i] = 0;
}
int groupNo = 0;
int groupPos = G_SIZE - 1;
final int eob = this.nInUse + 1;
int nextSym = getAndMoveToFrontDecode0(0);
int bsBuffShadow = this.bsBuff;
int bsLiveShadow = this.bsLive;
int lastShadow = -1;
int zt = selector[groupNo] & 0xff;
int[] baseZT = base[zt];
int[] limitZT = limit[zt];
int[] permZT = perm[zt];
int minLensZT = minLens[zt];
while (nextSym != eob) {
if ((nextSym == RUNA) || (nextSym == RUNB)) {
int s = -1;
for (int n = 1; true; n <<= 1) {
if (nextSym == RUNA) s += n;
else if (nextSym == RUNB) s += n << 1;
else break;
if (groupPos == 0) {
groupPos = G_SIZE - 1;
zt = selector[++groupNo] & 0xff;
baseZT = base[zt];
limitZT = limit[zt];
permZT = perm[zt];
minLensZT = minLens[zt];
}
else groupPos--;
int zn = minLensZT;
// Inlined:
// int zvec = bsR(zn);
while (bsLiveShadow < zn) {
final int thech = inShadow.read();
if (thech >= 0) {
bsBuffShadow = (bsBuffShadow << 8) | thech;
bsLiveShadow += 8;
continue;
}
throw new IOException("unexpected end of stream");
}
int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 << zn) - 1);
bsLiveShadow -= zn;
while (zvec > limitZT[zn]) {
zn++;
while (bsLiveShadow < 1) {
final int thech = inShadow.read();
if (thech >= 0) {
bsBuffShadow = (bsBuffShadow << 8) | thech;
bsLiveShadow += 8;
continue;
}
throw new IOException("unexpected end of stream");
}
bsLiveShadow--;
zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
}
nextSym = permZT[zvec - baseZT[zn]];
}
final byte ch = seqToUnseq[yy[0]];
unzftab[ch & 0xff] += s + 1;
while (s-- >= 0) ll8[++lastShadow] = ch;
if (lastShadow >= limitLast) throw new IOException("block overrun");
}
else {
if (++lastShadow >= limitLast) {
throw new IOException("block overrun");
}
final char tmp = yy[nextSym - 1];
unzftab[seqToUnseq[tmp] & 0xff]++;
ll8[lastShadow] = seqToUnseq[tmp];
/*
This loop is hammered during decompression,
hence avoid native method call overhead of
System.arraycopy for very small ranges to copy.
*/
if (nextSym <= 16) {
for (int j = nextSym - 1; j > 0;) yy[j] = yy[--j];
}
else System.arraycopy(yy, 0, yy, 1, nextSym - 1);
yy[0] = tmp;
if (groupPos == 0) {
groupPos = G_SIZE - 1;
zt = selector[++groupNo] & 0xff;
baseZT = base[zt];
limitZT = limit[zt];
permZT = perm[zt];
minLensZT = minLens[zt];
}
else groupPos--;
int zn = minLensZT;
// Inlined:
// int zvec = bsR(zn);
while (bsLiveShadow < zn) {
final int thech = inShadow.read();
if (thech >= 0) {
bsBuffShadow = (bsBuffShadow << 8) | thech;
bsLiveShadow += 8;
continue;
}
throw new IOException("unexpected end of stream");
}
int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 << zn) - 1);
bsLiveShadow -= zn;
while (zvec > limitZT[zn]) {
zn++;
while (bsLiveShadow < 1) {
final int thech = inShadow.read();
if (thech >= 0) {
bsBuffShadow = (bsBuffShadow << 8) | thech;
bsLiveShadow += 8;
continue;
}
throw new IOException("unexpected end of stream");
}
bsLiveShadow--;
zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
}
nextSym = permZT[zvec - baseZT[zn]];
}
}
this.last = lastShadow;
this.bsLive = bsLiveShadow;
this.bsBuff = bsBuffShadow;
}
private int getAndMoveToFrontDecode0(final int groupNo)
throws IOException
{
final InputStream inShadow = this.in;
final Data dataShadow = this.data;
final int zt = dataShadow.selector[groupNo] & 0xff;
final int[] limitZT = dataShadow.limit[zt];
int zn = dataShadow.minLens[zt];
int zvec = bsR(zn);
int bsLiveShadow = this.bsLive;
int bsBuffShadow = this.bsBuff;
while (zvec > limitZT[zn]) {
zn++;
while (bsLiveShadow < 1) {
final int thech = inShadow.read();
if (thech >= 0) {
bsBuffShadow = (bsBuffShadow << 8) | thech;
bsLiveShadow += 8;
continue;
}
throw new IOException("unexpected end of stream");
}
bsLiveShadow--;
zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
}
this.bsLive = bsLiveShadow;
this.bsBuff = bsBuffShadow;
return dataShadow.perm[zt][zvec - dataShadow.base[zt][zn]];
}
private void setupBlock() throws IOException {
if (this.data == null) return;
final int[] cftab = this.data.cftab;
final int[] tt = this.data.initTT(this.last + 1);
final byte[] ll8 = this.data.ll8;
cftab[0] = 0;
System.arraycopy(this.data.unzftab, 0, cftab, 1, 256);
for (int i = 1, c = cftab[0]; i <= 256; i++) {
c += cftab[i];
cftab[i] = c;
}
for (int i = 0, lastShadow = this.last; i <= lastShadow; i++) {
tt[cftab[ll8[i] & 0xff]++] = i;
}
if ((this.origPtr < 0) || (this.origPtr >= tt.length)) {
throw new IOException("stream corrupted");
}
this.suTPos = tt[this.origPtr];
this.suCount = 0;
this.suI2 = 0;
this.suCh2 = 256; /* not a char and not EOF */
if (this.blockRandomised) {
this.suRNToGo = 0;
this.suRTPos = 0;
setupRandPartA();
}
else setupNoRandPartA();
}
private void setupRandPartA() throws IOException {
if (this.suI2 <= this.last) {
this.suChPrev = this.suCh2;
int suCh2Shadow = this.data.ll8[this.suTPos] & 0xff;
this.suTPos = this.data.tt[this.suTPos];
if (this.suRNToGo == 0) {
this.suRNToGo = R_NUMS[this.suRTPos] - 1;
if (++this.suRTPos == 512) this.suRTPos = 0;
}
else this.suRNToGo--;
this.suCh2 = suCh2Shadow ^= (this.suRNToGo == 1) ? 1 : 0;
this.suI2++;
this.currentChar = suCh2Shadow;
this.currentState = RAND_PART_B_STATE;
this.crc.updateCRC(suCh2Shadow);
}
else {
endBlock();
initBlock();
setupBlock();
}
}
private void setupNoRandPartA() throws IOException {
if (this.suI2 <= this.last) {
this.suChPrev = this.suCh2;
int suCh2Shadow = this.data.ll8[this.suTPos] & 0xff;
this.suCh2 = suCh2Shadow;
this.suTPos = this.data.tt[this.suTPos];
this.suI2++;
this.currentChar = suCh2Shadow;
this.currentState = NO_RAND_PART_B_STATE;
this.crc.updateCRC(suCh2Shadow);
}
else {
this.currentState = NO_RAND_PART_A_STATE;
endBlock();
initBlock();
setupBlock();
}
}
private void setupRandPartB() throws IOException {
if (this.suCh2 != this.suChPrev) {
this.currentState = RAND_PART_A_STATE;
this.suCount = 1;
setupRandPartA();
}
else if (++this.suCount >= 4) {
this.suZ = (char) (this.data.ll8[this.suTPos] & 0xff);
this.suTPos = this.data.tt[this.suTPos];
if (this.suRNToGo == 0) {
this.suRNToGo = R_NUMS[this.suRTPos] - 1;
if (++this.suRTPos == 512) {
this.suRTPos = 0;
}
}
else this.suRNToGo--;
this.suJ2 = 0;
this.currentState = RAND_PART_C_STATE;
if (this.suRNToGo == 1) this.suZ ^= 1;
setupRandPartC();
}
else {
this.currentState = RAND_PART_A_STATE;
setupRandPartA();
}
}
private void setupRandPartC() throws IOException {
if (this.suJ2 < this.suZ) {
this.currentChar = this.suCh2;
this.crc.updateCRC(this.suCh2);
this.suJ2++;
}
else {
this.currentState = RAND_PART_A_STATE;
this.suI2++;
this.suCount = 0;
setupRandPartA();
}
}
private void setupNoRandPartB() throws IOException {
if (this.suCh2 != this.suChPrev) {
this.suCount = 1;
setupNoRandPartA();
}
else if (++this.suCount >= 4) {
this.suZ = (char) (this.data.ll8[this.suTPos] & 0xff);
this.suTPos = this.data.tt[this.suTPos];
this.suJ2 = 0;
setupNoRandPartC();
}
else setupNoRandPartA();
}
private void setupNoRandPartC() throws IOException {
if (this.suJ2 < this.suZ) {
int suCh2Shadow = this.suCh2;
this.currentChar = suCh2Shadow;
this.crc.updateCRC(suCh2Shadow);
this.suJ2++;
this.currentState = NO_RAND_PART_C_STATE;
}
else {
this.suI2++;
this.suCount = 0;
setupNoRandPartA();
}
}
private static final class Data extends Object {
// (with blockSize 900k)
final boolean[] inUse = new boolean[256]; // 256 byte
final byte[] seqToUnseq = new byte[256]; // 256 byte
final byte[] selector = new byte[MAX_SELECTORS]; // 18002 byte
final byte[] selectorMtf = new byte[MAX_SELECTORS]; // 18002 byte
/**
* Freq table collected to save a pass over the data during
* decompression.
*/
final int[] unzftab = new int[256]; // 1024 byte
final int[][] limit = new int[N_GROUPS][MAX_ALPHA_SIZE]; // 6192 byte
final int[][] base = new int[N_GROUPS][MAX_ALPHA_SIZE]; // 6192 byte
final int[][] perm = new int[N_GROUPS][MAX_ALPHA_SIZE]; // 6192 byte
final int[] minLens = new int[N_GROUPS]; // 24 byte
final int[] cftab = new int[257]; // 1028 byte
final char[] getAndMoveToFrontDecodeYY = new char[256]; // 512 byte
// 3096 byte
final char[][] tempCharArray2d = new char[N_GROUPS][MAX_ALPHA_SIZE];
final byte[] recvDecodingTablesPos = new byte[N_GROUPS]; // 6 byte
//---------------
// 60798 byte
int[] tt; // 3600000 byte
byte[] ll8; // 900000 byte
//---------------
// 4560782 byte
//===============
Data(int blockSize100k) {
super();
this.ll8 = new byte[blockSize100k * BASE_BLOCK_SIZE];
}
/**
* Initializes the {@link #tt} array.
*
* This method is called when the required length of the array
* is known. I don't initialize it at construction time to
* avoid unneccessary memory allocation when compressing small
* files.
*/
int[] initTT(int length) {
int[] ttShadow = this.tt;
// tt.length should always be >= length, but theoretically
// it can happen, if the compressor mixed small and large
// blocks. Normally only the last block will be smaller
// than others.
if ((ttShadow == null) || (ttShadow.length < length)) {
this.tt = ttShadow = new int[length];
}
return ttShadow;
}
}
}