Revision: 21643
http://sourceforge.net/p/jmol/code/21643
Author: hansonr
Date: 2017-06-27 07:36:29 +0000 (Tue, 27 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.1"
new feature: BZ2 compressed file reader
-- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
-- Apache license
bug fix: SMILES generator can show wrong @/@@ or stereochemical type for some
allenes and cumulenes
bug fix: CIPChirality Rule 4b fixes
Modified Paths:
--------------
trunk/Jmol/src/javajs/api/GenericZipTools.java
trunk/Jmol/src/javajs/util/Rdr.java
trunk/Jmol/src/javajs/util/ZipTools.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Added Paths:
-----------
trunk/Jmol/src/org/apache/
trunk/Jmol/src/org/apache/tools/
trunk/Jmol/src/org/apache/tools/bzip2/
trunk/Jmol/src/org/apache/tools/bzip2/BZip2Constants.java
trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
trunk/Jmol/src/org/apache/tools/bzip2/CRC.java
Modified: trunk/Jmol/src/javajs/api/GenericZipTools.java
===================================================================
--- trunk/Jmol/src/javajs/api/GenericZipTools.java 2017-06-27 04:28:53 UTC
(rev 21642)
+++ trunk/Jmol/src/javajs/api/GenericZipTools.java 2017-06-27 07:36:29 UTC
(rev 21643)
@@ -15,6 +15,8 @@
public InputStream newGZIPInputStream(InputStream bis) throws IOException;
+ public InputStream newBZip2InputStream(InputStream bis) throws IOException;
+
public Object getZipFileDirectory(BufferedInputStream bis,
String[] subFileList, int listPtr,
boolean asBufferedInputStream);
Modified: trunk/Jmol/src/javajs/util/Rdr.java
===================================================================
--- trunk/Jmol/src/javajs/util/Rdr.java 2017-06-27 04:28:53 UTC (rev 21642)
+++ trunk/Jmol/src/javajs/util/Rdr.java 2017-06-27 07:36:29 UTC (rev 21643)
@@ -152,10 +152,19 @@
&& (bytes[7] & 0xFF) == 0xE1);
}
+ public static boolean isBZip2S(InputStream is) {
+ return isBZip2B(getMagic(is, 3));
+ }
+
public static boolean isGzipS(InputStream is) {
return isGzipB(getMagic(is, 2));
}
+ public static boolean isBZip2B(byte[] bytes) {
+ return (bytes != null && bytes.length >= 3 // BZh
+ && (bytes[0] & 0xFF) == 0x42 && (bytes[1] & 0xFF) == 0x5A &&
(bytes[2] & 0xFF) == 0x68);
+}
+
public static boolean isGzipB(byte[] bytes) {
return (bytes != null && bytes.length >= 2
&& (bytes[0] & 0xFF) == 0x1F && (bytes[1] & 0xFF) == 0x8B);
@@ -269,6 +278,14 @@
return bis;
}
+ public static BufferedInputStream
getUnzippedInputStreamBZip2(GenericZipTools jzt,
+
BufferedInputStream bis) throws IOException {
+ while (isBZip2S(bis))
+ bis = new BufferedInputStream(jzt.newBZip2InputStream(bis));
+ return bis;
+ }
+
+
/**
* Allow for base64-encoding check.
*
Modified: trunk/Jmol/src/javajs/util/ZipTools.java
===================================================================
--- trunk/Jmol/src/javajs/util/ZipTools.java 2017-06-27 04:28:53 UTC (rev
21642)
+++ trunk/Jmol/src/javajs/util/ZipTools.java 2017-06-27 07:36:29 UTC (rev
21643)
@@ -33,6 +33,7 @@
import javajs.J2SIgnoreImport;
import javajs.api.GenericZipInputStream;
import javajs.api.GenericZipTools;
+import javajs.api.Interface;
import javajs.api.ZInputStream;
import java.util.Map;
@@ -42,7 +43,10 @@
import java.util.zip.ZipInputStream;
import java.util.zip.ZipOutputStream;
+import org.apache.tools.bzip2.CBZip2InputStreamFactory;
+import org.jmol.viewer.Viewer;
+
/**
* Note the JSmol/HTML5 must use its own version of
java.util.zip.ZipOutputStream.
*
@@ -284,6 +288,11 @@
}
@Override
+ public InputStream newBZip2InputStream(InputStream is) throws IOException {
+ return new BufferedInputStream(((CBZip2InputStreamFactory)
Interface.getInterface("org.apache.tools.bzip2.CBZip2InputStreamFactory")).getStream(is));
+ }
+
+ @Override
public BufferedInputStream getUnGzippedInputStream(byte[] bytes) {
try {
return Rdr.getUnzippedInputStream(this, Rdr.getBIS(bytes));
Added: trunk/Jmol/src/org/apache/tools/bzip2/BZip2Constants.java
===================================================================
--- trunk/Jmol/src/org/apache/tools/bzip2/BZip2Constants.java
(rev 0)
+++ trunk/Jmol/src/org/apache/tools/bzip2/BZip2Constants.java 2017-06-27
07:36:29 UTC (rev 21643)
@@ -0,0 +1,109 @@
+/*
+ * 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
+ * <kei...@aftexsw.com> to whom the Ant project is very grateful for his
+ * great code.
+ */
+
+package org.apache.tools.bzip2;
+
+/**
+ * Base class for both the compress and decompress classes.
+ * Holds common arrays, and static data.
+ * <p>
+ * This interface is public for historical purposes.
+ * You should have no need to use it.
+ * </p>
+ */
+public interface BZip2Constants {
+
+ int baseBlockSize = 100000;
+ int MAX_ALPHA_SIZE = 258;
+ int MAX_CODE_LEN = 23;
+ int RUNA = 0;
+ int RUNB = 1;
+ int N_GROUPS = 6;
+ int G_SIZE = 50;
+ int N_ITERS = 4;
+ int MAX_SELECTORS = (2 + (900000 / G_SIZE));
+ int NUM_OVERSHOOT_BYTES = 20;
+
+ /**
+ * This array really shouldn't be here.
+ * Again, for historical purposes it is.
+ *
+ * <p>FIXME: This array should be in a private or package private
+ * location, since it could be modified by malicious code.</p>
+ */
+ int[] rNums = {
+ 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
+ };
+}
Property changes on: trunk/Jmol/src/org/apache/tools/bzip2/BZip2Constants.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
===================================================================
--- trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
(rev 0)
+++ trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
2017-06-27 07:36:29 UTC (rev 21643)
@@ -0,0 +1,1062 @@
+/*
+ * 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
+ * <kei...@aftexsw.com> to whom the Ant project is very grateful for his
+ * great code.
+ */
+package org.apache.tools.bzip2;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+/**
+ * An input stream that decompresses from the BZip2 format (without the file
+ * header chars) to be read as any other stream.
+ *
+ * <p>The decompression requires large amounts of memory. Thus you
+ * should call the {@link #close() close()} method as soon as
+ * possible, to force <tt>CBZip2InputStream</tt> to release the
+ * allocated memory. See {@link CBZip2OutputStream
+ * CBZip2OutputStream} for information about memory usage.</p>
+ *
+ * <p><tt>CBZip2InputStream</tt> reads bytes from the compressed
+ * source stream via the single byte {@link java.io.InputStream#read()
+ * read()} method exclusively. Thus you should consider to use a
+ * buffered source stream.</p>
+ *
+ * <p>Instances of this class are not threadsafe.</p>
+ */
+public class CBZip2InputStream extends InputStream implements BZip2Constants {
+
+ /**
+ * 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 final boolean decompressConcatenated;
+
+ 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 su_count;
+ private int su_ch2;
+ private int su_chPrev;
+ private int su_i2;
+ private int su_j2;
+ private int su_rNToGo;
+ private int su_rTPos;
+ private int su_tPos;
+ private char su_z;
+
+ /**
+ * All memory intensive stuff.
+ * This field is initialized by initBlock().
+ */
+ private CBZip2InputStream.Data data;
+
+ /**
+ * Constructs a new CBZip2InputStream which decompresses bytes read from
+ * the specified stream. This doesn't suppprt decompressing
+ * concatenated .bz2 files.
+ *
+ * <p>Although BZip2 headers are marked with the magic
+ * <tt>"Bz"</tt> 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. </p>
+ *
+ * @throws IOException
+ * if the stream content is malformed or an I/O error occurs.
+ * @throws NullPointerException
+ * if <tt>in == null</tt>
+ */
+ public CBZip2InputStream(final InputStream in) throws IOException {
+ this(in, false);
+ }
+
+ /**
+ * Constructs a new CBZip2InputStream which decompresses bytes
+ * read from the specified stream.
+ *
+ * <p>Although BZip2 headers are marked with the magic
+ * <tt>"Bz"</tt> 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. </p>
+ *
+ * @param in the InputStream from which this object should be created
+ * @param decompressConcatenated
+ * if true, decompress until the end of the input;
+ * if false, stop after the first .bz2 stream and
+ * leave the input position to point to the next
+ * byte after the .bz2 stream
+ *
+ * @throws IOException
+ * if the stream content is malformed or an I/O error occurs.
+ * @throws NullPointerException
+ * if <tt>in == null</tt>
+ */
+ public CBZip2InputStream(final InputStream in,
+ final boolean decompressConcatenated)
+ throws IOException {
+ super();
+
+ this.in = in;
+ this.decompressConcatenated = decompressConcatenated;
+
+ init(true);
+ initBlock();
+ setupBlock();
+ }
+
+ /** {@inheritDoc} */
+ @Override
+ public int read() throws IOException {
+ if (this.in != null) {
+ return read0();
+ } else {
+ throw new IOException("stream closed");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.io.InputStream#read(byte[], int, int)
+ */
+ @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 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;
+ }
+
+ 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 boolean init(boolean isFirstStream) throws IOException {
+ if (null == in) {
+ throw new IOException("No InputStream");
+ }
+
+ if (isFirstStream) {
+ if (in.available() == 0) {
+ throw new IOException("Empty InputStream");
+ }
+ } else {
+ int magic0 = this.in.read();
+ if (magic0 == -1) {
+ return false;
+ }
+ int magic1 = this.in.read();
+ if (magic0 != 'B' || magic1 != 'Z') {
+ throw new IOException("Garbage after a valid BZip2 stream");
+ }
+ }
+
+ int magic2 = this.in.read();
+ if (magic2 != 'h') {
+ throw new IOException(isFirstStream
+ ? "Stream is not in the BZip2 format"
+ : "Garbage after a valid BZip2 stream");
+ }
+
+ 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';
+
+ this.bsLive = 0;
+ this.computedCombinedCRC = 0;
+
+ return true;
+ }
+
+ private void initBlock() throws IOException {
+ char magic0;
+ char magic1;
+ char magic2;
+ char magic3;
+ char magic4;
+ char magic5;
+
+ while (true) {
+ // Get the block magic bytes.
+ magic0 = bsGetUByte();
+ magic1 = bsGetUByte();
+ magic2 = bsGetUByte();
+ magic3 = bsGetUByte();
+ magic4 = bsGetUByte();
+ magic5 = bsGetUByte();
+
+ // If isn't end of stream magic, break out of the loop.
+ if (magic0 != 0x17 || magic1 != 0x72 || magic2 != 0x45
+ || magic3 != 0x38 || magic4 != 0x50 || magic5 != 0x90) {
+ break;
+ }
+
+ // End of stream was reached. Check the combined CRC and
+ // advance to the next .bz2 stream if decoding concatenated
+ // streams.
+ if (complete()) {
+ return;
+ }
+ }
+
+ 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() throws IOException {
+ 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 boolean complete() throws IOException {
+ this.storedCombinedCRC = bsGetInt();
+ this.currentState = EOF;
+ this.data = null;
+
+ if (this.storedCombinedCRC != this.computedCombinedCRC) {
+ reportCRCError();
+ }
+
+ // Look for the next .bz2 stream if decompressing
+ // concatenated files.
+ return !decompressConcatenated || !init(false);
+ }
+
+ @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 {
+ int bsLiveShadow = this.bsLive;
+ int bsBuffShadow = this.bsBuff;
+
+ if (bsLiveShadow < 1) {
+ int thech = this.in.read();
+
+ if (thech < 0) {
+ throw new IOException("unexpected end of stream");
+ }
+
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ this.bsBuff = bsBuffShadow;
+ }
+
+ this.bsLive = bsLiveShadow - 1;
+ return ((bsBuffShadow >> (bsLiveShadow - 1)) & 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.recvDecodingTables_pos;
+ 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.temp_charArray2d;
+
+ /* Now the coding tables */
+ for (int t = 0; t < nGroups; t++) {
+ int curr = bsR(5);
+ final char[] len_t = len[t];
+ for (int i = 0; i < alphaSize; i++) {
+ while (bsGetBit()) {
+ curr += bsGetBit() ? -1 : 1;
+ }
+ len_t[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.temp_charArray2d;
+ 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[] len_t = len[t];
+ for (int i = alphaSize; --i >= 0;) {
+ final char lent = len_t[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.getAndMoveToFrontDecode_yy;
+ 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[] base_zt = base[zt];
+ int[] limit_zt = limit[zt];
+ int[] perm_zt = perm[zt];
+ int minLens_zt = 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;
+ base_zt = base[zt];
+ limit_zt = limit[zt];
+ perm_zt = perm[zt];
+ minLens_zt = minLens[zt];
+ } else {
+ groupPos--;
+ }
+
+ int zn = minLens_zt;
+
+ // Inlined:
+ // int zvec = bsR(zn);
+ while (bsLiveShadow < zn) {
+ final int thech = inShadow.read();
+ if (thech >= 0) {
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ } else {
+ throw new IOException("unexpected end of stream");
+ }
+ }
+ int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 <<
zn) - 1);
+ bsLiveShadow -= zn;
+
+ while (zvec > limit_zt[zn]) {
+ zn++;
+ while (bsLiveShadow < 1) {
+ final int thech = inShadow.read();
+ if (thech >= 0) {
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ } else {
+ throw new IOException("unexpected end of
stream");
+ }
+ }
+ bsLiveShadow--;
+ zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) &
1);
+ }
+ nextSym = perm_zt[zvec - base_zt[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;
+ base_zt = base[zt];
+ limit_zt = limit[zt];
+ perm_zt = perm[zt];
+ minLens_zt = minLens[zt];
+ } else {
+ groupPos--;
+ }
+
+ int zn = minLens_zt;
+
+ // Inlined:
+ // int zvec = bsR(zn);
+ while (bsLiveShadow < zn) {
+ final int thech = inShadow.read();
+ if (thech >= 0) {
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ } else {
+ throw new IOException("unexpected end of stream");
+ }
+ }
+ int zvec = (bsBuffShadow >> (bsLiveShadow - zn)) & ((1 << zn)
- 1);
+ bsLiveShadow -= zn;
+
+ while (zvec > limit_zt[zn]) {
+ zn++;
+ while (bsLiveShadow < 1) {
+ final int thech = inShadow.read();
+ if (thech >= 0) {
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ } else {
+ throw new IOException("unexpected end of stream");
+ }
+ }
+ bsLiveShadow--;
+ zvec = (zvec << 1) | ((bsBuffShadow >> bsLiveShadow) & 1);
+ }
+ nextSym = perm_zt[zvec - base_zt[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[] limit_zt = dataShadow.limit[zt];
+ int zn = dataShadow.minLens[zt];
+ int zvec = bsR(zn);
+ int bsLiveShadow = this.bsLive;
+ int bsBuffShadow = this.bsBuff;
+
+ while (zvec > limit_zt[zn]) {
+ zn++;
+ while (bsLiveShadow < 1) {
+ final int thech = inShadow.read();
+
+ if (thech >= 0) {
+ bsBuffShadow = (bsBuffShadow << 8) | thech;
+ bsLiveShadow += 8;
+ continue;
+ } else {
+ 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.su_tPos = tt[this.origPtr];
+ this.su_count = 0;
+ this.su_i2 = 0;
+ this.su_ch2 = 256; /* not a char and not EOF */
+
+ if (this.blockRandomised) {
+ this.su_rNToGo = 0;
+ this.su_rTPos = 0;
+ setupRandPartA();
+ } else {
+ setupNoRandPartA();
+ }
+ }
+
+ private void setupRandPartA() throws IOException {
+ if (this.su_i2 <= this.last) {
+ this.su_chPrev = this.su_ch2;
+ int su_ch2Shadow = this.data.ll8[this.su_tPos] & 0xff;
+ this.su_tPos = this.data.tt[this.su_tPos];
+ if (this.su_rNToGo == 0) {
+ this.su_rNToGo = BZip2Constants.rNums[this.su_rTPos] - 1;
+ if (++this.su_rTPos == 512) {
+ this.su_rTPos = 0;
+ }
+ } else {
+ this.su_rNToGo--;
+ }
+ this.su_ch2 = su_ch2Shadow ^= (this.su_rNToGo == 1) ? 1 : 0;
+ this.su_i2++;
+ this.currentChar = su_ch2Shadow;
+ this.currentState = RAND_PART_B_STATE;
+ this.crc.updateCRC(su_ch2Shadow);
+ } else {
+ endBlock();
+ initBlock();
+ setupBlock();
+ }
+ }
+
+ private void setupNoRandPartA() throws IOException {
+ if (this.su_i2 <= this.last) {
+ this.su_chPrev = this.su_ch2;
+ int su_ch2Shadow = this.data.ll8[this.su_tPos] & 0xff;
+ this.su_ch2 = su_ch2Shadow;
+ this.su_tPos = this.data.tt[this.su_tPos];
+ this.su_i2++;
+ this.currentChar = su_ch2Shadow;
+ this.currentState = NO_RAND_PART_B_STATE;
+ this.crc.updateCRC(su_ch2Shadow);
+ } else {
+ this.currentState = NO_RAND_PART_A_STATE;
+ endBlock();
+ initBlock();
+ setupBlock();
+ }
+ }
+
+ private void setupRandPartB() throws IOException {
+ if (this.su_ch2 != this.su_chPrev) {
+ this.currentState = RAND_PART_A_STATE;
+ this.su_count = 1;
+ setupRandPartA();
+ } else if (++this.su_count >= 4) {
+ this.su_z = (char) (this.data.ll8[this.su_tPos] & 0xff);
+ this.su_tPos = this.data.tt[this.su_tPos];
+ if (this.su_rNToGo == 0) {
+ this.su_rNToGo = BZip2Constants.rNums[this.su_rTPos] - 1;
+ if (++this.su_rTPos == 512) {
+ this.su_rTPos = 0;
+ }
+ } else {
+ this.su_rNToGo--;
+ }
+ this.su_j2 = 0;
+ this.currentState = RAND_PART_C_STATE;
+ if (this.su_rNToGo == 1) {
+ this.su_z ^= 1;
+ }
+ setupRandPartC();
+ } else {
+ this.currentState = RAND_PART_A_STATE;
+ setupRandPartA();
+ }
+ }
+
+ private void setupRandPartC() throws IOException {
+ if (this.su_j2 < this.su_z) {
+ this.currentChar = this.su_ch2;
+ this.crc.updateCRC(this.su_ch2);
+ this.su_j2++;
+ } else {
+ this.currentState = RAND_PART_A_STATE;
+ this.su_i2++;
+ this.su_count = 0;
+ setupRandPartA();
+ }
+ }
+
+ private void setupNoRandPartB() throws IOException {
+ if (this.su_ch2 != this.su_chPrev) {
+ this.su_count = 1;
+ setupNoRandPartA();
+ } else if (++this.su_count >= 4) {
+ this.su_z = (char) (this.data.ll8[this.su_tPos] & 0xff);
+ this.su_tPos = this.data.tt[this.su_tPos];
+ this.su_j2 = 0;
+ setupNoRandPartC();
+ } else {
+ setupNoRandPartA();
+ }
+ }
+
+ private void setupNoRandPartC() throws IOException {
+ if (this.su_j2 < this.su_z) {
+ int su_ch2Shadow = this.su_ch2;
+ this.currentChar = su_ch2Shadow;
+ this.crc.updateCRC(su_ch2Shadow);
+ this.su_j2++;
+ this.currentState = NO_RAND_PART_C_STATE;
+ } else {
+ this.su_i2++;
+ this.su_count = 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[] getAndMoveToFrontDecode_yy = new char[256];
// 512 byte
+ final char[][] temp_charArray2d = new
char[N_GROUPS][MAX_ALPHA_SIZE]; // 3096 byte
+ final byte[] recvDecodingTables_pos = 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 * BZip2Constants.baseBlockSize];
+ }
+
+ /**
+ * 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 unnecessary memory allocation when compressing small
+ * files.
+ */
+ final 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;
+ }
+
+ }
+
+ private static void reportCRCError() throws IOException {
+ // The clean way would be to throw an exception.
+ //throw new IOException("crc error");
+
+ // Just print a message, like the previous versions of this class did
+ System.err.println("BZip2 CRC error");
+ }
+
+}
+
Property changes on:
trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStream.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
===================================================================
--- trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
(rev 0)
+++ trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
2017-06-27 07:36:29 UTC (rev 21643)
@@ -0,0 +1,21 @@
+package org.apache.tools.bzip2;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+public class CBZip2InputStreamFactory {
+
+ /**
+ * jsjava addition for reflection
+ *
+ * @param is
+ * @return BZip2 input stream
+ * @throws IOException
+ */
+ public CBZip2InputStream getStream(InputStream is) throws IOException {
+ is.read(new byte[2]);
+ return new CBZip2InputStream(is);
+ }
+
+}
+
Property changes on:
trunk/Jmol/src/org/apache/tools/bzip2/CBZip2InputStreamFactory.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: trunk/Jmol/src/org/apache/tools/bzip2/CRC.java
===================================================================
--- trunk/Jmol/src/org/apache/tools/bzip2/CRC.java
(rev 0)
+++ trunk/Jmol/src/org/apache/tools/bzip2/CRC.java 2017-06-27 07:36:29 UTC
(rev 21643)
@@ -0,0 +1,141 @@
+/*
+ * 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
+ * <kei...@aftexsw.com> to whom the Ant project is very grateful for his
+ * great code.
+ */
+
+package org.apache.tools.bzip2;
+
+/**
+ * A simple class the hold and calculate the CRC for sanity checking
+ * of the data.
+ *
+ */
+final class CRC {
+ static final int crc32Table[] = {
+ 0x00000000, 0x04c11db7, 0x09823b6e, 0x0d4326d9,
+ 0x130476dc, 0x17c56b6b, 0x1a864db2, 0x1e475005,
+ 0x2608edb8, 0x22c9f00f, 0x2f8ad6d6, 0x2b4bcb61,
+ 0x350c9b64, 0x31cd86d3, 0x3c8ea00a, 0x384fbdbd,
+ 0x4c11db70, 0x48d0c6c7, 0x4593e01e, 0x4152fda9,
+ 0x5f15adac, 0x5bd4b01b, 0x569796c2, 0x52568b75,
+ 0x6a1936c8, 0x6ed82b7f, 0x639b0da6, 0x675a1011,
+ 0x791d4014, 0x7ddc5da3, 0x709f7b7a, 0x745e66cd,
+ 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e, 0x95609039,
+ 0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5,
+ 0xbe2b5b58, 0xbaea46ef, 0xb7a96036, 0xb3687d81,
+ 0xad2f2d84, 0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d,
+ 0xd4326d90, 0xd0f37027, 0xddb056fe, 0xd9714b49,
+ 0xc7361b4c, 0xc3f706fb, 0xceb42022, 0xca753d95,
+ 0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1,
+ 0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d,
+ 0x34867077, 0x30476dc0, 0x3d044b19, 0x39c556ae,
+ 0x278206ab, 0x23431b1c, 0x2e003dc5, 0x2ac12072,
+ 0x128e9dcf, 0x164f8078, 0x1b0ca6a1, 0x1fcdbb16,
+ 0x018aeb13, 0x054bf6a4, 0x0808d07d, 0x0cc9cdca,
+ 0x7897ab07, 0x7c56b6b0, 0x71159069, 0x75d48dde,
+ 0x6b93dddb, 0x6f52c06c, 0x6211e6b5, 0x66d0fb02,
+ 0x5e9f46bf, 0x5a5e5b08, 0x571d7dd1, 0x53dc6066,
+ 0x4d9b3063, 0x495a2dd4, 0x44190b0d, 0x40d816ba,
+ 0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e,
+ 0xbfa1b04b, 0xbb60adfc, 0xb6238b25, 0xb2e29692,
+ 0x8aad2b2f, 0x8e6c3698, 0x832f1041, 0x87ee0df6,
+ 0x99a95df3, 0x9d684044, 0x902b669d, 0x94ea7b2a,
+ 0xe0b41de7, 0xe4750050, 0xe9362689, 0xedf73b3e,
+ 0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2,
+ 0xc6bcf05f, 0xc27dede8, 0xcf3ecb31, 0xcbffd686,
+ 0xd5b88683, 0xd1799b34, 0xdc3abded, 0xd8fba05a,
+ 0x690ce0ee, 0x6dcdfd59, 0x608edb80, 0x644fc637,
+ 0x7a089632, 0x7ec98b85, 0x738aad5c, 0x774bb0eb,
+ 0x4f040d56, 0x4bc510e1, 0x46863638, 0x42472b8f,
+ 0x5c007b8a, 0x58c1663d, 0x558240e4, 0x51435d53,
+ 0x251d3b9e, 0x21dc2629, 0x2c9f00f0, 0x285e1d47,
+ 0x36194d42, 0x32d850f5, 0x3f9b762c, 0x3b5a6b9b,
+ 0x0315d626, 0x07d4cb91, 0x0a97ed48, 0x0e56f0ff,
+ 0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623,
+ 0xf12f560e, 0xf5ee4bb9, 0xf8ad6d60, 0xfc6c70d7,
+ 0xe22b20d2, 0xe6ea3d65, 0xeba91bbc, 0xef68060b,
+ 0xd727bbb6, 0xd3e6a601, 0xdea580d8, 0xda649d6f,
+ 0xc423cd6a, 0xc0e2d0dd, 0xcda1f604, 0xc960ebb3,
+ 0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7,
+ 0xae3afba2, 0xaafbe615, 0xa7b8c0cc, 0xa379dd7b,
+ 0x9b3660c6, 0x9ff77d71, 0x92b45ba8, 0x9675461f,
+ 0x8832161a, 0x8cf30bad, 0x81b02d74, 0x857130c3,
+ 0x5d8a9099, 0x594b8d2e, 0x5408abf7, 0x50c9b640,
+ 0x4e8ee645, 0x4a4ffbf2, 0x470cdd2b, 0x43cdc09c,
+ 0x7b827d21, 0x7f436096, 0x7200464f, 0x76c15bf8,
+ 0x68860bfd, 0x6c47164a, 0x61043093, 0x65c52d24,
+ 0x119b4be9, 0x155a565e, 0x18197087, 0x1cd86d30,
+ 0x029f3d35, 0x065e2082, 0x0b1d065b, 0x0fdc1bec,
+ 0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088,
+ 0x2497d08d, 0x2056cd3a, 0x2d15ebe3, 0x29d4f654,
+ 0xc5a92679, 0xc1683bce, 0xcc2b1d17, 0xc8ea00a0,
+ 0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb, 0xdbee767c,
+ 0xe3a1cbc1, 0xe760d676, 0xea23f0af, 0xeee2ed18,
+ 0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4,
+ 0x89b8fd09, 0x8d79e0be, 0x803ac667, 0x84fbdbd0,
+ 0x9abc8bd5, 0x9e7d9662, 0x933eb0bb, 0x97ffad0c,
+ 0xafb010b1, 0xab710d06, 0xa6322bdf, 0xa2f33668,
+ 0xbcb4666d, 0xb8757bda, 0xb5365d03, 0xb1f740b4
+ };
+
+ CRC() {
+ initialiseCRC();
+ }
+
+ void initialiseCRC() {
+ globalCrc = 0xffffffff;
+ }
+
+ int getFinalCRC() {
+ return ~globalCrc;
+ }
+
+ int getGlobalCRC() {
+ return globalCrc;
+ }
+
+ void setGlobalCRC(int newCrc) {
+ globalCrc = newCrc;
+ }
+
+ void updateCRC(int inCh) {
+ int temp = (globalCrc >> 24) ^ inCh;
+ if (temp < 0) {
+ temp = 256 + temp;
+ }
+ globalCrc = (globalCrc << 8) ^ CRC.crc32Table[temp];
+ }
+
+ void updateCRC(int inCh, int repeat) {
+ int globalCrcShadow = this.globalCrc;
+ while (repeat-- > 0) {
+ int temp = (globalCrcShadow >> 24) ^ inCh;
+ globalCrcShadow = (globalCrcShadow << 8) ^ crc32Table[(temp >= 0)
+ ? temp
+ : (temp + 256)];
+ }
+ this.globalCrc = globalCrcShadow;
+ }
+
+ int globalCrc;
+}
+
Property changes on: trunk/Jmol/src/org/apache/tools/bzip2/CRC.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2017-06-27 04:28:53 UTC
(rev 21642)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2017-06-27 07:36:29 UTC
(rev 21643)
@@ -669,6 +669,9 @@
if (Rdr.isGzipS(bis))
bis = Rdr.getUnzippedInputStream(vwr.getJzt(), bis);
// if we have a subFileList, we don't want to return the stream for the
zip file itself
+ else if (Rdr.isBZip2S(bis))
+ bis = Rdr.getUnzippedInputStreamBZip2(vwr.getJzt(), bis);
+ // if we have a subFileList, we don't want to return the stream for the
zip file itself
if (forceInputStream && subFileList == null)
return bis;
if (Rdr.isCompoundDocumentS(bis)) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-27 04:28:53 UTC
(rev 21642)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-27 07:36:29 UTC
(rev 21643)
@@ -56,9 +56,14 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.19.2"
+Jmol.___JmolVersion="14.20.1"
+new feature: BZ2 compressed file reader
+ -- uses org.apache.tools.bzip2.CBZip2InputStream v. 1.9.6
+ -- Apache license
+
bug fix: SMILES generator can show wrong @/@@ or stereochemical type for some
allenes and cumulenes
+bug fix: CIPChirality Rule 4b fixes
JmolVersion="14.19.1" // 2017.06.25
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