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- cataloged all the licenses for the libraries Gridworks depends on

Browse Source 
- added the secondstring libraries that contains all sorts of useful string distance functions
- added a java arithmetic coding library (used to implement a string distance based on PPM arithmetic coding)
- added the vicino kNN string clustering library (from MIT's SIMILE)


git-svn-id: http://google-refine.googlecode.com/svn/trunk@181 7d457c2a-affb-35e4-300a-418c747d4874
This commit is contained in:
Stefano Mazzocchi 2010-03-04 00:29:52 +00:00
parent 5a0a8bea4f
commit c07431fb88
39 changed files with 4130 additions and 2 deletions
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.classpath
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<classpathentry kind="lib" path="lib/json-20100208.jar" sourcepath="lib-src/json-20100208-sources.jar"/> <classpathentry kind="lib" path="lib/json-20100208.jar" sourcepath="lib-src/json-20100208-sources.jar"/>
<classpathentry kind="lib" path="lib/icu4j-4.2.1.jar" sourcepath="lib-src/icu4j-4.2.1-sources.jar"/> <classpathentry kind="lib" path="lib/icu4j-4.2.1.jar" sourcepath="lib-src/icu4j-4.2.1-sources.jar"/>
<classpathentry kind="lib" path="lib/cos-20081226.jar" sourcepath="lib-src/cos-20081226-sources.jar"/> <classpathentry kind="lib" path="lib/cos-20081226.jar" sourcepath="lib-src/cos-20081226-sources.jar"/>
<classpathentry kind="lib" path="lib/arithcode-1.1.jar" sourcepath="lib-src/arithcode-1.1-sources.jar"/>
<classpathentry kind="lib" path="lib/jdatapath-alpha2.jar" sourcepath="lib-src/jdatapath-alpha2-sources.jar"/>
<classpathentry kind="lib" path="lib/secondstring-20100303.jar" sourcepath="lib-src/secondstring-20100303-sources.jar"/>
<classpathentry kind="lib" path="lib/poi-3.6.jar"/> <classpathentry kind="lib" path="lib/poi-3.6.jar"/>
<classpathentry kind="lib" path="lib/poi-ooxml-3.6.jar"/> <classpathentry kind="lib" path="lib/poi-ooxml-3.6.jar"/>
<classpathentry kind="lib" path="lib/jdatapath-alpha2.jar" sourcepath="lib-src/jdatapath-alpha2-sources.jar"/>
<classpathentry kind="output" path="build/classes"/> <classpathentry kind="output" path="build/classes"/>
</classpath> </classpath>

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/* /*
* (c) Copyright 2010 Metaweb Technologies, Inc. All rights reserved. * (c) Copyright 2010 Metaweb Technologies, Inc. All rights reserved.
*
*/ */
See the 'licenses' directory for a list of the licenses for the libraries we depend on,
ordered here by license:
licenses/apache2.0.LICENSE.txt
jetty
jetty-util
servlet-api
commons-lang
commons-codec
log4j
xmlbeans
poi
poi-ooxml
poi-ooxml-schemas
jdatapath
licenses/secondstring.LICENSE.txt (BSD family)
secondstring
licenses/dom4j.LICENSE.txt (BSD family)
dom4j
licenses/simile.LICENSE.txt (BSD family)
vicino
licenses/arithcode.LICENSE.txt (BSD family)
arithcode
licenses/icu4j.LICENSE.txt (MIT family)
icu4j
licenses/slf4j.LICENSE.txt (MIT family)
slf4j-api
slf4j-log4j12
jcl-over-slf4j
licenses/json.LICENSE.txt (MIT family)
json
licenses/cos.LICENSE.txt
cos

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Copyright (c) 2002, Bob Carpenter.
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Redistribution and use of this software and associated documentation ("Software"),
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Copyright 2001-2005 (C) MetaStuff, Ltd. All Rights Reserved.

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@ -0,0 +1,28 @@
ICU License - ICU 1.8.1 and later
COPYRIGHT AND PERMISSION NOTICE
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Copyright (c) 2002 JSON.org
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copies or substantial portions of the Software.
The Software shall be used for Good, not Evil.
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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Copyright (c) 2003 Carnegie Mellon University
All rights reserved.
Developed by: Center for Automated Learning and Discovery
Carnegie Mellon University
http://www.cald.cs.cmu.edu
The design and implementation of this software was supported in
part by National Science Foundation Grant No. EIA-0131884 to the
National Institute of Statistical Sciences, and by a contract
from the Army Research Office to the Center for Computer and
Communications Security with Carnegie Mellon University.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal with the Software without restriction, including
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distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
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or Carnegie Mellon University, nor the names of its contributors may
be used to endorse or promote products derived from this Software
without specific prior written permission. THE SOFTWARE IS PROVIDED
"AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
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PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS WITH THE SOFTWARE.
[This is an instance of the University of Illinois/NCSA Open Source
agreement, obtained from http://www.opensource.org/licenses/UoI-NCSA.php]

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/*
* (c) Copyright Massachusetts Institute of Technology & Contributors.
*
* 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.
*
* 3. The name of the author may not be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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.
*
*/

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Copyright (c) 2004-2008 QOS.ch
All rights reserved.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
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The above copyright notice and this permission notice shall be
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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package edu.mit.simile.vicino;
public interface Distance {
public float d(String x, String y);
}

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package edu.mit.simile.vicino;
import java.util.List;
import edu.mit.simile.vicino.Distance;
public class Distributor extends Operator {
private static final int COLUMNS = 70;
private static final char CHAR = '=';
public static void main(String[] args) throws Exception {
Distance d = getDistance(args[0]);
List<String> strings = getStrings(args[1]);
int buckets = Integer.parseInt(args[2]);
long start = System.currentTimeMillis();
int[] values = new int[buckets];
int size = strings.size();
for (int i = 0; i < size; i++) {
String x = (String) strings.get((int) (Math.random() * size));
String y = (String) strings.get((int) (Math.random() * size));
int dist = (int) (buckets * d.d(x, y));
values[dist]++;
System.out.print(".");
}
System.out.println();
long stop = System.currentTimeMillis();
float m = ((float) (stop - start)) / (float) size;
int maxValue = 0;
for (int i = 0; i < buckets; i++) {
if (values[i] > maxValue) {
maxValue = values[i];
}
}
System.out
.println("+-------------------------------------------------------------------");
for (int i = 0; i < buckets; i++) {
System.out.println("|" + bar(COLUMNS * values[i] / maxValue));
}
System.out
.println("+-------------------------------------------------------------------");
System.out.println("\n Each distance calculation took: " + m + " millis");
}
static private String bar(int value) {
StringBuffer b = new StringBuffer(value);
for (int i = 0; i < value; i++) {
b.append(CHAR);
}
return b.toString();
}
}

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package edu.mit.simile.vicino;
public class Meter extends Operator {
public static void main(String[] args) throws Exception {
Distance d = getDistance(args[0]);
System.out.println(args[1] + " <- " + d.d(args[1], args[2]) + " -> " + args[2]);
}
}

47
src/main/java/edu/mit/simile/vicino/Operator.java Normal file
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package edu.mit.simile.vicino;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
public class Operator {
static void log(String msg) {
System.out.println(msg);
}
static Distance getDistance(String distance) throws Exception {
return (Distance) Class.forName("edu.mit.simile.vicino.distances." + distance + "Distance").newInstance();
}
static List<String> getStrings(String fileName) throws IOException {
ArrayList<String> strings = new ArrayList<String>();
File file = new File(fileName);
if (file.isDirectory()) {
File[] files = file.listFiles();
for (int i = 0; i < files.length; i++) {
BufferedReader input = new BufferedReader(new FileReader(files[i]));
StringBuffer b = new StringBuffer();
String line;
while ((line = input.readLine()) != null) {
b.append(line.trim());
}
input.close();
strings.add(b.toString());
}
} else {
BufferedReader input = new BufferedReader(new FileReader(fileName));
String line;
while ((line = input.readLine()) != null) {
strings.add(line.trim());
}
input.close();
}
return strings;
}
}

52
src/main/java/edu/mit/simile/vicino/Seeker.java Normal file
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package edu.mit.simile.vicino;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.util.Iterator;
import java.util.List;
import edu.mit.simile.vicino.vptree.VPTree;
import edu.mit.simile.vicino.vptree.VPTreeBuilder;
import edu.mit.simile.vicino.vptree.VPTreeSeeker;
public class Seeker extends Operator {
public static void main(String[] args) throws Exception {
Distance d = getDistance(args[0]);
log("Working with distance: " + d);
List<String> strings = getStrings(args[1]);
log("Obtained " + strings.size() + " from " + args[1]);
log("Building VPTree...");
VPTreeBuilder builder = new VPTreeBuilder(d);
VPTree tree = builder.buildVPTree(strings);
log("..done");
VPTreeSeeker seeker = new VPTreeSeeker(d, tree);
log("type a string|range then hit return:");
BufferedReader input = new BufferedReader(new InputStreamReader(
System.in));
String line = null;
while ((line = input.readLine()) != null) {
int index = line.indexOf('|');
String query = line.substring(0, index);
float range = Float.parseFloat(line.substring(index + 1));
long start = System.currentTimeMillis();
List<? extends Serializable> results = seeker.range(query, range);
long stop = System.currentTimeMillis();
Iterator<? extends Serializable> j = results.iterator();
if (j.hasNext()) {
while (j.hasNext()) {
String r = (String) j.next();
log(" " + r);
}
log(" [done in " + (stop - start) + "ms]");
} else {
log(" [no results found in " + (stop - start) + "ms]");
}
}
}
}

50
src/main/java/edu/mit/simile/vicino/Tester.java Normal file
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package edu.mit.simile.vicino;
import java.util.List;
public class Tester extends Operator {
public static void main(String[] args) throws Exception {
Distance d = getDistance(args[0]);
List<String> strings = getStrings(args[1]);
long start = System.currentTimeMillis();
int size = strings.size();
for (int i = 0; i < size; i++) {
String x = (String) strings.get((int) (Math.random() * size));
String y = (String) strings.get((int) (Math.random() * size));
String z = (String) strings.get((int) (Math.random() * size));
boolean metric = metric(x, y, z, d);
if (metric) {
System.out.println("metric");
} else {
System.out.println("***** NOT METRIC *****");
}
}
long stop = System.currentTimeMillis();
float m = ((float) (stop - start)) / (float) size;
System.out.println("\n Each metric evaluation took: " + m + " millis");
}
static boolean metric(String x, String y, String z, Distance d) {
float dxx = d.d(x, x);
boolean identity = (dxx == 0.0f);
float dxy = d.d(x, y);
float dyx = d.d(y, x);
boolean simmetrical = (dxy == dyx);
float dxz = d.d(x, z);
float dyz = d.d(y, z);
boolean triangular = (dxz <= dxy + dyz);
return (identity && simmetrical && triangular);
}
static Distance getDistance(String distance) throws Exception {
return (Distance) Class.forName(
"edu.mit.simile.vicino.distances." + distance + "Distance")
.newInstance();
}
}

26
src/main/java/edu/mit/simile/vicino/distances/BZip2Distance.java Normal file
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package edu.mit.simile.vicino.distances;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import org.apache.tools.bzip2.CBZip2OutputStream;
public class BZip2Distance extends PseudoMetricDistance {
public float d2(String x, String y) {
String str = x + y;
float result = 0.0f;
try {
ByteArrayOutputStream baos = new ByteArrayOutputStream(str.length());
CBZip2OutputStream os = new CBZip2OutputStream(baos);
os.write(str.getBytes());
os.close();
baos.close();
result = baos.toByteArray().length;
} catch (IOException e) {
e.printStackTrace();
}
return result;
}
}

26
src/main/java/edu/mit/simile/vicino/distances/GZipDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.zip.GZIPOutputStream;
public class GZipDistance extends PseudoMetricDistance {
public float d2(String x, String y) {
String str = x + y;
float result = 0.0f;
try {
ByteArrayOutputStream baos = new ByteArrayOutputStream(str.length());
GZIPOutputStream os = new GZIPOutputStream(baos);
os.write(str.getBytes());
os.close();
baos.close();
result = baos.toByteArray().length;
} catch (IOException e) {
e.printStackTrace();
}
return result;
}
}

18
src/main/java/edu/mit/simile/vicino/distances/JaccardDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import com.wcohen.ss.Jaccard;
import com.wcohen.ss.api.StringDistance;
public class JaccardDistance extends MetricDistance {
StringDistance distance;
public JaccardDistance() {
this.distance = new Jaccard();
}
protected float d2(String x, String y) {
return Math.abs((float) this.distance.score(x, y) - 1.0f);
}
}

18
src/main/java/edu/mit/simile/vicino/distances/JaroDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import com.wcohen.ss.Jaro;
import com.wcohen.ss.api.StringDistance;
public class JaroDistance extends MetricDistance {
StringDistance distance;
public JaroDistance() {
this.distance = new Jaro();
}
protected float d2(String x, String y) {
return Math.abs((float) this.distance.score(x, y) - 1.0f);
}
}

22
src/main/java/edu/mit/simile/vicino/distances/LevensteinDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import com.wcohen.ss.Levenstein;
import com.wcohen.ss.api.StringDistance;
import edu.mit.simile.vicino.Distance;
public class LevensteinDistance implements Distance {
StringDistance distance;
public LevensteinDistance() {
this.distance = new Levenstein();
}
public float d(String x, String y) {
float d = Math.abs((float) this.distance.score(x, y));
// System.out.println(this.distance.explainScore(x,y));
return d / (x.length() + y.length());
}
}

19
src/main/java/edu/mit/simile/vicino/distances/MetricDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import edu.mit.simile.vicino.Distance;
public abstract class MetricDistance implements Distance {
/*
* public float d(String x,String y) { float dxy = d2(x,y); float dx =
* d2(x,""); float dy = d2(y,""); float result = dxy / (dx + dy); return
* result; }
*/
public float d(String x, String y) {
return d2(x, y);
}
abstract float d2(String x, String y);
}

27
src/main/java/edu/mit/simile/vicino/distances/PPMDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import com.colloquial.arithcode.ArithCodeOutputStream;
import com.colloquial.arithcode.PPMModel;
public class PPMDistance extends PseudoMetricDistance {
public float d2(String x, String y) {
String str = x + y;
float result = 0.0f;
try {
ByteArrayOutputStream baos = new ByteArrayOutputStream(str.length());
ArithCodeOutputStream os = new ArithCodeOutputStream(baos,new PPMModel(8));
os.write(str.getBytes());
os.close();
baos.close();
result = baos.toByteArray().length;
} catch (IOException e) {
e.printStackTrace();
}
return result;
}
}

17
src/main/java/edu/mit/simile/vicino/distances/PseudoMetricDistance.java Normal file
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package edu.mit.simile.vicino.distances;
import edu.mit.simile.vicino.Distance;
public abstract class PseudoMetricDistance implements Distance {
public float d(String x, String y) {
float cxx = d2(x, x);
float cyy = d2(y, y);
float cxy = d2(x, y);
float cyx = d2(y, x);
float result1 = (cxy + cyx) / (cxx + cyy) - 1.0f;
return result1;
}
protected abstract float d2(String x, String y);
}

42
src/main/java/edu/mit/simile/vicino/vptree/Node.java Executable file
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package edu.mit.simile.vicino.vptree;
import java.io.Serializable;
/**
* This class represent a couple (Object, distance) value of that Object from
* the Vp in each step of the algorithm.
*
* @author Paolo Ciccarese
*/
public class Node implements Serializable {
private static final long serialVersionUID = -2077473220894258550L;
private final Serializable obj;
private float distance;
public Node(Serializable obj, int i) {
this.obj = obj;
this.distance = i;
}
public Node(Serializable obj) {
this.obj = obj;
}
public Serializable get() {
return this.obj;
}
public void setDistance(float distance) {
this.distance = distance;
}
public float getDistance() {
return distance;
}
public String toString() {
return obj.toString();
}
}

94
src/main/java/edu/mit/simile/vicino/vptree/NodeSorter.java Executable file
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package edu.mit.simile.vicino.vptree;
public class NodeSorter {
/**
* Sort array of Objects using the QuickSort algorithm.
*
* @param s
* An Object[].
* @param lo
* The current lower bound.
* @param hi
* The current upper bound.
*/
public static void sort(Node nodes[], int lo, int hi) {
if (lo >= hi) {
return;
}
/*
* Use median-of-three(lo, mid, hi) to pick a partition. Also swap them
* into relative order while we are at it.
*/
int mid = (lo + hi) / 2;
if (nodes[lo].getDistance() > nodes[mid].getDistance()) {
// Swap.
Node tmp = nodes[lo];
nodes[lo] = nodes[mid];
nodes[mid] = tmp;
}
if (nodes[mid].getDistance() > nodes[hi].getDistance()) {
// Swap .
Node tmp = nodes[mid];
nodes[mid] = nodes[hi];
nodes[hi] = tmp;
if (nodes[lo].getDistance() > nodes[mid].getDistance()) {
// Swap.
Node tmp2 = nodes[lo];
nodes[lo] = nodes[mid];
nodes[mid] = tmp2;
}
}
// Start one past lo since already handled lo.
int left = lo + 1;
// Similarly, end one before hi since already handled hi.
int right = hi - 1;
// If there are three or fewer elements, we are done.
if (left >= right) {
return;
}
Node partition = nodes[mid];
while (true) {
while (nodes[right].getDistance() > partition.getDistance()) {
--right;
}
while (left < right && nodes[left].getDistance() <= partition.getDistance()) {
++left;
}
if (left < right) {
// Swap.
Node tmp = nodes[left];
nodes[left] = nodes[right];
nodes[right] = tmp;
--right;
} else {
break;
}
}
sort(nodes, lo, left);
sort(nodes, left + 1, hi);
}
/**
* Sorts and array of objects.
*/
public void sort(Node nodes[]) {
NodeSorter.sort(nodes, 0, nodes.length - 1);
}
}

52
src/main/java/edu/mit/simile/vicino/vptree/TNode.java Executable file
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package edu.mit.simile.vicino.vptree;
import java.io.Serializable;
/**
* @author Paolo Ciccarese
*/
public class TNode implements Serializable {
private static final long serialVersionUID = -217604190976851241L;
private final Serializable obj;
private float median;
private TNode left;
private TNode right;
/**
* The Object will be fixed during the instantiation of the node, while the
* children will be defined in another iteration of the algorithm,
*/
public TNode(Serializable obj) {
this.obj = obj;
}
public Serializable get() {
return this.obj;
}
public void setMedian(float median) {
this.median = median;
}
public float getMedian() {
return median;
}
public void setLeft(TNode leftNode) {
this.left = leftNode;
}
public TNode getLeft() {
return left;
}
public void setRight(TNode rightNode) {
this.right = rightNode;
}
public TNode getRight() {
return right;
}
}

33
src/main/java/edu/mit/simile/vicino/vptree/VPTree.java Executable file
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package edu.mit.simile.vicino.vptree;
import java.io.Serializable;
/**
* The VPTree class.
*
* @author Paolo Ciccarese
*/
public class VPTree implements Serializable {
private static final long serialVersionUID = 1291056732155841123L;
private TNode root;
/**
* Sets the root of the VPTree.
*
* @param root The VPTree root.
*/
public void setRoot(TNode root) {
this.root = root;
}
/**
* Get the root of the VPTree.
*
* @return The VPTree root.
*/
public TNode getRoot() {
return root;
}
}

101
src/main/java/edu/mit/simile/vicino/vptree/VPTreeBuilder.java Executable file
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package edu.mit.simile.vicino.vptree;
import java.io.Serializable;
import java.util.Collection;
import java.util.Iterator;
import java.util.Random;
import edu.mit.simile.vicino.Distance;
/**
* @author Paolo Ciccarese
* @author Stefano Mazzocchi
*/
public class VPTreeBuilder {
private static final boolean DEBUG = false;
private Random generator = new Random(System.currentTimeMillis());
private VPTree tree;
private final Distance distance;
/**
* Defines a VPTree Builder for a specific distance.
*
* @param distance The class implementing the distance.
*/
public VPTreeBuilder(Distance distance) {
this.distance = distance;
}
public VPTree buildVPTree(Collection<? extends Serializable> col) {
Node nodes[] = new Node[col.size()];
Iterator<? extends Serializable> i = col.iterator();
int counter = 0;
while (i.hasNext()) {
Serializable s = (Serializable) i.next();
nodes[counter++] = new Node(s);
}
tree = new VPTree();
tree.setRoot(addNode(nodes, 0, nodes.length - 1));
return tree;
}
private TNode addNode(Node nodes[], int begin, int end) {
int delta = end - begin;
int middle = begin + delta / 2;
TNode node = new TNode(nodes[begin + getRandomIndex(delta)].get());
if (DEBUG) System.out.println("\nnode: " + node.get().toString());
calculateDistances(node, nodes, begin, end);
orderDistances(nodes, begin, end);
if (DEBUG) {
for (int i = begin; i <= end; i++) {
System.out.println(" +-- " + nodes[i].getDistance() + " --> " + nodes[i].get());
}
}
if (delta + 1 > 0) {
if (middle - (begin + 1) >= 1) {
node.setLeft(addNode(nodes, begin + 1, middle));
if (DEBUG) System.out.println(" L --> " + node.getLeft().get());
} else if (middle - (begin + 1) == 0) {
node.setLeft(new TNode(nodes[middle].get()));
if (DEBUG) System.out.println(" L --> " + node.getLeft().get());
}
if ((end - (middle + 1)) >= 1) {
node.setRight(addNode(nodes, middle + 1, end));
if (DEBUG) System.out.println(" R --> " + node.getRight().get());
} else if (end - (middle + 1) == 0) {
node.setRight(new TNode(nodes[middle + 1].get()));
if (DEBUG) System.out.println(" R --> " + node.getRight().get());
}
}
return node;
}
private void calculateDistances(TNode pivot, Node nodes[], int begin, int end) {
for (int i = begin; i <= end; i++) {
Object x = pivot.get();
Object y = nodes[i].get();
float d = (x == y) ? 0.0f : distance.d(x.toString(), y.toString());
nodes[i].setDistance(d);
}
}
private void orderDistances(Node nodes[], int begin, int end) {
NodeSorter.sort(nodes, begin, end);
}
private int getRandomIndex(int max) {
return generator.nextInt(max);
}
}

48
src/main/java/edu/mit/simile/vicino/vptree/VPTreeSeeker.java Executable file
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package edu.mit.simile.vicino.vptree;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import edu.mit.simile.vicino.Distance;
/**
* @author Paolo Ciccarese
*/
public class VPTreeSeeker {
VPTree tree;
Distance distance;
public VPTreeSeeker(Distance distance, VPTree tree) {
this.distance = distance;
this.tree = tree;
}
public List<? extends Serializable> range(Object query, float range) {
return rangeTraversal(query, range, tree.getRoot(), new ArrayList<Serializable>());
}
private List<Serializable> rangeTraversal(Object query, float range, TNode tNode, List<Serializable> results) {
if (tNode != null) {
float distance = this.distance.d(query.toString(), tNode.toString());
if (distance < range) {
results.add(tNode.get());
}
if ((distance + range) < tNode.getMedian()) {
rangeTraversal(query, range, tNode.getLeft(), results);
} else if ((distance - range) > tNode.getMedian()) {
rangeTraversal(query, range, tNode.getRight(), results);
} else {
rangeTraversal(query, range, tNode.getLeft(), results);
rangeTraversal(query, range, tNode.getRight(), results);
}
}
return results;
}
}

136
src/main/java/org/apache/tools/bzip2/BZip2Constants.java Normal file
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/*
* The Apache Software License, Version 1.1
*
* Copyright (c) 2001 The Apache Software Foundation. All rights
* reserved.
*
* 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.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "Ant" and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Group.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 APACHE SOFTWARE FOUNDATION OR
* ITS 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.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
/*
* This package is based on the work done by Keiron Liddle, Aftex Software
* <keiron@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.
*
* @author <a href="mailto:keiron@aftexsw.com">Keiron Liddle</a>
*/
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;
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
};
}

865
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@ -0,0 +1,865 @@
/*
* The Apache Software License, Version 1.1
*
* Copyright (c) 2001-2003 The Apache Software Foundation. All rights
* reserved.
*
* 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.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "Ant" and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Group.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 APACHE SOFTWARE FOUNDATION OR
* ITS 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.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
/*
* This package is based on the work done by Keiron Liddle, Aftex Software
* <keiron@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.
*
* @author <a href="mailto:keiron@aftexsw.com">Keiron Liddle</a>
*/
public class CBZip2InputStream extends InputStream implements BZip2Constants {
private static void cadvise() {
System.out.println("CRC Error");
//throw new CCoruptionError();
}
private static void compressedStreamEOF() {
cadvise();
}
private void makeMaps() {
int i;
nInUse = 0;
for (i = 0; i < 256; i++) {
if (inUse[i]) {
seqToUnseq[nInUse] = (char) i;
unseqToSeq[i] = (char) nInUse;
nInUse++;
}
}
}
/*
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 CRC mCrc = new CRC();
private boolean[] inUse = new boolean[256];
private int nInUse;
private char[] seqToUnseq = new char[256];
private char[] unseqToSeq = new char[256];
private char[] selector = new char[MAX_SELECTORS];
private char[] selectorMtf = new char[MAX_SELECTORS];
private int[] tt;
private char[] ll8;
/*
freq table collected to save a pass over the data
during decompression.
*/
private int[] unzftab = new int[256];
private int[][] limit = new int[N_GROUPS][MAX_ALPHA_SIZE];
private int[][] base = new int[N_GROUPS][MAX_ALPHA_SIZE];
private int[][] perm = new int[N_GROUPS][MAX_ALPHA_SIZE];
private int[] minLens = new int[N_GROUPS];
private InputStream bsStream;
private boolean streamEnd = false;
private int currentChar = -1;
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;
int i2, count, chPrev, ch2;
int i, tPos;
int rNToGo = 0;
int rTPos = 0;
int j2;
char z;
public CBZip2InputStream(InputStream zStream) {
ll8 = null;
tt = null;
bsSetStream(zStream);
initialize();
initBlock();
setupBlock();
}
public int read() {
if (streamEnd) {
return -1;
} else {
int retChar = currentChar;
switch(currentState) {
case START_BLOCK_STATE:
break;
case RAND_PART_A_STATE:
break;
case RAND_PART_B_STATE:
setupRandPartB();
break;
case RAND_PART_C_STATE:
setupRandPartC();
break;
case NO_RAND_PART_A_STATE:
break;
case NO_RAND_PART_B_STATE:
setupNoRandPartB();
break;
case NO_RAND_PART_C_STATE:
setupNoRandPartC();
break;
default:
break;
}
return retChar;
}
}
private void initialize() {
char magic3, magic4;
magic3 = bsGetUChar();
magic4 = bsGetUChar();
if (magic3 != 'h' || magic4 < '1' || magic4 > '9') {
bsFinishedWithStream();
streamEnd = true;
return;
}
setDecompressStructureSizes(magic4 - '0');
computedCombinedCRC = 0;
}
private void initBlock() {
char magic1, magic2, magic3, magic4;
char magic5, magic6;
magic1 = bsGetUChar();
magic2 = bsGetUChar();
magic3 = bsGetUChar();
magic4 = bsGetUChar();
magic5 = bsGetUChar();
magic6 = bsGetUChar();
if (magic1 == 0x17 && magic2 == 0x72 && magic3 == 0x45
&& magic4 == 0x38 && magic5 == 0x50 && magic6 == 0x90) {
complete();
return;
}
if (magic1 != 0x31 || magic2 != 0x41 || magic3 != 0x59
|| magic4 != 0x26 || magic5 != 0x53 || magic6 != 0x59) {
badBlockHeader();
streamEnd = true;
return;
}
storedBlockCRC = bsGetInt32();
if (bsR(1) == 1) {
blockRandomised = true;
} else {
blockRandomised = false;
}
// currBlockNo++;
getAndMoveToFrontDecode();
mCrc.initialiseCRC();
currentState = START_BLOCK_STATE;
}
private void endBlock() {
computedBlockCRC = mCrc.getFinalCRC();
/* A bad CRC is considered a fatal error. */
if (storedBlockCRC != computedBlockCRC) {
crcError();
}
computedCombinedCRC = (computedCombinedCRC << 1)
| (computedCombinedCRC >>> 31);
computedCombinedCRC ^= computedBlockCRC;
}
private void complete() {
storedCombinedCRC = bsGetInt32();
if (storedCombinedCRC != computedCombinedCRC) {
crcError();
}
bsFinishedWithStream();
streamEnd = true;
}
private static void blockOverrun() {
cadvise();
}
private static void badBlockHeader() {
cadvise();
}
private static void crcError() {
cadvise();
}
private void bsFinishedWithStream() {
try {
if (this.bsStream != null) {
if (this.bsStream != System.in) {
this.bsStream.close();
this.bsStream = null;
}
}
} catch (IOException ioe) {
//ignore
}
}
private void bsSetStream(InputStream f) {
bsStream = f;
bsLive = 0;
bsBuff = 0;
}
private int bsR(int n) {
int v;
while (bsLive < n) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
if (thech == -1) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
v = (bsBuff >> (bsLive - n)) & ((1 << n) - 1);
bsLive -= n;
return v;
}
private char bsGetUChar() {
return (char) bsR(8);
}
private int bsGetint() {
int u = 0;
u = (u << 8) | bsR(8);
u = (u << 8) | bsR(8);
u = (u << 8) | bsR(8);
u = (u << 8) | bsR(8);
return u;
}
private int bsGetIntVS(int numBits) {
return (int) bsR(numBits);
}
private int bsGetInt32() {
return (int) bsGetint();
}
private void hbCreateDecodeTables(int[] limit, int[] base,
int[] perm, char[] length,
int minLen, int maxLen, int alphaSize) {
int pp, i, j, vec;
pp = 0;
for (i = minLen; i <= maxLen; i++) {
for (j = 0; j < alphaSize; j++) {
if (length[j] == i) {
perm[pp] = j;
pp++;
}
}
}
for (i = 0; i < MAX_CODE_LEN; i++) {
base[i] = 0;
}
for (i = 0; i < alphaSize; i++) {
base[length[i] + 1]++;
}
for (i = 1; i < MAX_CODE_LEN; i++) {
base[i] += base[i - 1];
}
for (i = 0; i < MAX_CODE_LEN; i++) {
limit[i] = 0;
}
vec = 0;
for (i = minLen; i <= maxLen; i++) {
vec += (base[i + 1] - base[i]);
limit[i] = vec - 1;
vec <<= 1;
}
for (i = minLen + 1; i <= maxLen; i++) {
base[i] = ((limit[i - 1] + 1) << 1) - base[i];
}
}
private void recvDecodingTables() {
char len[][] = new char[N_GROUPS][MAX_ALPHA_SIZE];
int i, j, t, nGroups, nSelectors, alphaSize;
int minLen, maxLen;
boolean[] inUse16 = new boolean[16];
/* Receive the mapping table */
for (i = 0; i < 16; i++) {
if (bsR(1) == 1) {
inUse16[i] = true;
} else {
inUse16[i] = false;
}
}
for (i = 0; i < 256; i++) {
inUse[i] = false;
}
for (i = 0; i < 16; i++) {
if (inUse16[i]) {
for (j = 0; j < 16; j++) {
if (bsR(1) == 1) {
inUse[i * 16 + j] = true;
}
}
}
}
makeMaps();
alphaSize = nInUse + 2;
/* Now the selectors */
nGroups = bsR(3);
nSelectors = bsR(15);
for (i = 0; i < nSelectors; i++) {
j = 0;
while (bsR(1) == 1) {
j++;
}
selectorMtf[i] = (char) j;
}
/* Undo the MTF values for the selectors. */
{
char[] pos = new char[N_GROUPS];
char tmp, v;
for (v = 0; v < nGroups; v++) {
pos[v] = v;
}
for (i = 0; i < nSelectors; i++) {
v = selectorMtf[i];
tmp = pos[v];
while (v > 0) {
pos[v] = pos[v - 1];
v--;
}
pos[0] = tmp;
selector[i] = tmp;
}
}
/* Now the coding tables */
for (t = 0; t < nGroups; t++) {
int curr = bsR(5);
for (i = 0; i < alphaSize; i++) {
while (bsR(1) == 1) {
if (bsR(1) == 0) {
curr++;
} else {
curr--;
}
}
len[t][i] = (char) curr;
}
}
/* Create the Huffman decoding tables */
for (t = 0; t < nGroups; t++) {
minLen = 32;
maxLen = 0;
for (i = 0; i < alphaSize; i++) {
if (len[t][i] > maxLen) {
maxLen = len[t][i];
}
if (len[t][i] < minLen) {
minLen = len[t][i];
}
}
hbCreateDecodeTables(limit[t], base[t], perm[t], len[t], minLen,
maxLen, alphaSize);
minLens[t] = minLen;
}
}
private void getAndMoveToFrontDecode() {
char[] yy = new char[256];
int i, j, nextSym, limitLast;
int EOB, groupNo, groupPos;
limitLast = baseBlockSize * blockSize100k;
origPtr = bsGetIntVS(24);
recvDecodingTables();
EOB = nInUse + 1;
groupNo = -1;
groupPos = 0;
/*
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 (i = 0; i <= 255; i++) {
unzftab[i] = 0;
}
for (i = 0; i <= 255; i++) {
yy[i] = (char) i;
}
last = -1;
{
int zt, zn, zvec, zj;
if (groupPos == 0) {
groupNo++;
groupPos = G_SIZE;
}
groupPos--;
zt = selector[groupNo];
zn = minLens[zt];
zvec = bsR(zn);
while (zvec > limit[zt][zn]) {
zn++;
{
{
while (bsLive < 1) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
if (thech == -1) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
}
zj = (bsBuff >> (bsLive - 1)) & 1;
bsLive--;
}
zvec = (zvec << 1) | zj;
}
nextSym = perm[zt][zvec - base[zt][zn]];
}
while (true) {
if (nextSym == EOB) {
break;
}
if (nextSym == RUNA || nextSym == RUNB) {
char ch;
int s = -1;
int N = 1;
do {
if (nextSym == RUNA) {
s = s + (0 + 1) * N;
} else if (nextSym == RUNB) {
s = s + (1 + 1) * N;
}
N = N * 2;
{
int zt, zn, zvec, zj;
if (groupPos == 0) {
groupNo++;
groupPos = G_SIZE;
}
groupPos--;
zt = selector[groupNo];
zn = minLens[zt];
zvec = bsR(zn);
while (zvec > limit[zt][zn]) {
zn++;
{
{
while (bsLive < 1) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
if (thech == -1) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
}
zj = (bsBuff >> (bsLive - 1)) & 1;
bsLive--;
}
zvec = (zvec << 1) | zj;
}
nextSym = perm[zt][zvec - base[zt][zn]];
}
} while (nextSym == RUNA || nextSym == RUNB);
s++;
ch = seqToUnseq[yy[0]];
unzftab[ch] += s;
while (s > 0) {
last++;
ll8[last] = ch;
s--;
}
if (last >= limitLast) {
blockOverrun();
}
continue;
} else {
char tmp;
last++;
if (last >= limitLast) {
blockOverrun();
}
tmp = yy[nextSym - 1];
unzftab[seqToUnseq[tmp]]++;
ll8[last] = seqToUnseq[tmp];
/*
This loop is hammered during decompression,
hence the unrolling.
for (j = nextSym-1; j > 0; j--) yy[j] = yy[j-1];
*/
j = nextSym - 1;
for (; j > 3; j -= 4) {
yy[j] = yy[j - 1];
yy[j - 1] = yy[j - 2];
yy[j - 2] = yy[j - 3];
yy[j - 3] = yy[j - 4];
}
for (; j > 0; j--) {
yy[j] = yy[j - 1];
}
yy[0] = tmp;
{
int zt, zn, zvec, zj;
if (groupPos == 0) {
groupNo++;
groupPos = G_SIZE;
}
groupPos--;
zt = selector[groupNo];
zn = minLens[zt];
zvec = bsR(zn);
while (zvec > limit[zt][zn]) {
zn++;
{
{
while (bsLive < 1) {
int zzi;
char thech = 0;
try {
thech = (char) bsStream.read();
} catch (IOException e) {
compressedStreamEOF();
}
zzi = thech;
bsBuff = (bsBuff << 8) | (zzi & 0xff);
bsLive += 8;
}
}
zj = (bsBuff >> (bsLive - 1)) & 1;
bsLive--;
}
zvec = (zvec << 1) | zj;
}
nextSym = perm[zt][zvec - base[zt][zn]];
}
continue;
}
}
}
private void setupBlock() {
int[] cftab = new int[257];
char ch;
cftab[0] = 0;
for (i = 1; i <= 256; i++) {
cftab[i] = unzftab[i - 1];
}
for (i = 1; i <= 256; i++) {
cftab[i] += cftab[i - 1];
}
for (i = 0; i <= last; i++) {
ch = (char) ll8[i];
tt[cftab[ch]] = i;
cftab[ch]++;
}
cftab = null;
tPos = tt[origPtr];
count = 0;
i2 = 0;
ch2 = 256; /* not a char and not EOF */
if (blockRandomised) {
rNToGo = 0;
rTPos = 0;
setupRandPartA();
} else {
setupNoRandPartA();
}
}
private void setupRandPartA() {
if (i2 <= last) {
chPrev = ch2;
ch2 = ll8[tPos];
tPos = tt[tPos];
if (rNToGo == 0) {
rNToGo = rNums[rTPos];
rTPos++;
if (rTPos == 512) {
rTPos = 0;
}
}
rNToGo--;
ch2 ^= (int) ((rNToGo == 1) ? 1 : 0);
i2++;
currentChar = ch2;
currentState = RAND_PART_B_STATE;
mCrc.updateCRC(ch2);
} else {
endBlock();
initBlock();
setupBlock();
}
}
private void setupNoRandPartA() {
if (i2 <= last) {
chPrev = ch2;
ch2 = ll8[tPos];
tPos = tt[tPos];
i2++;
currentChar = ch2;
currentState = NO_RAND_PART_B_STATE;
mCrc.updateCRC(ch2);
} else {
endBlock();
initBlock();
setupBlock();
}
}
private void setupRandPartB() {
if (ch2 != chPrev) {
currentState = RAND_PART_A_STATE;
count = 1;
setupRandPartA();
} else {
count++;
if (count >= 4) {
z = ll8[tPos];
tPos = tt[tPos];
if (rNToGo == 0) {
rNToGo = rNums[rTPos];
rTPos++;
if (rTPos == 512) {
rTPos = 0;
}
}
rNToGo--;
z ^= ((rNToGo == 1) ? 1 : 0);
j2 = 0;
currentState = RAND_PART_C_STATE;
setupRandPartC();
} else {
currentState = RAND_PART_A_STATE;
setupRandPartA();
}
}
}
private void setupRandPartC() {
if (j2 < (int) z) {
currentChar = ch2;
mCrc.updateCRC(ch2);
j2++;
} else {
currentState = RAND_PART_A_STATE;
i2++;
count = 0;
setupRandPartA();
}
}
private void setupNoRandPartB() {
if (ch2 != chPrev) {
currentState = NO_RAND_PART_A_STATE;
count = 1;
setupNoRandPartA();
} else {
count++;
if (count >= 4) {
z = ll8[tPos];
tPos = tt[tPos];
currentState = NO_RAND_PART_C_STATE;
j2 = 0;
setupNoRandPartC();
} else {
currentState = NO_RAND_PART_A_STATE;
setupNoRandPartA();
}
}
}
private void setupNoRandPartC() {
if (j2 < (int) z) {
currentChar = ch2;
mCrc.updateCRC(ch2);
j2++;
} else {
currentState = NO_RAND_PART_A_STATE;
i2++;
count = 0;
setupNoRandPartA();
}
}
private void setDecompressStructureSizes(int newSize100k) {
if (!(0 <= newSize100k && newSize100k <= 9 && 0 <= blockSize100k
&& blockSize100k <= 9)) {
// throw new IOException("Invalid block size");
}
blockSize100k = newSize100k;
if (newSize100k == 0) {
return;
}
int n = baseBlockSize * newSize100k;
ll8 = new char[n];
tt = new int[n];
}
}

1665
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167
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/*
* The Apache Software License, Version 1.1
*
* Copyright (c) 2001-2002 The Apache Software Foundation. All rights
* reserved.
*
* 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.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "Ant" and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Group.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 APACHE SOFTWARE FOUNDATION OR
* ITS 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.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
/*
* This package is based on the work done by Keiron Liddle, Aftex Software
* <keiron@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.
*
* @author <a href="mailto:keiron@aftexsw.com">Keiron Liddle</a>
*/
class CRC {
public static 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
};
public 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];
}
int globalCrc;
}