Merge pull request #38 from sdk2/master

change all files "iso-8859-1" to "UTF-8"

jplag.frontend-utils/src/main/java/jplag/UnicodeReader.java

@@ -27,7 +27,7 @@ import java.io.Reader;
  * default is used if: BOM mark is not found and defaultEnc is NULL.<br />
  * 
  * Usage pattern:<pre>
- * String defaultEnc = "ISO-8859-1"; // or NULL to use system default
+ * String defaultEnc = "UTF-8"; // or NULL to use system default
  * FileInputStream fis = new FileInputStream(file);
  * Reader in = new UnicodeReader(fis, defaultEnc);</pre>
  */

jplag.frontend.csharp-1.2/src/main/java/jplag/csharp/Parser.java

@@ -72,7 +72,7 @@ public class Parser extends jplag.Parser implements CSharpTokenConstants {
 			FileInputStream fis = new FileInputStream(new File(dir, file));
 			currentFile = file;
 			// Create a scanner that reads from the input stream passed to us
-			CSharpLexer lexer = new CSharpLexer(new UnicodeReader(fis, "ISO-8859-1"));
+			CSharpLexer lexer = new CSharpLexer(new UnicodeReader(fis, "UTF-8"));
 			lexer.setFilename(file);
 			lexer.setTabSize(1);
 

jplag.frontend.java-1.5/src/main/javacc/Java1.5.jj

@@ -137,11 +137,11 @@ public class JavaParser implements JavaTokenConstants
         try {
             FileInputStream in = new FileInputStream(new File(dir,fileName));
             if (parser == null) {
-                JavaTabModCharStream charStream = new JavaTabModCharStream(new UnicodeReader(in, "ISO-8859-1"));
+                JavaTabModCharStream charStream = new JavaTabModCharStream(new UnicodeReader(in, "UTF-8"));
                 parser = new JavaParser(charStream);
                 parser.charStream = charStream;
             } else {
-                parser.charStream.ReInit(new UnicodeReader(in, "ISO-8859-1"));
+                parser.charStream.ReInit(new UnicodeReader(in, "UTF-8"));
                 parser.ReInit(parser.charStream);
             }
             parser.parser2 = parserX;

jplag.homepage/src/main/webapp/WEB-INF/web.xml

@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="ISO-8859-1"?>
+<?xml version="1.0" encoding="UTF-8"?>
 
 <!DOCTYPE web-app
     PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN"

jplag/pom.xml

@@ -1,230 +1,230 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<artifactId>jplag</artifactId>
-	<version>2.11.9-SNAPSHOT</version>
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <artifactId>jplag</artifactId>
+    <version>2.11.9-SNAPSHOT</version>
 
-	<parent>
-		<groupId>edu.kit.ipd.jplag</groupId>
-		<artifactId>parent</artifactId>
-		<version>0.3-SNAPSHOT</version>
-		<relativePath>../jplag.parent/pom.xml</relativePath>
-	</parent>
+    <parent>
+        <groupId>edu.kit.ipd.jplag</groupId>
+        <artifactId>parent</artifactId>
+        <version>0.3-SNAPSHOT</version>
+        <relativePath>../jplag.parent/pom.xml</relativePath>
+    </parent>
 
-	<repositories>
-		<repository>
-			<id>ipdNexus</id>
-			<name>Recaa Repository</name>
-			<url>http://bob.ipd.kit.edu/nexus/content/repositories/public/</url>
-		</repository>
-	</repositories>
+    <repositories>
+        <repository>
+            <id>ipdNexus</id>
+            <name>Recaa Repository</name>
+            <url>http://bob.ipd.kit.edu/nexus/content/repositories/public/</url>
+        </repository>
+    </repositories>
 
-	<build>
-		<resources>
-			<resource>
-				<directory>src/main/resources</directory>
-				<filtering>true</filtering>
-				<includes>
-					<include>jplag/version.properties</include>
-				</includes>
-			</resource>
-			<resource>
-				<directory>src/main/resources</directory>
-				<filtering>false</filtering>
-				<excludes>
-					<exclude>jplag/version.properties</exclude>
-				</excludes>
-			</resource>
-		</resources>
+    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <filtering>true</filtering>
+                <includes>
+                    <include>jplag/version.properties</include>
+                </includes>
+            </resource>
+            <resource>
+                <directory>src/main/resources</directory>
+                <filtering>false</filtering>
+                <excludes>
+                    <exclude>jplag/version.properties</exclude>
+                </excludes>
+            </resource>
+        </resources>
 
-		<plugins>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>build-helper-maven-plugin</artifactId>
-				<version>1.7</version>
-				<executions>
-					<execution>
-						<id>add-antlr-source</id>
-						<phase>generate-sources</phase>
-						<goals>
-							<goal>add-source</goal>
-						</goals>
-						<configuration>
-							<sources>
-								<source>target/generated-sources/antlr</source>
-								<source>target/generated-sources/javacc</source>
-							</sources>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
+        <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>1.7</version>
+                <executions>
+                    <execution>
+                        <id>add-antlr-source</id>
+                        <phase>generate-sources</phase>
+                        <goals>
+                            <goal>add-source</goal>
+                        </goals>
+                        <configuration>
+                            <sources>
+                                <source>target/generated-sources/antlr</source>
+                                <source>target/generated-sources/javacc</source>
+                            </sources>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
 
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>javacc-maven-plugin</artifactId>
-				<!-- If you need javacc version 3.2 (as did the original jplag) use plugin 
-					version 2.0; plugin version 2.6 uses javacc version 5.0 -->
-				<version>2.6</version>
-				<configuration>
-					<debugParser>false</debugParser>
-					<isStatic>false</isStatic>
-					<!-- we need this since the old plugin does not read the package from 
-						the grammar; as of 2.4 the plugin does that on its own <packageName>jplag.filter</packageName> -->
-				</configuration>
-				<executions>
-					<execution>
-						<id>javacc</id>
-						<goals>
-							<goal>javacc</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>javacc-maven-plugin</artifactId>
+                <!-- If you need javacc version 3.2 (as did the original jplag) use plugin
+                    version 2.0; plugin version 2.6 uses javacc version 5.0 -->
+                <version>2.6</version>
+                <configuration>
+                    <debugParser>false</debugParser>
+                    <isStatic>false</isStatic>
+                    <!-- we need this since the old plugin does not read the package from
+                        the grammar; as of 2.4 the plugin does that on its own <packageName>jplag.filter</packageName> -->
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>javacc</id>
+                        <goals>
+                            <goal>javacc</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
 
-			<plugin>
-				<artifactId>maven-jar-plugin</artifactId>
-				<configuration>
-					<archive>
-						<manifest>
-							<mainClass>jplag.JPlag</mainClass>
-							<packageName>jplag</packageName>
-						</manifest>
-					</archive>
-				</configuration>
-			</plugin>
+            <plugin>
+                <artifactId>maven-jar-plugin</artifactId>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <mainClass>jplag.JPlag</mainClass>
+                            <packageName>jplag</packageName>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
 
-			<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<version>2.4</version>
-				<configuration>
-					<descriptorRefs>
-						<descriptorRef>jar-with-dependencies</descriptorRef>
-					</descriptorRefs>
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <version>2.4</version>
+                <configuration>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
 
-					<archive>
-						<manifest>
-							<mainClass>jplag.JPlag</mainClass>
-							<packageName>jplag</packageName>
-						</manifest>
-					</archive>
-				</configuration>
-			</plugin>
+                    <archive>
+                        <manifest>
+                            <mainClass>jplag.JPlag</mainClass>
+                            <packageName>jplag</packageName>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
 
-			<plugin>
-				<groupId>com.github.wvengen</groupId>
-				<artifactId>proguard-maven-plugin</artifactId>
-				<version>2.0.11</version>
-				<!-- executions>
-					<execution>
-						<phase>package</phase>
-						<goals>
-							<goal>proguard</goal>
-						</goals>
-					</execution>
-				</executions-->
-				<configuration>
-					<proguardVersion>4.8</proguardVersion>
-					<options>
-						<option>-allowaccessmodification</option>
-						<option>-keep public class * extends java.applet.Applet { *; }</option>
-					</options>
-					<libs>
-						<lib>${java.home}/lib/rt.jar</lib>
-					</libs>
-				</configuration>
-				<dependencies>
-				<dependency>
-					<groupId>net.sf.proguard</groupId>
-					<artifactId>proguard-base</artifactId>
-					<version>4.9</version>
-					<scope>runtime</scope>
-					</dependency>
-				</dependencies>
-			</plugin>
+            <plugin>
+                <groupId>com.github.wvengen</groupId>
+                <artifactId>proguard-maven-plugin</artifactId>
+                <version>2.0.11</version>
+                <!-- executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>proguard</goal>
+                        </goals>
+                    </execution>
+                </executions-->
+                <configuration>
+                    <proguardVersion>4.8</proguardVersion>
+                    <options>
+                        <option>-allowaccessmodification</option>
+                        <option>-keep public class * extends java.applet.Applet { *; }</option>
+                    </options>
+                    <libs>
+                        <lib>${java.home}/lib/rt.jar</lib>
+                    </libs>
+                </configuration>
+                <dependencies>
+                    <dependency>
+                        <groupId>net.sf.proguard</groupId>
+                        <artifactId>proguard-base</artifactId>
+                        <version>4.9</version>
+                        <scope>runtime</scope>
+                    </dependency>
+                </dependencies>
+            </plugin>
 
-		</plugins>
-		<pluginManagement>
-			<plugins>
-				<!--This plugin's configuration is used to store Eclipse m2e settings 
-					only. It has no influence on the Maven build itself. -->
-				<plugin>
-					<groupId>org.eclipse.m2e</groupId>
-					<artifactId>lifecycle-mapping</artifactId>
-					<version>1.0.0</version>
-					<configuration>
-						<lifecycleMappingMetadata>
-							<pluginExecutions>
-								<pluginExecution>
-									<pluginExecutionFilter>
-										<groupId>
-											org.codehaus.mojo
-										</groupId>
-										<artifactId>
-											javacc-maven-plugin
-										</artifactId>
-										<versionRange>
-											[2.0],[2.6]
-										</versionRange>
-										<goals>
-											<goal>javacc</goal>
-										</goals>
-									</pluginExecutionFilter>
-									<action>
-										<ignore></ignore>
-									</action>
-								</pluginExecution>
-							</pluginExecutions>
-						</lifecycleMappingMetadata>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-	</build>
+        </plugins>
+        <pluginManagement>
+            <plugins>
+                <!--This plugin's configuration is used to store Eclipse m2e settings
+                    only. It has no influence on the Maven build itself. -->
+                <plugin>
+                    <groupId>org.eclipse.m2e</groupId>
+                    <artifactId>lifecycle-mapping</artifactId>
+                    <version>1.0.0</version>
+                    <configuration>
+                        <lifecycleMappingMetadata>
+                            <pluginExecutions>
+                                <pluginExecution>
+                                    <pluginExecutionFilter>
+                                        <groupId>
+                                            org.codehaus.mojo
+                                        </groupId>
+                                        <artifactId>
+                                            javacc-maven-plugin
+                                        </artifactId>
+                                        <versionRange>
+                                            [2.0],[2.6]
+                                        </versionRange>
+                                        <goals>
+                                            <goal>javacc</goal>
+                                        </goals>
+                                    </pluginExecutionFilter>
+                                    <action>
+                                        <ignore></ignore>
+                                    </action>
+                                </pluginExecution>
+                            </pluginExecutions>
+                        </lifecycleMappingMetadata>
+                    </configuration>
+                </plugin>
+            </plugins>
+        </pluginManagement>
+    </build>
 
-	<dependencies>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>frontend-utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>java-1.1exp</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>utils</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>text</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>java-1.5</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>java-1.7</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>python-3</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>csharp-1.2</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>cpp</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>scheme</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>edu.kit.ipd.jplag</groupId>
-			<artifactId>chars</artifactId>
-		</dependency>
-	</dependencies>
+    <dependencies>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>frontend-utils</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>java-1.1exp</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>utils</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>text</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>java-1.5</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>java-1.7</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>python-3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>csharp-1.2</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>cpp</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>scheme</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>edu.kit.ipd.jplag</groupId>
+            <artifactId>chars</artifactId>
+        </dependency>
+    </dependencies>
 </project>

jplag/src/main/java/jplag/HTMLFile.java

@@ -10,7 +10,7 @@ public class HTMLFile extends PrintWriter {
   /* This static method has to be used to instanciate HTMLFile objects. */
   public static HTMLFile createHTMLFile(File f) throws IOException {
     BufferedCounter new_bc = new BufferedCounter(
-        new OutputStreamWriter(new FileOutputStream(f), "ISO-8859-1"));
+        new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));
     HTMLFile htmlfile = new HTMLFile(new_bc);
     htmlfile.bc = new_bc;
 //      if (Program.verbose_details)

jplag/src/main/java/jplag/JPlag.java

@@ -17,7 +17,7 @@ public class JPlag {
             }
             catch(ExitException ex) {
                 System.out.println("Error: "+ex.getReport());
-		System.exit(1);
+                System.exit(1);
             }
 		}
 	}

jplag/src/main/java/jplag/Program.java

@@ -29,1417 +29,1421 @@ import jplagUtils.PropertiesLoader;
 
 /*
  * This class coordinates the whole program flow.
- * The revision history can be found on https://svn.ipd.kit.edu/trac/jplag/wiki/JPlag/History 
+ * The revision history can be found on https://svn.ipd.kit.edu/trac/jplag/wiki/JPlag/History
  *
  */
 
 public class Program implements ProgramI {
-	private static final Properties versionProps = PropertiesLoader.loadProps("jplag/version.properties");
-	public static final String name = "JPlag" + versionProps.getProperty("version", "devel");
-	public static final String name_long = "JPlag (Version " + versionProps.getProperty("version", "devel") + ")";
-
-	public DateFormat dateFormat;
-	public DateFormat dateTimeFormat;
-
-	public String currentSubmissionName = "<Unknown submission>";
-	public Vector<String> errorVector = new Vector<String>();
-
-	public void addError(String errorMsg) {
-		errorVector.add("[" + currentSubmissionName + "]\n" + errorMsg);
-		print(errorMsg, null);
-	}
-
-	public void print(String normal, String lng) {
-		if (options.verbose_parser) {
-			if (lng != null)
-				myWrite(lng);
-			else if (normal != null)
-				myWrite(normal);
-		}
-		if (options.verbose_quiet)
-			return;
-		try {
-			if (normal != null) {
-				System.out.print(normal);
-			}
-
-			if (lng != null) {
-				if (options.verbose_long)
-					System.out.print(lng);
-			}
-		} catch (Throwable e) {
-			System.out.println(e.getMessage());
-		}
-	}
-
-	private Submission basecodeSubmission = null;
-
-	// Used Objects of anothers jplag.Classes ,they muss be just one time
-	// instantiate
-	public Clusters clusters = null;
-
-	private int errors = 0;
-	private String invalidSubmissionNames = null;
-
-	private HashSet<String> excluded = null;
-
-	protected GSTiling gSTiling = new GSTiling(this);
-
-	private Hashtable<String, AllBasecodeMatches> htBasecodeMatches = new Hashtable<String, AllBasecodeMatches>(30);
-
-	private Vector<String> included = null;
-
-	// experiment end
-
-	private jplag.options.Options options;
-
-	public Report report;
-
-	public Messages msg;
-
-	private Runtime runtime = Runtime.getRuntime();
-
-	private Vector<Submission> submissions;
-
-	private FileWriter writer = null;
-
-	public Program(Options options) throws jplag.ExitException {
-		this.options = options;
-		this.options.initializeSecondStep(this);
-		if (this.options.language == null)
-			throw new ExitException("Language not initialized!", ExitException.BAD_LANGUAGE_ERROR);
-
-		msg = new Messages(this.options.getCountryTag());
-
-		if (this.options.getCountryTag().equals("de")) {
-			dateFormat = new SimpleDateFormat("dd.MM.yyyy");
-			dateTimeFormat = new SimpleDateFormat("dd.MM.yyyy HH:mm:ss 'GMT'");
-		} else {
-			dateFormat = new SimpleDateFormat("yyyy-MM-dd");
-			dateTimeFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss 'GMT'");
-		}
-		dateFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
-		dateTimeFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
-
-		report = new Report(this, get_language());
-	}
-
-	/**
-	 * All submission with no errors are counted. (unsure if this is still
-	 * necessary.)
-	 */
-	protected int validSubmissions() {
-		if (submissions == null)
-			return 0;
-		int size = 0;
-		for (int i = submissions.size() - 1; i >= 0; i--) {
-			if (!submissions.elementAt(i).errors)
-				size++;
-		}
-		return size;
-	}
-
-	/**
-	 * Like the validSubmissions(), but this time all the submissions are
-	 * returned as a string, separated by "separator".
-	 */
-	protected String allValidSubmissions(String separator) {
-		String res = "";
-		int size = submissions.size();
-		boolean firsterr = true;
-		for (int i = 0; i < size; i++) {
-			Submission subm = submissions.elementAt(i);
-			if (!subm.errors) {
-				res += ((!firsterr) ? separator : "") + subm.name;
-				firsterr = false;
-			}
-		}
-		return res;
-	}
-
-	/**
-	 * Returns a " - " separated list of invalid submission names
-	 */
-	protected String allInvalidSubmissions() {
-		return invalidSubmissionNames;
-	}
-
-	public void closeWriter() {
-		try {
-			if (writer != null)
-				writer.close();
-		} catch (IOException ex) {
-			ex.printStackTrace();
-		}
-		writer = null;
-	}
-
-	private void throwNotEnoughSubmissions() throws jplag.ExitException {
-		StringBuilder errorStr = new StringBuilder();
-		for (String str : errorVector) {
-			errorStr.append(str);
-			errorStr.append('\n');
-		}
-
-		throw new ExitException("Not enough valid submissions! (only " + validSubmissions() + " "
-				+ (validSubmissions() != 1 ? "are" : "is") + " valid):\n" + errorStr.toString(), ExitException.NOT_ENOUGH_SUBMISSIONS_ERROR);
-	}
-
-	private void throwBadBasecodeSubmission() throws jplag.ExitException {
-		StringBuilder errorStr = new StringBuilder();
-		for (String str : errorVector) {
-			errorStr.append(str);
-			errorStr.append('\n');
-		}
-
-		throw new ExitException("Bad basecode submission:\n" + errorStr.toString());
-	}
-
-	// COMPARE
-
-	/**
-	 * Now the actual comparison: All submissions are compared pairwise.
-	 */
-	private void compare() throws jplag.ExitException {
-		int size = submissions.size();
-
-		SortedVector<AllMatches> avgmatches, maxmatches;
-		int[] dist = new int[10];
-
-		// Result vector
-		avgmatches = new SortedVector<AllMatches>(new AllMatches.AvgComparator());
-		maxmatches = new SortedVector<AllMatches>(new AllMatches.MaxComparator());
-
-		long msec;
-
-		AllBasecodeMatches bcmatch;
-		Submission s1, s2;
-
-		options.setState(Options.COMPARING);
-		options.setProgress(0);
-
-		if (this.options.useBasecode) {
-			//			print("\nComparing with Basecode:\n", validSubmissions()
-			//					+ " submissions");
-			int countBC = 0;
-			// System.out.println("BC size: "+basecodeSubmission.size());
-			msec = System.currentTimeMillis();
-			for (int i = 0; i < (size); i++) {
-				s1 = submissions.elementAt(i);
-				// System.out.println("basecode recognition for: "+s1.name);
-				bcmatch = this.gSTiling.compareWithBasecode(s1, basecodeSubmission);
-				htBasecodeMatches.put(s1.name, bcmatch);
-				this.gSTiling.resetBaseSubmission(basecodeSubmission);
-				countBC++;
-				options.setProgress(countBC * 100 / size);
-			}
-			long timebc = System.currentTimeMillis() - msec;
-			print("\n\n", "\nTime for comparing with Basecode: " + ((timebc / 3600000 > 0) ? (timebc / 3600000) + " h " : "")
-					+ ((timebc / 60000 > 0) ? ((timebc / 60000) % 60000) + " min " : "") + (timebc / 1000 % 60) + " sec\n"
-					+ "Time per basecode comparison: " + (timebc / size) + " msec\n\n");
-		}
-
-		//		print("\nComparing:\n", validSubmissions() + " submissions");
-
-		int totalcomps = (size - 1) * size / 2;
-		int i, j, anz = 0, count = 0;
-		AllMatches match;
-
-		options.setProgress(0);
-		msec = System.currentTimeMillis();
-
-		for (i = 0; i < (size - 1); i++) {
-			s1 = submissions.elementAt(i);
-			if (s1.struct == null) {
-				count += (size - i - 1);
-				continue;
-			}
-
-			for (j = (i + 1); j < size; j++) {
-				s2 = submissions.elementAt(j);
-				if (s2.struct == null) {
-					count++;
-					continue;
-				}
-
-				match = this.gSTiling.compare(s1, s2);
-
-				anz++;
-
-				System.out.println("Comparing " + s1.name + "-" + s2.name + ": " + match.percent());
-
-				// histogram:
-				if (options.useBasecode) {
-					match.bcmatchesA = htBasecodeMatches.get(match.subA.name);
-					match.bcmatchesB = htBasecodeMatches.get(match.subB.name);
-				}
-
-				registerMatch(match, dist, avgmatches, maxmatches, null, i, j);
-				count++;
-				options.setProgress(count * 100 / totalcomps);
-			}
-		}
-		options.setProgress(100);
-		long time = System.currentTimeMillis() - msec;
-
-		print("\n", "Total time for comparing submissions: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
-				+ ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n" + "Time per comparison: "
-				+ (time / anz) + " msec\n");
-
-		Cluster cluster = null;
-		if (options.clustering)
-			cluster = this.clusters.calculateClustering(submissions);
-
-		writeResults(dist, avgmatches, maxmatches, null, cluster);
-	}
-
-	/**
-	 * Revision compare mode: Compare each submission only with its next
-	 * submission.
-	 */
-	private void revisionCompare() throws jplag.ExitException {
-		int size = submissions.size();
-
-		SortedVector<AllMatches> avgmatches, maxmatches, minmatches;
-		int[] dist = new int[10];
-
-		// Result vector
-		avgmatches = new SortedVector<AllMatches>(new AllMatches.AvgReversedComparator());
-		maxmatches = new SortedVector<AllMatches>(new AllMatches.MaxReversedComparator());
-		minmatches = new SortedVector<AllMatches>(new AllMatches.MinReversedComparator());
-
-		long msec;
-
-		AllBasecodeMatches bcmatch;
-		Submission s1, s2;
-
-		options.setState(Options.COMPARING);
-		options.setProgress(0);
-
-		if (options.useBasecode) {
-			msec = System.currentTimeMillis();
-			for (int i = 0; i < size; i++) {
-				s1 = submissions.elementAt(i);
-				bcmatch = gSTiling.compareWithBasecode(s1, basecodeSubmission);
-				htBasecodeMatches.put(s1.name, bcmatch);
-				gSTiling.resetBaseSubmission(basecodeSubmission);
-				options.setProgress((i + 1) * 100 / size);
-			}
-			long timebc = System.currentTimeMillis() - msec;
-			print("\n\n", "\nTime for comparing with Basecode: " + ((timebc / 3600000 > 0) ? (timebc / 3600000) + " h " : "")
-					+ ((timebc / 60000 > 0) ? ((timebc / 60000) % 60000) + " min " : "") + (timebc / 1000 % 60) + " sec\n"
-					+ "Time per basecode comparison: " + (timebc / size) + " msec\n\n");
-		}
-
-		int totalcomps = size - 1;
-		int anz = 0, count = 0;
-		AllMatches match;
-
-		options.setProgress(0);
-		msec = System.currentTimeMillis();
-
-		s1loop: for (int i = 0; i < size - 1;) {
-			s1 = submissions.elementAt(i);
-			if (s1.struct == null) {
-				count++;
-				continue;
-			}
-
-			// Find next valid submission
-			int j = i;
-			do {
-				j++;
-				if (j >= size)
-					break s1loop; // no more comparison pairs available
-				s2 = submissions.elementAt(j);
-			} while (s2.struct == null);
-
-			match = this.gSTiling.compare(s1, s2);
-
-			anz++;
-
-			/*
-			 * System.out.println("Comparing "+s1.name+"-"+s2.name+": "+
-			 * match.percent());
-			 */
-			// histogram:
-			if (options.useBasecode) {
-				match.bcmatchesA = htBasecodeMatches.get(match.subA.name);
-				match.bcmatchesB = htBasecodeMatches.get(match.subB.name);
-			}
-
-			registerMatch(match, dist, avgmatches, maxmatches, minmatches, i, j);
-			count++;
-			options.setProgress(count * 100 / totalcomps);
-
-			i = j;
-		}
-		options.setProgress(100);
-		long time = System.currentTimeMillis() - msec;
-
-		print("\n", "Total time for comparing submissions: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
-				+ ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n" + "Time per comparison: "
-				+ (time / anz) + " msec\n");
-
-		Cluster cluster = null;
-		if (options.clustering)
-			cluster = this.clusters.calculateClustering(submissions);
-
-		writeResults(dist, avgmatches, maxmatches, minmatches, cluster);
-	}
-
-	private void createSubmissions() throws jplag.ExitException {
-		submissions = new Vector<Submission>();
-		File f = new File(options.root_dir);
-		if (f == null || !f.isDirectory()) {
-			throw new jplag.ExitException("\"" + options.root_dir + "\" is not a directory!");
-		}
-		String[] list = null;
-		try {
-			list = f.list();
-		} catch (SecurityException e) {
-			throw new jplag.ExitException("Unable to retrieve directory: " + options.root_dir + " Cause : " + e.toString());
-		}
-		Arrays.sort(list);
-
-		for (int i = 0; i < list.length; i++) {
-			File subm_dir = new File(f, list[i]);
-			if (!subm_dir.isDirectory()) {
-				if (options.sub_dir != null)
-					continue;
-
-				boolean ok = false;
-				String name = subm_dir.getName();
-				for (int j = 0; j < options.suffixes.length; j++)
-					if (name.endsWith(options.suffixes[j])) {
-						ok = true;
-						break;
-					}
-
-				if (!ok)
-					continue;
-
-				submissions.addElement(new Submission(name, f, this, get_language()));
-				continue;
-			}
-			if (options.exp && excludeFile(subm_dir.toString())) { // EXPERIMENT
-				// !!
-				System.err.println("excluded: " + subm_dir);
-				continue;
-			}
-
-			File file_dir = ((options.sub_dir == null) ? // - S option
-			subm_dir
-					: new File(subm_dir, options.sub_dir));
-			if (file_dir.isDirectory()) {
-				if (options.basecode.equals(subm_dir.getName())) {
-					basecodeSubmission = new Submission(subm_dir.getName(), file_dir, options.read_subdirs, this, get_language());
-				} else {
-					submissions.addElement(new Submission(subm_dir.getName(), file_dir, options.read_subdirs, this, get_language())); // -s
-				}
-			} else
-				throw new ExitException("Cannot find directory: " + file_dir.toString());
-		}
-	}
-
-	/**
-	 * THIS IS FOR THE EMPIRICAL STUDY
-	 */
-	private void createSubmissionsExp() throws jplag.ExitException {
-		// ES IST SICHER, DASS EIN INCLUDE-FILE ANGEGEBEN WURDE!
-		readIncludeFile();
-		submissions = new Vector<Submission>();
-		File f = new File(options.root_dir);
-		if (f == null || !f.isDirectory()) {
-			throw new jplag.ExitException(options.root_dir + " is not a directory!");
-		}
-		String[] list = new String[included.size()];
-		included.copyInto(list);
-		for (int i = 0; i < list.length; i++) {
-			File subm_dir = new File(f, list[i]);
-			if (subm_dir == null || !subm_dir.isDirectory())
-				continue;
-			if (options.exp && excludeFile(subm_dir.toString())) { // EXPERIMENT
-				// !!
-				System.err.println("excluded: " + subm_dir);
-				continue;
-			}
-			File file_dir = ((options.sub_dir == null) ? // - S option
-			subm_dir
-					: new File(subm_dir, options.sub_dir));
-			if (file_dir != null && file_dir.isDirectory())
-				submissions.addElement(new Submission(subm_dir.getName(), file_dir, options.read_subdirs, this, this.get_language())); // -s
-			else if (options.sub_dir == null) {
-				throw new jplag.ExitException(options.root_dir + " is not a directory!");
-			}
-		}
-	}
-
-	/**
-	 * Check if a file is excluded or not
-	 */
-	protected boolean excludeFile(String file) {
-		if (excluded == null)
-			return false;
-		Iterator<String> iter = excluded.iterator();
-		while (iter.hasNext())
-			if (file.endsWith(iter.next()))
-				return true;
-		return false;
-	}
-
-	// EXPERIMENT !!!!! special compare routine!
-	private void expCompare() throws jplag.ExitException {
-		int size = validSubmissions();
-		int[] similarity = new int[(size * size - size) / 2];
-
-		int anzSub = submissions.size();
-		int i, j, count = 0;
-		Submission s1, s2;
-		AllMatches match;
-		long msec = System.currentTimeMillis();
-		for (i = 0; i < (anzSub - 1); i++) {
-			s1 = submissions.elementAt(i);
-			if (s1.struct == null)
-				continue;
-			for (j = (i + 1); j < anzSub; j++) {
-				s2 = submissions.elementAt(j);
-				if (s2.struct == null)
-					continue;
-
-				match = this.gSTiling.compare(s1, s2);
-				similarity[count++] = (int) match.percent();
-			}
-		}
-		long time = System.currentTimeMillis() - msec;
-		// output
-		System.out.print(options.root_dir + " ");
-		System.out.print(options.min_token_match + " ");
-		System.out.print(options.filtername + " ");
-		System.out.print((time) + " ");
-		for (i = 0; i < similarity.length; i++)
-			System.out.print(similarity[i] + " ");
-		System.out.println();
-	}
-
-	/**
-	 * This is the special external comparison routine
-	 */
-	private void externalCompare() throws jplag.ExitException {
-		int size = submissions.size();
-		// Progress progress;
-		// Result vector
-		SortedVector<AllMatches> avgmatches = new SortedVector<AllMatches>(new AllMatches.AvgComparator());
-		SortedVector<AllMatches> maxmatches = new SortedVector<AllMatches>(new AllMatches.MaxComparator());
-		int[] dist = new int[10];
-
-		print("Comparing: " + size + " submissions\n", null);
-		options.setState(Options.COMPARING);
-		options.setProgress(0);
-		long totalComparisons = (size * (size - 1)) / 2, count = 0, comparisons = 0;
-		int index = 0;
-		AllMatches match;
-		Submission s1, s2;
-		long remain;
-		String totalTimeStr, remainTime;
-
-		print("Checking memory size...\n", null);
-		// First try to load as many submissions as possible
-		index = fillMemory(0, size);
-
-		long startTime;
-		long totalTime = 0;
-		int startA = 0;
-		int endA = index / 2;
-		int startB = endA + 1;
-		int endB = index;
-		int i, j;
-		//		long progStart;
-
-		do {
-			// compare A to A
-			startTime = System.currentTimeMillis();
-			print("Comparing block A (" + startA + "-" + endA + ") to block A\n", null);
-			//progStart = (endA - startA + 1) * (endA - startA) / 2;
-			//      progress = new Progress(progStart > 0 ? progStart : 1, this);
-			//progStart = count;
-			for (i = startA; i <= endA; i++) {
-				//        progress.set(count - progStart);
-				options.setProgress((int) (count * 100 / totalComparisons));
-				s1 = submissions.elementAt(i);
-				if (s1.struct == null) {
-					count += (endA - i);
-					continue;
-				}
-				for (j = (i + 1); j <= endA; j++) {
-					s2 = submissions.elementAt(j);
-					if (s2.struct == null) {
-						count++;
-						continue;
-					}
-
-					match = this.gSTiling.compare(s1, s2);
-					registerMatch(match, dist, avgmatches, maxmatches, null, i, j);
-					comparisons++;
-					count++;
-				}
-			}
-			//      progress.set(count - progStart);
-			options.setProgress((int) (count * 100 / totalComparisons));
-			print("\n", null);
-			totalTime += System.currentTimeMillis() - startTime;
-
-			// Are we finished?
-			if (startA == startB)
-				break;
-
-			do {
-				totalTimeStr = "" + ((totalTime / 3600000 > 0) ? (totalTime / 3600000) + " h " : "")
-						+ ((totalTime / 60000 > 0) ? ((totalTime / 60000) % 60) + " min " : "") + (totalTime / 1000 % 60) + " sec";
-				if (comparisons != 0)
-					remain = totalTime * (totalComparisons - count) / comparisons;
-				else
-					remain = 0;
-				remainTime = "" + ((remain / 3600000 > 0) ? (remain / 3600000) + " h " : "")
-						+ ((remain / 60000 > 0) ? ((remain / 60000) % 60) + " min " : "") + (remain / 1000 % 60) + " sec";
-
-				print("Progress: " + (100 * count) / totalComparisons + "%\nTime used for comparisons: " + totalTimeStr
-						+ "\nRemaining time (estimate): " + remainTime + "\n", null);
-
-				// compare A to B
-				startTime = System.currentTimeMillis();
-				print("Comparing block A (" + startA + "-" + endA + ") to block B (" + startB + "-" + endB + ")\n", null);
-				//progStart = (endA - startA + 1) * (endB - startB + 1);
-				//        progress = new Progress(progStart > 0 ? progStart : 1, this);
-				//progStart = count;
-				for (i = startB; i <= endB; i++) {
-					//          progress.set(count - progStart);
-					options.setProgress((int) (count * 100 / totalComparisons));
-					s1 = submissions.elementAt(i);
-					if (s1.struct == null) {
-						count += (endA - startA + 1);
-						continue;
-					}
-					for (j = startA; j <= endA; j++) {
-						s2 = submissions.elementAt(j);
-						if (s2.struct == null) {
-							count++;
-							continue;
-						}
-
-						match = this.gSTiling.compare(s1, s2);
-						registerMatch(match, dist, avgmatches, maxmatches, null, i, j);
-						comparisons++;
-						count++;
-					}
-					s1.struct = null; // remove B
-				}
-				//        progress.set(count - progStart);
-				options.setProgress((int) (count * 100 / totalComparisons));
-				print("\n", null);
-				totalTime += System.currentTimeMillis() - startTime;
-
-				if (endB == size - 1) {
-					totalTimeStr = "" + ((totalTime / 3600000 > 0) ? (totalTime / 3600000) + " h " : "")
-							+ ((totalTime / 60000 > 0) ? ((totalTime / 60000) % 60) + " min " : "") + (totalTime / 1000 % 60) + " sec";
-					remain = totalTime * (totalComparisons - count) / comparisons;
-					remainTime = "" + ((remain / 3600000 > 0) ? (remain / 3600000) + " h " : "")
-							+ ((remain / 60000 > 0) ? ((remain / 60000) % 60) + " min " : "") + (remain / 1000 % 60) + " sec";
-
-					print("Progress: " + (100 * count) / totalComparisons + "%\nTime used for comparisons: " + totalTimeStr
-							+ "\nRemaining time (estimate): " + remainTime + "\n", null);
-					break;
-				}
-
-				// Remove B -> already done...
-				// for (i=startB; i<=endB; i++)
-				// ((Submission)submissions.elementAt(i)).struct = null;
-				runtime.runFinalization();
-				runtime.gc();
-				Thread.yield();
-				// Try to find the next B
-				print("Finding next B\n", null);
-
-				index = fillMemory(endB + 1, size);
-
-				startB = endB + 1;
-				endB = index;
-
-			} while (true);
-
-			// Remove A
-			for (i = startA; i <= endA; i++)
-				submissions.elementAt(i).struct = null;
-			runtime.runFinalization();
-			runtime.gc();
-			Thread.yield();
-			print("Find next A.\n", null);
-			// First try to load as many submissions as possible
-
-			index = fillMemory(endA + 1, size);
-
-			if (index != size - 1) {
-				startA = endA + 1;
-				endA = startA + (index - startA + 1) / 2;
-				startB = endA + 1;
-				endB = index;
-			} else {
-				startA = startB; // last block
-				endA = endB = index;
-			}
-		} while (true);
-
-		totalTime += System.currentTimeMillis() - startTime;
-		totalTimeStr = "" + ((totalTime / 3600000 > 0) ? (totalTime / 3600000) + " h " : "")
-				+ ((totalTime / 60000 > 0) ? ((totalTime / 60000) % 60000) + " min " : "") + (totalTime / 1000 % 60) + " sec";
-
-		print("Total comparison time: " + totalTimeStr + "\nComparisons: " + count + "/" + comparisons + "/" + totalComparisons + "\n",
-				null);
-
-		// free remaining memory
-		for (i = startA; i <= endA; i++)
-			submissions.elementAt(i).struct = null;
-		runtime.runFinalization();
-		runtime.gc();
-		Thread.yield();
-
-		// System.out.println("Matrix:\n"+ similarity);
-		Cluster cluster = null;
-		if (options.clustering)
-			cluster = this.clusters.calculateClustering(submissions);
-
-		writeResults(dist, avgmatches, maxmatches, null, cluster);
-	}
-
-	private int fillMemory(int from, int size) {
-		Submission sub = null;
-		int index = from;
-
-		runtime.runFinalization();
-		runtime.gc();
-		Thread.yield();
-		long freeBefore = runtime.freeMemory();
-		try {
-			for (; index < size; index++) {
-				sub = submissions.elementAt(index);
-				sub.struct = new Structure();
-				if (!sub.struct.load(new File("temp", sub.dir.getName() + sub.name)))
-					sub.struct = null;
-			}
-		} catch (java.lang.OutOfMemoryError e) {
-			sub.struct = null;
-			print("Memory overflow after loading " + (index - from + 1) + " submissions.\n", null);
-		}
-		if (index >= size)
-			index = size - 1;
-
-		if (freeBefore / runtime.freeMemory() <= 2)
-			return index;
-		for (int i = (index - from) / 2; i > 0; i--) {
-			submissions.elementAt(index--).struct = null;
-		}
-		runtime.runFinalization();
-		runtime.gc();
-		Thread.yield();
-
-		// make sure we freed half of the "available" memory.
-		long free;
-		while (freeBefore / (free = runtime.freeMemory()) > 2) {
-			submissions.elementAt(index--).struct = null;
-			runtime.runFinalization();
-			runtime.gc();
-			Thread.yield();
-		}
-		print(free / 1024 / 1024 + "MByte freed. Current index: " + index + "\n", null);
-
-		return index;
-	}
-
-	public String get_basecode() {
-		return this.options.basecode;
-	}
-
-	public int get_clusterType() {
-		return this.options.clusterType;
-	}
-
-	public String get_commandLine() {
-		return this.options.commandLine;
-	}
-
-	public String getCountryTag() {
-		return options.getCountryTag();
-	}
-
-	/*
-	 * Distribution: Program given away to:
-	 * 
-	 * 0: Server version
-	 * 
-	 * 1: David Klausner 2: Ronald Kostoff 3: Bob Carlson 4: Neville Newman
-	 */
-
-	public int get_distri() {
-		return 0;
-	}
-
-	public File get_jplagResult() {
-		return new File(options.result_dir);
-
-	}
-
-	public Language get_language() {
-		return this.options.language;
-	}
-
-	public int get_min_token_match() {
-		return this.options.min_token_match;
-	}
-
-	public String get_title() {
-		return this.options.title;
-	}
-
-	public String get_original_dir() {
-		return this.options.original_dir;
-	}
-
-	public String get_result_dir() {
-		return this.options.result_dir;
-	}
-
-	public String get_root_dir() {
-		return this.options.root_dir;
-	}
-
-	public SimilarityMatrix get_similarity() {
-		return this.options.similarity;
-	}
-
-	public String get_sub_dir() {
-		return this.options.sub_dir;
-	}
-
-	public String[] get_suffixes() {
-		return this.options.suffixes;
-	}
-
-	public int[] get_themewords() {
-		return this.options.themewords;
-	}
-
-	public float[] get_threshold() {
-		return this.options.threshold;
-	}
-
-	public int getErrors() {
-		return errors;
-	}
-
-	public void hash_distribution() {
-		int[] dist = new int[20];
-		int count = 0;
-		Enumeration<Submission> enum1 = submissions.elements();
-
-		while (enum1.hasMoreElements()) {
-			Structure struct = enum1.nextElement().struct;
-			if (struct != null) {
-				struct.table.count_dist(dist);
-				count++;
-			}
-		}
-
-		System.out.println("Count: " + count);
-		for (int i = 0; i < dist.length; i++)
-			System.out.println(i + "\t" + dist[i]);
-	}
-
-	private void makeTempDir() throws jplag.ExitException {
-		print(null, "Creating temporary dir.\n");
-		File f = new File("temp");
-		if (!f.exists()) {
-			if (!f.mkdirs()) {
-				throw new jplag.ExitException("Cannot create temporary directory!");
-			}
-		}
-		if (!f.isDirectory()) {
-			throw new ExitException("'temp' is not a directory!");
-		}
-		if (!f.canWrite()) {
-			throw new ExitException("Cannot write directory: 'temp'");
-		}
-	}
-
-	private void myWrite(String str) {
-		if (writer != null) {
-			try {
-				writer.write(str);
-			} catch (IOException e) {
-				e.printStackTrace();
-			}
-		} else
-			System.out.print(str);
-	}
-
-	// PARSE
-	/*
-	 * Compiles all "submissions"
-	 */
-	private void parseAll() throws jplag.ExitException {
-		if (submissions == null) {
-			System.out.println("  Nothing to parse!");
-			return;
-		}
-		// lets go:)
-		int count = 0;
-		int totalcount = submissions.size();
-		options.setState(Options.PARSING);
-		options.setProgress(0);
-		long msec = System.currentTimeMillis();
-		Iterator<Submission> iter = submissions.iterator();
-
-		if (options.externalSearch)
-			makeTempDir();
-		int invalid = 0;
-		while (iter.hasNext()) {
-			boolean ok = true;
-			boolean removed = false;
-			Submission subm = iter.next();
-			print(null, "------ Parsing submission: " + subm.name + "\n");
-			currentSubmissionName = subm.name;
-			options.setProgress(count * 100 / totalcount);
-			if (!(ok = subm.parse()))
-				errors++;
-
-			if (options.exp && options.filter != null)
-				subm.struct = options.filter.filter(subm.struct); // EXPERIMENT
-			count++;
-			if (subm.struct != null && subm.size() < options.min_token_match) {
-				print(null, "Submission contains fewer tokens than minimum match " + "length allows!\n");
-				subm.struct = null;
-				invalid++;
-				removed = true;
-			}
-			if (options.externalSearch) {
-				if (subm.struct != null) {
-					this.gSTiling.create_hashes(subm.struct, options.min_token_match, false);
-					subm.struct.save(new File("temp", subm.dir.getName() + subm.name));
-					subm.struct = null;
-				}
-			}
-			if (!options.externalSearch && subm.struct == null) {
-				invalidSubmissionNames = (invalidSubmissionNames == null) ? subm.name : invalidSubmissionNames + " - " + subm.name;
-				iter.remove();
-			}
-			if (ok && !removed)
-				print(null, "OK\n");
-			else
-				print(null, "ERROR -> Submission removed\n");
-		}
-
-		options.setProgress(100);
-		print("\n" + (count - errors - invalid) + " submissions parsed successfully!\n" + errors + " parser error"
-				+ (errors != 1 ? "s!\n" : "!\n"), null);
-		if (invalid != 0) {
-			print(null, invalid
-					+ ((invalid == 1) ? " submission is not valid because it contains" : " submissions are not valid because they contain")
-					+ " fewer tokens\nthan minimum match length allows.\n");
-		}
-		long time = System.currentTimeMillis() - msec;
-		print("\n\n", "\nTotal time for parsing: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
-				+ ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n"
-				+ "Time per parsed submission: " + (count > 0 ? (time / count) : "n/a") + " msec\n\n");
-	}
-
-	private void parseBasecodeSubmission() throws jplag.ExitException {
-		Submission subm = basecodeSubmission;
-		if (subm == null) {
-			options.useBasecode = false;
-			return;
-		}
-		long msec = System.currentTimeMillis();
-		print("----- Parsing basecode submission: " + subm.name + "\n", null);
-
-		// lets go:
-		if (options.externalSearch)
-			makeTempDir();
-
-		if (!subm.parse())
-			throwBadBasecodeSubmission();
-
-		if (options.exp && options.filter != null)
-			subm.struct = options.filter.filter(subm.struct); // EXPERIMENT
-
-		if (subm.struct != null && subm.size() < options.min_token_match)
-			throw new ExitException("Basecode submission contains fewer tokens " + "than minimum match length allows!\n");
-
-		if (options.useBasecode)
-			gSTiling.create_hashes(subm.struct, options.min_token_match, true);
-		if (options.externalSearch) {
-			if (subm.struct != null) {
-				gSTiling.create_hashes(subm.struct, options.min_token_match, false);
-				subm.struct.save(new File("temp", subm.dir.getName() + subm.name));
-				subm.struct = null;
-			}
-		}
-
-		print("\nBasecode submission parsed!\n", null);
-		long time = System.currentTimeMillis() - msec;
-		print("\n", "\nTime for parsing Basecode: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
-				+ ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n");
-	}
-
-	// Excluded files:
-
-	/*
-	 * If an exclusion file is given, it is read in and all stings are saved in
-	 * the set "excluded".
-	 */
-	private void readExclusionFile() {
-		if (options.exclude_file == null)
-			return;
-		excluded = new HashSet<String>();
-
-		try {
-			BufferedReader in = new BufferedReader(new FileReader(options.exclude_file));
-			String line;
-			while ((line = in.readLine()) != null) {
-				excluded.add(line.trim());
-			}
-			in.close();
-		} catch (FileNotFoundException e) {
-			System.out.println("Exclusion file not found: " + options.exclude_file);
-		} catch (IOException e) {
-		}
-		print(null, "Excluded files:\n");
-		if (options.verbose_long) {
-			Iterator<String> iter = excluded.iterator();
-			while (iter.hasNext()) {
-				print(null, "  " + iter.next() + "\n");
-			}
-		}
-	}
-
-	/*
-	 * If an include file is given, read it in and store all the strings in
-	 * "included".
-	 */
-	private void readIncludeFile() {
-		if (options.include_file == null)
-			return;
-		included = new Vector<String>();
-		try {
-			BufferedReader in = new BufferedReader(new FileReader(options.include_file));
-			String line;
-			while ((line = in.readLine()) != null) {
-				included.addElement(line.trim());
-			}
-			in.close();
-		} catch (FileNotFoundException e) {
-			System.out.println("Include file not found: " + options.include_file);
-		} catch (IOException e) {
-		}
-		print(null, "Included dirs:\n");
-		if (options.verbose_long) {
-			Enumeration<String> enum1 = included.elements();
-			while (enum1.hasMoreElements())
-				print(null, "  " + enum1.nextElement() + "\n");
-		}
-	}
-
-	private void registerMatch(AllMatches match, int[] dist, SortedVector<AllMatches> avgmatches, SortedVector<AllMatches> maxmatches,
-			SortedVector<AllMatches> minmatches, int a, int b) {
-		float avgpercent = match.percent();
-		float maxpercent = match.percentMaxAB();
-		float minpercent = match.percentMinAB();
-
-		dist[((((int) avgpercent) / 10) == 10) ? 9 : (((int) avgpercent) / 10)]++;
-		if (!options.store_percent) {
-			if ((avgmatches.size() < options.store_matches || avgpercent > avgmatches.lastElement().percent()) && avgpercent > 0) {
-				avgmatches.insert(match);
-				if (avgmatches.size() > options.store_matches)
-					avgmatches.removeElementAt(options.store_matches);
-			}
-			if (maxmatches != null && (maxmatches.size() < options.store_matches || maxpercent > maxmatches.lastElement().percent())
-					&& maxpercent > 0) {
-				maxmatches.insert(match);
-				if (maxmatches.size() > options.store_matches)
-					maxmatches.removeElementAt(options.store_matches);
-			}
-			if (minmatches != null && (minmatches.size() < options.store_matches || minpercent > minmatches.lastElement().percent())
-					&& minpercent > 0) {
-				minmatches.insert(match);
-				if (minmatches.size() > options.store_matches)
-					minmatches.removeElementAt(options.store_matches);
-			}
-		} else { // store_percent
-			if (avgpercent > options.store_matches) {
-				avgmatches.insert(match);
-				if (avgmatches.size() > Options.MAX_RESULT_PAIRS)
-					avgmatches.removeElementAt(Options.MAX_RESULT_PAIRS);
-			}
-
-			if (maxmatches != null && maxpercent > options.store_matches) {
-				maxmatches.insert(match);
-				if (maxmatches.size() > Options.MAX_RESULT_PAIRS)
-					maxmatches.removeElementAt(Options.MAX_RESULT_PAIRS);
-			}
-
-			if (minmatches != null && minpercent > options.store_matches) {
-				minmatches.insert(match);
-				if (minmatches.size() > Options.MAX_RESULT_PAIRS)
-					minmatches.removeElementAt(Options.MAX_RESULT_PAIRS);
-			}
-		}
-		if (options.clustering)
-			options.similarity.setSimilarity(a, b, avgpercent);
-	}
-
-	private String toUTF8(String str) {
-		byte[] utf8 = null;
-		try {
-			utf8 = str.getBytes("UTF-8");
-		} catch (UnsupportedEncodingException e) {
-		}
-		return new String(utf8);
-	}
-
-	/** *************************** */
-	/* THE MAIN PROCEDURE */
-	/** *************************** */
-	public void run() throws jplag.ExitException {
-		if (options.output_file != null) {
-			try {
-				writer = new FileWriter(new File(options.output_file));
-				writer.write(name_long + "\n");
-				writer.write(dateTimeFormat.format(new Date()) + "\n\n");
-			} catch (IOException ex) {
-				System.out.println("Unable to open or write to log file: " + options.output_file);
-				throw new ExitException("Unable to create log file!");
-			}
-		} else
-			print(null, name_long + "\n\n");
-		print(null, "Language: " + options.language.name() + "\n\n");
-		if (options.original_dir == null)
-			print(null, "Root-dir: " + options.root_dir + "\n"); // server
-		// this file contains all files names which are excluded
-		readExclusionFile();
-		if (options.include_file == null) {
-			createSubmissions();
-			System.out.println(submissions.size() + " submissions");
-		} else
-			createSubmissionsExp();
-
-		if (!options.skipParse) {
-			try {
-				parseAll();
-				System.gc();
-				parseBasecodeSubmission();
-			} catch (OutOfMemoryError e) {
-				submissions = null;
-				System.gc();
-				System.out.println("[" + new Date() + "] OutOfMemoryError " + "during parsing of submission \"" + currentSubmissionName
-						+ "\"");
-				throw new ExitException("Out of memory during parsing of submission \"" + currentSubmissionName + "\"");
-			} catch (ExitException e) {
-				throw e;
-			} catch (Throwable e) {
-				System.out.println("[" + new Date() + "] Unknown exception " + "during parsing of submission \"" + currentSubmissionName
-						+ "\"");
-				e.printStackTrace();
-				throw new ExitException("Unknown exception during parsing of " + "submission \"" + currentSubmissionName + "\"");
-			}
-		} else
-			print("Skipping parsing...\n", null);
-
-		if (validSubmissions() < 2) {
-			throwNotEnoughSubmissions();
-		}
-		errorVector = null; // errorVector is not needed anymore
-
-		if (options.clustering) {
-			clusters = new Clusters(this);
-			options.similarity = new SimilarityMatrix(submissions.size());
-		}
-		System.gc();
-		if (options.exp) { // EXPERIMENT
-			expCompare();
-		} else if (options.externalSearch) {
-			try {
-				externalCompare();
-			} catch (OutOfMemoryError e) {
-				e.printStackTrace();
-			}
-		} else {
-			if (options.compare > 0)
-				specialCompare(); // compare every submission to x others
-			else {
-				switch (options.comparisonMode) {
-				case Options.COMPMODE_NORMAL:
-					compare();
-					break;
-
-				case Options.COMPMODE_REVISION:
-					revisionCompare();
-					break;
-
-				default:
-					throw new ExitException("Illegal comparison mode: \"" + options.comparisonMode + "\"");
-				}
-			}
-		}
-		closeWriter();
-
-		String str = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>";
-		str += "<jplag_infos>\n";
-		str += "<infos \n";
-
-		String sp = "\"";
-		str += " title = " + sp + toUTF8(options.getTitle()) + sp;
-		str += " source = " + sp + (get_original_dir() != null ? toUTF8(get_original_dir()) : "") + sp;
-		str += " n_of_programs = " + sp + submissions.size() + sp;
-		str += " errors = " + sp + get_language().errorsCount() + sp;
-		str += " path_to_files = " + sp + toUTF8((options.sub_dir != null) ? options.sub_dir : "") + sp;
-		str += " basecode_dir = " + sp + toUTF8((options.basecode != null) ? options.basecode : "") + sp;
-		str += " read_subdirs = " + sp + this.options.read_subdirs + sp;
-		str += " clustertype = " + sp + this.options.getClusterTyp() + sp;
-		str += " store_matches = " + sp + this.options.store_matches + ((this.options.store_percent) ? "%" : "") + sp;
-		String suf = "";
-		for (int s = 0; s < this.options.suffixes.length; s++)
-			suf += "," + this.options.suffixes[s];
-		str += " suffixes = " + sp + suf.substring(1) + sp;
-		str += " language_name = " + sp + this.options.languageName + sp;
-		str += " comparison_mode = " + sp + this.options.comparisonMode + sp;
-		str += " country_tag = " + sp + this.options.getCountryTag() + sp;
-		str += " min_token = " + sp + this.options.min_token_match + sp;
-		str += " date = " + sp + System.currentTimeMillis() + sp;
-
-		str += "/>\n";
-		str += "</jplag_infos>";
-
-		try {
-			FileWriter fw = new FileWriter(new File(this.options.result_dir + File.separator + "result.xml"));
-			fw.write(str);
-			fw.close();
-		} catch (IOException ex) {
-			System.out.println("Unable to create result.xml");
-		}
-	}
-
-	public void set_result_dir(String result_dir) {
-		this.options.result_dir = result_dir;
-	}
-
-	/*
-	 * Now the special comparison:
-	 */
-	private void specialCompare() throws jplag.ExitException {
-		File root = new File(options.result_dir);
-		HTMLFile f = this.report.openHTMLFile(root, "index.html");
-		this.report.copyFixedFiles(root);
-
-		this.report.writeIndexBegin(f, "Special Search Results"); // start HTML
-		f.println("<P><A NAME=\"matches\"><H4>Matches:</H4><P>");
-
-		int size = submissions.size();
-		int matchIndex = 0;
-
-		print("Comparing: ", validSubmissions() + " submissions");
-		print("\n(Writing results at the same time.)\n", null);
-
-		options.setState(Options.COMPARING);
-		options.setProgress(0);
-		int totalcomps = size * size;
-		int i, j, anz = 0, count = 0;
-		AllMatches match;
-		Submission s1, s2;
-		long msec = System.currentTimeMillis();
-		for (i = 0; i < (size - 1); i++) {
-			// Result vector
-			SortedVector<AllMatches> matches = new SortedVector<AllMatches>(new AllMatches.AvgComparator());
-
-			s1 = submissions.elementAt(i);
-			if (s1.struct == null) {
-				count += (size - 1);
-				continue;
-			}
-			for (j = 0; j < size; j++) {
-				s2 = submissions.elementAt(j);
-				if ((i == j) || (s2.struct == null)) {
-					count++;
-					continue;
-				}
-
-				match = this.gSTiling.compare(s1, s2);
-				anz++;
-
-				float percent = match.percent();
-
-				if ((matches.size() < options.compare || matches.size() == 0 || match.moreThan(matches.lastElement().percent()))
-						&& match.moreThan(0)) {
-					matches.insert(match);
-					if (matches.size() > options.compare)
-						matches.removeElementAt(options.compare);
-				}
-
-				if (options.clustering)
-					options.similarity.setSimilarity(i, j, percent);
-
-				count++;
-				options.setProgress(count * 100 / totalcomps);
-			}
-
-			// now output matches:
-			f.println("<TABLE CELLPADDING=3 CELLSPACING=2>");
-			boolean once = true;
-			for (Iterator<AllMatches> iter = matches.iterator(); iter.hasNext();) {
-				match = iter.next();
-				if (once) {
-					f.println("<TR><TD BGCOLOR=" + this.report.color(match.percent(), 128, 192, 128, 192, 255, 255) + ">" + s1.name
-							+ "<TD WIDTH=\"10\">-&gt;");
-					once = false;
-				}
-
-				int other = (match.subName(0).equals(s1.name) ? 1 : 0);
-				f.println(" <TD BGCOLOR=" + this.report.color(match.percent(), 128, 192, 128, 192, 255, 255)
-						+ " ALIGN=center><A HREF=\"match" + matchIndex + ".html\">" + match.subName(other) + "</A><BR><FONT COLOR=\""
-						+ this.report.color(match.percent(), 0, 255, 0, 0, 0, 0) + "\"><B>(" + match.roundedPercent() + "%)</B></FONT>");
-				this.report.writeMatch(root, matchIndex++, match);
-			}
-			f.println("</TR>");
-		}
-		f.println("</TABLE><P>\n");
-		f.println("<!---->");
-		this.report.writeIndexEnd(f);
-		f.close();
-
-		options.setProgress(100);
-		long time = System.currentTimeMillis() - msec;
-		print("\n", "Total time: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
-				+ ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n" + "Time per comparison: "
-				+ (time / anz) + " msec\n");
-
-	}
-
-	// DEBUG !!!
-	public void token_distribution() {
-		int[] count = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-				0, 0, 0 }; // to
-		// count
-		// the
-		// distribution
-
-		Enumeration<Submission> enum1 = submissions.elements();
-
-		while (enum1.hasMoreElements()) {
-			Structure struct = enum1.nextElement().struct;
-			if (struct != null)
-				for (int i = struct.size() - 1; i >= 0; i--)
-					count[struct.tokens[i].type]++;
-		}
-
-		int tot = 0;
-		for (int i = 0; i < 0; i++) { // !!!!!!!!!!!!!!!
-			int c = count[i];
-			tot += c;
-			// System.out.println(Token.type2string(i)+"\t"+c);
-		}
-		System.out.println((tot > 999 ? "" : (tot > 99 ? " " : (tot > 9 ? "  " : "   "))) + tot);
-	}
-
-	public boolean use_clustering() {
-		return this.options.clustering;
-	}
-
-	public boolean use_debugParser() {
-		return this.options.debugParser;
-	}
-
-	public boolean use_diff_report() {
-		return this.options.diff_report;
-	}
-
-	public boolean use_externalSearch() {
-		return this.options.externalSearch;
-	}
-
-	public boolean use_verbose_details() {
-		return this.options.verbose_details;
-	}
-
-	public boolean use_verbose_long() {
-		return this.options.verbose_long;
-	}
-
-	public boolean use_verbose_parser() {
-		return this.options.verbose_parser;
-	}
-
-	public boolean use_verbose_quiet() {
-		return this.options.verbose_quiet;
-	}
-
-	public boolean useBasecode() {
-		return this.options.useBasecode;
-	}
-
-	// RESULT
-
-	/*
-	 * Erst wird die Existenz des Ergebnis-Verzeichnisses sichergestellt, dann
-	 * wird die Erstellung der Dateien durch die Klasse "Report" erledigt.
-	 */
-	private void writeResults(int[] dist, SortedVector<AllMatches> avgmatches, SortedVector<AllMatches> maxmatches,
-			SortedVector<AllMatches> minmatches, Cluster clustering) throws jplag.ExitException {
-		options.setState(Options.GENERATING_RESULT_FILES);
-		options.setProgress(0);
-		if (options.original_dir == null)
-			print("Writing results to: " + options.result_dir + "\n", null);
-		File f = new File(options.result_dir);
-		if (!f.exists())
-			if (!f.mkdirs()) {
-				throw new jplag.ExitException("Cannot create directory!");
-			}
-		if (!f.isDirectory()) {
-			throw new jplag.ExitException(options.result_dir + " is not a directory!");
-		}
-		if (!f.canWrite()) {
-			throw new jplag.ExitException("Cannot write directory: " + options.result_dir);
-		}
-
-		this.report.write(f, dist, avgmatches, maxmatches, minmatches, clustering, options);
-
-		if (options.externalSearch)
-			writeTextResult(f, avgmatches);
-	}
-
-	private void writeTextResult(File dir, SortedVector<AllMatches> matches) {
-		Iterator<AllMatches> iter = matches.iterator();
-
-		print("Writing special 'matches.txt' file\n", null);
-
-		try {
-			File f = new File(dir, "matches.txt");
-			PrintWriter writer = new PrintWriter(new FileWriter(f));
-
-			while (iter.hasNext()) {
-				AllMatches match = iter.next();
-
-				String file1, file2, tmp;
-				file1 = match.subA.name;
-				file2 = match.subB.name;
-
-				if (file1.compareTo(file2) > 0) {
-					tmp = file2;
-					file2 = file1;
-					file1 = tmp;
-				}
-
-				writer.println(file1 + "\t" + file2 + "\t" + match.percent());
-			}
-			writer.close();
-		} catch (IOException e) {
-			print("IOException while writing file\n", null);
-		}
-	}
+    private static final Properties versionProps = PropertiesLoader.loadProps("jplag/version.properties");
+    public static final String name = "JPlag" + versionProps.getProperty("version", "devel");
+    public static final String name_long = "JPlag (Version " + versionProps.getProperty("version", "devel") + ")";
+
+    public DateFormat dateFormat;
+    public DateFormat dateTimeFormat;
+
+    public String currentSubmissionName = "<Unknown submission>";
+    public Vector<String> errorVector = new Vector<String>();
+
+    public void addError(String errorMsg) {
+        errorVector.add("[" + currentSubmissionName + "]\n" + errorMsg);
+        print(errorMsg, null);
+    }
+
+    public void print(String normal, String lng) {
+        if (options.verbose_parser) {
+            if (lng != null)
+                myWrite(lng);
+            else if (normal != null)
+                myWrite(normal);
+        }
+        if (options.verbose_quiet)
+            return;
+        try {
+            if (normal != null) {
+                System.out.print(normal);
+            }
+
+            if (lng != null) {
+                if (options.verbose_long)
+                    System.out.print(lng);
+            }
+        } catch (Throwable e) {
+            System.out.println(e.getMessage());
+        }
+    }
+
+    private Submission basecodeSubmission = null;
+
+    // Used Objects of anothers jplag.Classes ,they muss be just one time
+    // instantiate
+    public Clusters clusters = null;
+
+    private int errors = 0;
+    private String invalidSubmissionNames = null;
+
+    private HashSet<String> excluded = null;
+
+    protected GSTiling gSTiling = new GSTiling(this);
+
+    private Hashtable<String, AllBasecodeMatches> htBasecodeMatches = new Hashtable<String, AllBasecodeMatches>(30);
+
+    private Vector<String> included = null;
+
+    // experiment end
+
+    private jplag.options.Options options;
+
+    public Report report;
+
+    public Messages msg;
+
+    private Runtime runtime = Runtime.getRuntime();
+
+    private Vector<Submission> submissions;
+
+    private FileWriter writer = null;
+
+    public Program(Options options) throws jplag.ExitException {
+        this.options = options;
+        this.options.initializeSecondStep(this);
+        if (this.options.language == null)
+            throw new ExitException("Language not initialized!", ExitException.BAD_LANGUAGE_ERROR);
+
+        msg = new Messages(this.options.getCountryTag());
+
+        if (this.options.getCountryTag().equals("de")) {
+            dateFormat = new SimpleDateFormat("dd.MM.yyyy");
+            dateTimeFormat = new SimpleDateFormat("dd.MM.yyyy HH:mm:ss 'GMT'");
+        } else {
+            dateFormat = new SimpleDateFormat("yyyy-MM-dd");
+            dateTimeFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss 'GMT'");
+        }
+        dateFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
+        dateTimeFormat.setTimeZone(TimeZone.getTimeZone("GMT"));
+
+        report = new Report(this, get_language());
+    }
+
+    /**
+     * All submission with no errors are counted. (unsure if this is still
+     * necessary.)
+     */
+    protected int validSubmissions() {
+        if (submissions == null)
+            return 0;
+        int size = 0;
+        for (int i = submissions.size() - 1; i >= 0; i--) {
+            if (!submissions.elementAt(i).errors)
+                size++;
+        }
+        return size;
+    }
+
+    /**
+     * Like the validSubmissions(), but this time all the submissions are
+     * returned as a string, separated by "separator".
+     */
+    protected String allValidSubmissions(String separator) {
+        String res = "";
+        int size = submissions.size();
+        boolean firsterr = true;
+        for (int i = 0; i < size; i++) {
+            Submission subm = submissions.elementAt(i);
+            if (!subm.errors) {
+                res += ((!firsterr) ? separator : "") + subm.name;
+                firsterr = false;
+            }
+        }
+        return res;
+    }
+
+    /**
+     * Returns a " - " separated list of invalid submission names
+     */
+    protected String allInvalidSubmissions() {
+        return invalidSubmissionNames;
+    }
+
+    public void closeWriter() {
+        try {
+            if (writer != null)
+                writer.close();
+        } catch (IOException ex) {
+            ex.printStackTrace();
+        }
+        writer = null;
+    }
+
+    private void throwNotEnoughSubmissions() throws jplag.ExitException {
+        StringBuilder errorStr = new StringBuilder();
+        for (String str : errorVector) {
+            errorStr.append(str);
+            errorStr.append('\n');
+        }
+
+        throw new ExitException("Not enough valid submissions! (only " + validSubmissions() + " "
+                + (validSubmissions() != 1 ? "are" : "is") + " valid):\n" + errorStr.toString(), ExitException.NOT_ENOUGH_SUBMISSIONS_ERROR);
+    }
+
+    private void throwBadBasecodeSubmission() throws jplag.ExitException {
+        StringBuilder errorStr = new StringBuilder();
+        for (String str : errorVector) {
+            errorStr.append(str);
+            errorStr.append('\n');
+        }
+
+        throw new ExitException("Bad basecode submission:\n" + errorStr.toString());
+    }
+
+    // COMPARE
+
+    /**
+     * Now the actual comparison: All submissions are compared pairwise.
+     */
+    private void compare() throws jplag.ExitException {
+        int size = submissions.size();
+
+        SortedVector<AllMatches> avgmatches, maxmatches;
+        int[] dist = new int[10];
+
+        // Result vector
+        avgmatches = new SortedVector<AllMatches>(new AllMatches.AvgComparator());
+        maxmatches = new SortedVector<AllMatches>(new AllMatches.MaxComparator());
+
+        long msec;
+
+        AllBasecodeMatches bcmatch;
+        Submission s1, s2;
+
+        options.setState(Options.COMPARING);
+        options.setProgress(0);
+
+        if (this.options.useBasecode) {
+            //			print("\nComparing with Basecode:\n", validSubmissions()
+            //					+ " submissions");
+            int countBC = 0;
+            // System.out.println("BC size: "+basecodeSubmission.size());
+            msec = System.currentTimeMillis();
+            for (int i = 0; i < (size); i++) {
+                s1 = submissions.elementAt(i);
+                // System.out.println("basecode recognition for: "+s1.name);
+                bcmatch = this.gSTiling.compareWithBasecode(s1, basecodeSubmission);
+                htBasecodeMatches.put(s1.name, bcmatch);
+                this.gSTiling.resetBaseSubmission(basecodeSubmission);
+                countBC++;
+                options.setProgress(countBC * 100 / size);
+            }
+            long timebc = System.currentTimeMillis() - msec;
+            print("\n\n", "\nTime for comparing with Basecode: " + ((timebc / 3600000 > 0) ? (timebc / 3600000) + " h " : "")
+                    + ((timebc / 60000 > 0) ? ((timebc / 60000) % 60000) + " min " : "") + (timebc / 1000 % 60) + " sec\n"
+                    + "Time per basecode comparison: " + (timebc / size) + " msec\n\n");
+        }
+
+        //		print("\nComparing:\n", validSubmissions() + " submissions");
+
+        int totalcomps = (size - 1) * size / 2;
+        int i, j, anz = 0, count = 0;
+        AllMatches match;
+
+        options.setProgress(0);
+        msec = System.currentTimeMillis();
+
+        for (i = 0; i < (size - 1); i++) {
+            s1 = submissions.elementAt(i);
+            if (s1.struct == null) {
+                count += (size - i - 1);
+                continue;
+            }
+
+            for (j = (i + 1); j < size; j++) {
+                s2 = submissions.elementAt(j);
+                if (s2.struct == null) {
+                    count++;
+                    continue;
+                }
+
+                match = this.gSTiling.compare(s1, s2);
+
+                anz++;
+
+                System.out.println("Comparing " + s1.name + "-" + s2.name + ": " + match.percent());
+
+                // histogram:
+                if (options.useBasecode) {
+                    match.bcmatchesA = htBasecodeMatches.get(match.subA.name);
+                    match.bcmatchesB = htBasecodeMatches.get(match.subB.name);
+                }
+
+                registerMatch(match, dist, avgmatches, maxmatches, null, i, j);
+                count++;
+                options.setProgress(count * 100 / totalcomps);
+            }
+        }
+        options.setProgress(100);
+        long time = System.currentTimeMillis() - msec;
+
+        print("\n", "Total time for comparing submissions: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
+                + ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n" + "Time per comparison: "
+                + (time / anz) + " msec\n");
+
+        Cluster cluster = null;
+        if (options.clustering)
+            cluster = this.clusters.calculateClustering(submissions);
+
+        writeResults(dist, avgmatches, maxmatches, null, cluster);
+    }
+
+    /**
+     * Revision compare mode: Compare each submission only with its next
+     * submission.
+     */
+    private void revisionCompare() throws jplag.ExitException {
+        int size = submissions.size();
+
+        SortedVector<AllMatches> avgmatches, maxmatches, minmatches;
+        int[] dist = new int[10];
+
+        // Result vector
+        avgmatches = new SortedVector<AllMatches>(new AllMatches.AvgReversedComparator());
+        maxmatches = new SortedVector<AllMatches>(new AllMatches.MaxReversedComparator());
+        minmatches = new SortedVector<AllMatches>(new AllMatches.MinReversedComparator());
+
+        long msec;
+
+        AllBasecodeMatches bcmatch;
+        Submission s1, s2;
+
+        options.setState(Options.COMPARING);
+        options.setProgress(0);
+
+        if (options.useBasecode) {
+            msec = System.currentTimeMillis();
+            for (int i = 0; i < size; i++) {
+                s1 = submissions.elementAt(i);
+                bcmatch = gSTiling.compareWithBasecode(s1, basecodeSubmission);
+                htBasecodeMatches.put(s1.name, bcmatch);
+                gSTiling.resetBaseSubmission(basecodeSubmission);
+                options.setProgress((i + 1) * 100 / size);
+            }
+            long timebc = System.currentTimeMillis() - msec;
+            print("\n\n", "\nTime for comparing with Basecode: " + ((timebc / 3600000 > 0) ? (timebc / 3600000) + " h " : "")
+                    + ((timebc / 60000 > 0) ? ((timebc / 60000) % 60000) + " min " : "") + (timebc / 1000 % 60) + " sec\n"
+                    + "Time per basecode comparison: " + (timebc / size) + " msec\n\n");
+        }
+
+        int totalcomps = size - 1;
+        int anz = 0, count = 0;
+        AllMatches match;
+
+        options.setProgress(0);
+        msec = System.currentTimeMillis();
+
+        s1loop:
+        for (int i = 0; i < size - 1; ) {
+            s1 = submissions.elementAt(i);
+            if (s1.struct == null) {
+                count++;
+                continue;
+            }
+
+            // Find next valid submission
+            int j = i;
+            do {
+                j++;
+                if (j >= size)
+                    break s1loop; // no more comparison pairs available
+                s2 = submissions.elementAt(j);
+            } while (s2.struct == null);
+
+            match = this.gSTiling.compare(s1, s2);
+
+            anz++;
+
+            /*
+             * System.out.println("Comparing "+s1.name+"-"+s2.name+": "+
+             * match.percent());
+             */
+            // histogram:
+            if (options.useBasecode) {
+                match.bcmatchesA = htBasecodeMatches.get(match.subA.name);
+                match.bcmatchesB = htBasecodeMatches.get(match.subB.name);
+            }
+
+            registerMatch(match, dist, avgmatches, maxmatches, minmatches, i, j);
+            count++;
+            options.setProgress(count * 100 / totalcomps);
+
+            i = j;
+        }
+        options.setProgress(100);
+        long time = System.currentTimeMillis() - msec;
+
+        print("\n", "Total time for comparing submissions: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
+                + ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n" + "Time per comparison: "
+                + (time / anz) + " msec\n");
+
+        Cluster cluster = null;
+        if (options.clustering)
+            cluster = this.clusters.calculateClustering(submissions);
+
+        writeResults(dist, avgmatches, maxmatches, minmatches, cluster);
+    }
+
+    private void createSubmissions() throws jplag.ExitException {
+        submissions = new Vector<Submission>();
+        File f = new File(options.root_dir);
+        if (f == null || !f.isDirectory()) {
+            throw new jplag.ExitException("\"" + options.root_dir + "\" is not a directory!");
+        }
+        String[] list = null;
+        try {
+            list = f.list();
+        } catch (SecurityException e) {
+            throw new jplag.ExitException("Unable to retrieve directory: " + options.root_dir + " Cause : " + e.toString());
+        }
+        Arrays.sort(list);
+
+        for (int i = 0; i < list.length; i++) {
+            File subm_dir = new File(f, list[i]);
+            if (!subm_dir.isDirectory()) {
+                if (options.sub_dir != null)
+                    continue;
+
+                boolean ok = false;
+                String name = subm_dir.getName();
+                for (int j = 0; j < options.suffixes.length; j++)
+                    if (name.endsWith(options.suffixes[j])) {
+                        ok = true;
+                        break;
+                    }
+
+                if (!ok)
+                    continue;
+
+                submissions.addElement(new Submission(name, f, this, get_language()));
+                continue;
+            }
+            if (options.exp && excludeFile(subm_dir.toString())) { // EXPERIMENT
+                // !!
+                System.err.println("excluded: " + subm_dir);
+                continue;
+            }
+
+            File file_dir = ((options.sub_dir == null) ? // - S option
+                    subm_dir
+                    : new File(subm_dir, options.sub_dir));
+            if (file_dir.isDirectory()) {
+                if (options.basecode.equals(subm_dir.getName())) {
+                    basecodeSubmission = new Submission(subm_dir.getName(), file_dir, options.read_subdirs, this, get_language());
+                } else {
+                    submissions.addElement(new Submission(subm_dir.getName(), file_dir, options.read_subdirs, this, get_language())); // -s
+                }
+            } else
+                throw new ExitException("Cannot find directory: " + file_dir.toString());
+        }
+    }
+
+    /**
+     * THIS IS FOR THE EMPIRICAL STUDY
+     */
+    private void createSubmissionsExp() throws jplag.ExitException {
+        // ES IST SICHER, DASS EIN INCLUDE-FILE ANGEGEBEN WURDE!
+        readIncludeFile();
+        submissions = new Vector<Submission>();
+        File f = new File(options.root_dir);
+        if (f == null || !f.isDirectory()) {
+            throw new jplag.ExitException(options.root_dir + " is not a directory!");
+        }
+        String[] list = new String[included.size()];
+        included.copyInto(list);
+        for (int i = 0; i < list.length; i++) {
+            File subm_dir = new File(f, list[i]);
+            if (subm_dir == null || !subm_dir.isDirectory())
+                continue;
+            if (options.exp && excludeFile(subm_dir.toString())) { // EXPERIMENT
+                // !!
+                System.err.println("excluded: " + subm_dir);
+                continue;
+            }
+            File file_dir = ((options.sub_dir == null) ? // - S option
+                    subm_dir
+                    : new File(subm_dir, options.sub_dir));
+            if (file_dir != null && file_dir.isDirectory())
+                submissions.addElement(new Submission(subm_dir.getName(), file_dir, options.read_subdirs, this, this.get_language())); // -s
+            else if (options.sub_dir == null) {
+                throw new jplag.ExitException(options.root_dir + " is not a directory!");
+            }
+        }
+    }
+
+    /**
+     * Check if a file is excluded or not
+     */
+    protected boolean excludeFile(String file) {
+        if (excluded == null)
+            return false;
+        Iterator<String> iter = excluded.iterator();
+        while (iter.hasNext())
+            if (file.endsWith(iter.next()))
+                return true;
+        return false;
+    }
+
+    // EXPERIMENT !!!!! special compare routine!
+    private void expCompare() throws jplag.ExitException {
+        int size = validSubmissions();
+        int[] similarity = new int[(size * size - size) / 2];
+
+        int anzSub = submissions.size();
+        int i, j, count = 0;
+        Submission s1, s2;
+        AllMatches match;
+        long msec = System.currentTimeMillis();
+        for (i = 0; i < (anzSub - 1); i++) {
+            s1 = submissions.elementAt(i);
+            if (s1.struct == null)
+                continue;
+            for (j = (i + 1); j < anzSub; j++) {
+                s2 = submissions.elementAt(j);
+                if (s2.struct == null)
+                    continue;
+
+                match = this.gSTiling.compare(s1, s2);
+                similarity[count++] = (int) match.percent();
+            }
+        }
+        long time = System.currentTimeMillis() - msec;
+        // output
+        System.out.print(options.root_dir + " ");
+        System.out.print(options.min_token_match + " ");
+        System.out.print(options.filtername + " ");
+        System.out.print((time) + " ");
+        for (i = 0; i < similarity.length; i++)
+            System.out.print(similarity[i] + " ");
+        System.out.println();
+    }
+
+    /**
+     * This is the special external comparison routine
+     */
+    private void externalCompare() throws jplag.ExitException {
+        int size = submissions.size();
+        // Progress progress;
+        // Result vector
+        SortedVector<AllMatches> avgmatches = new SortedVector<AllMatches>(new AllMatches.AvgComparator());
+        SortedVector<AllMatches> maxmatches = new SortedVector<AllMatches>(new AllMatches.MaxComparator());
+        int[] dist = new int[10];
+
+        print("Comparing: " + size + " submissions\n", null);
+        options.setState(Options.COMPARING);
+        options.setProgress(0);
+        long totalComparisons = (size * (size - 1)) / 2, count = 0, comparisons = 0;
+        int index = 0;
+        AllMatches match;
+        Submission s1, s2;
+        long remain;
+        String totalTimeStr, remainTime;
+
+        print("Checking memory size...\n", null);
+        // First try to load as many submissions as possible
+        index = fillMemory(0, size);
+
+        long startTime;
+        long totalTime = 0;
+        int startA = 0;
+        int endA = index / 2;
+        int startB = endA + 1;
+        int endB = index;
+        int i, j;
+        //		long progStart;
+
+        do {
+            // compare A to A
+            startTime = System.currentTimeMillis();
+            print("Comparing block A (" + startA + "-" + endA + ") to block A\n", null);
+            //progStart = (endA - startA + 1) * (endA - startA) / 2;
+            //      progress = new Progress(progStart > 0 ? progStart : 1, this);
+            //progStart = count;
+            for (i = startA; i <= endA; i++) {
+                //        progress.set(count - progStart);
+                options.setProgress((int) (count * 100 / totalComparisons));
+                s1 = submissions.elementAt(i);
+                if (s1.struct == null) {
+                    count += (endA - i);
+                    continue;
+                }
+                for (j = (i + 1); j <= endA; j++) {
+                    s2 = submissions.elementAt(j);
+                    if (s2.struct == null) {
+                        count++;
+                        continue;
+                    }
+
+                    match = this.gSTiling.compare(s1, s2);
+                    registerMatch(match, dist, avgmatches, maxmatches, null, i, j);
+                    comparisons++;
+                    count++;
+                }
+            }
+            //      progress.set(count - progStart);
+            options.setProgress((int) (count * 100 / totalComparisons));
+            print("\n", null);
+            totalTime += System.currentTimeMillis() - startTime;
+
+            // Are we finished?
+            if (startA == startB)
+                break;
+
+            do {
+                totalTimeStr = "" + ((totalTime / 3600000 > 0) ? (totalTime / 3600000) + " h " : "")
+                        + ((totalTime / 60000 > 0) ? ((totalTime / 60000) % 60) + " min " : "") + (totalTime / 1000 % 60) + " sec";
+                if (comparisons != 0)
+                    remain = totalTime * (totalComparisons - count) / comparisons;
+                else
+                    remain = 0;
+                remainTime = "" + ((remain / 3600000 > 0) ? (remain / 3600000) + " h " : "")
+                        + ((remain / 60000 > 0) ? ((remain / 60000) % 60) + " min " : "") + (remain / 1000 % 60) + " sec";
+
+                print("Progress: " + (100 * count) / totalComparisons + "%\nTime used for comparisons: " + totalTimeStr
+                        + "\nRemaining time (estimate): " + remainTime + "\n", null);
+
+                // compare A to B
+                startTime = System.currentTimeMillis();
+                print("Comparing block A (" + startA + "-" + endA + ") to block B (" + startB + "-" + endB + ")\n", null);
+                //progStart = (endA - startA + 1) * (endB - startB + 1);
+                //        progress = new Progress(progStart > 0 ? progStart : 1, this);
+                //progStart = count;
+                for (i = startB; i <= endB; i++) {
+                    //          progress.set(count - progStart);
+                    options.setProgress((int) (count * 100 / totalComparisons));
+                    s1 = submissions.elementAt(i);
+                    if (s1.struct == null) {
+                        count += (endA - startA + 1);
+                        continue;
+                    }
+                    for (j = startA; j <= endA; j++) {
+                        s2 = submissions.elementAt(j);
+                        if (s2.struct == null) {
+                            count++;
+                            continue;
+                        }
+
+                        match = this.gSTiling.compare(s1, s2);
+                        registerMatch(match, dist, avgmatches, maxmatches, null, i, j);
+                        comparisons++;
+                        count++;
+                    }
+                    s1.struct = null; // remove B
+                }
+                //        progress.set(count - progStart);
+                options.setProgress((int) (count * 100 / totalComparisons));
+                print("\n", null);
+                totalTime += System.currentTimeMillis() - startTime;
+
+                if (endB == size - 1) {
+                    totalTimeStr = "" + ((totalTime / 3600000 > 0) ? (totalTime / 3600000) + " h " : "")
+                            + ((totalTime / 60000 > 0) ? ((totalTime / 60000) % 60) + " min " : "") + (totalTime / 1000 % 60) + " sec";
+                    remain = totalTime * (totalComparisons - count) / comparisons;
+                    remainTime = "" + ((remain / 3600000 > 0) ? (remain / 3600000) + " h " : "")
+                            + ((remain / 60000 > 0) ? ((remain / 60000) % 60) + " min " : "") + (remain / 1000 % 60) + " sec";
+
+                    print("Progress: " + (100 * count) / totalComparisons + "%\nTime used for comparisons: " + totalTimeStr
+                            + "\nRemaining time (estimate): " + remainTime + "\n", null);
+                    break;
+                }
+
+                // Remove B -> already done...
+                // for (i=startB; i<=endB; i++)
+                // ((Submission)submissions.elementAt(i)).struct = null;
+                runtime.runFinalization();
+                runtime.gc();
+                Thread.yield();
+                // Try to find the next B
+                print("Finding next B\n", null);
+
+                index = fillMemory(endB + 1, size);
+
+                startB = endB + 1;
+                endB = index;
+
+            } while (true);
+
+            // Remove A
+            for (i = startA; i <= endA; i++)
+                submissions.elementAt(i).struct = null;
+            runtime.runFinalization();
+            runtime.gc();
+            Thread.yield();
+            print("Find next A.\n", null);
+            // First try to load as many submissions as possible
+
+            index = fillMemory(endA + 1, size);
+
+            if (index != size - 1) {
+                startA = endA + 1;
+                endA = startA + (index - startA + 1) / 2;
+                startB = endA + 1;
+                endB = index;
+            } else {
+                startA = startB; // last block
+                endA = endB = index;
+            }
+        } while (true);
+
+        totalTime += System.currentTimeMillis() - startTime;
+        totalTimeStr = "" + ((totalTime / 3600000 > 0) ? (totalTime / 3600000) + " h " : "")
+                + ((totalTime / 60000 > 0) ? ((totalTime / 60000) % 60000) + " min " : "") + (totalTime / 1000 % 60) + " sec";
+
+        print("Total comparison time: " + totalTimeStr + "\nComparisons: " + count + "/" + comparisons + "/" + totalComparisons + "\n",
+                null);
+
+        // free remaining memory
+        for (i = startA; i <= endA; i++)
+            submissions.elementAt(i).struct = null;
+        runtime.runFinalization();
+        runtime.gc();
+        Thread.yield();
+
+        // System.out.println("Matrix:\n"+ similarity);
+        Cluster cluster = null;
+        if (options.clustering)
+            cluster = this.clusters.calculateClustering(submissions);
+
+        writeResults(dist, avgmatches, maxmatches, null, cluster);
+    }
+
+    private int fillMemory(int from, int size) {
+        Submission sub = null;
+        int index = from;
+
+        runtime.runFinalization();
+        runtime.gc();
+        Thread.yield();
+        long freeBefore = runtime.freeMemory();
+        try {
+            for (; index < size; index++) {
+                sub = submissions.elementAt(index);
+                sub.struct = new Structure();
+                if (!sub.struct.load(new File("temp", sub.dir.getName() + sub.name)))
+                    sub.struct = null;
+            }
+        } catch (java.lang.OutOfMemoryError e) {
+            sub.struct = null;
+            print("Memory overflow after loading " + (index - from + 1) + " submissions.\n", null);
+        }
+        if (index >= size)
+            index = size - 1;
+
+        if (freeBefore / runtime.freeMemory() <= 2)
+            return index;
+        for (int i = (index - from) / 2; i > 0; i--) {
+            submissions.elementAt(index--).struct = null;
+        }
+        runtime.runFinalization();
+        runtime.gc();
+        Thread.yield();
+
+        // make sure we freed half of the "available" memory.
+        long free;
+        while (freeBefore / (free = runtime.freeMemory()) > 2) {
+            submissions.elementAt(index--).struct = null;
+            runtime.runFinalization();
+            runtime.gc();
+            Thread.yield();
+        }
+        print(free / 1024 / 1024 + "MByte freed. Current index: " + index + "\n", null);
+
+        return index;
+    }
+
+    public String get_basecode() {
+        return this.options.basecode;
+    }
+
+    public int get_clusterType() {
+        return this.options.clusterType;
+    }
+
+    public String get_commandLine() {
+        return this.options.commandLine;
+    }
+
+    public String getCountryTag() {
+        return options.getCountryTag();
+    }
+
+    /*
+     * Distribution: Program given away to:
+     *
+     * 0: Server version
+     *
+     * 1: David Klausner 2: Ronald Kostoff 3: Bob Carlson 4: Neville Newman
+     */
+
+    public int get_distri() {
+        return 0;
+    }
+
+    public File get_jplagResult() {
+        return new File(options.result_dir);
+
+    }
+
+    public Language get_language() {
+        return this.options.language;
+    }
+
+    public int get_min_token_match() {
+        return this.options.min_token_match;
+    }
+
+    public String get_title() {
+        return this.options.title;
+    }
+
+    public String get_original_dir() {
+        return this.options.original_dir;
+    }
+
+    public String get_result_dir() {
+        return this.options.result_dir;
+    }
+
+    public String get_root_dir() {
+        return this.options.root_dir;
+    }
+
+    public SimilarityMatrix get_similarity() {
+        return this.options.similarity;
+    }
+
+    public String get_sub_dir() {
+        return this.options.sub_dir;
+    }
+
+    public String[] get_suffixes() {
+        return this.options.suffixes;
+    }
+
+    public int[] get_themewords() {
+        return this.options.themewords;
+    }
+
+    public float[] get_threshold() {
+        return this.options.threshold;
+    }
+
+    public int getErrors() {
+        return errors;
+    }
+
+    public void hash_distribution() {
+        int[] dist = new int[20];
+        int count = 0;
+        Enumeration<Submission> enum1 = submissions.elements();
+
+        while (enum1.hasMoreElements()) {
+            Structure struct = enum1.nextElement().struct;
+            if (struct != null) {
+                struct.table.count_dist(dist);
+                count++;
+            }
+        }
+
+        System.out.println("Count: " + count);
+        for (int i = 0; i < dist.length; i++)
+            System.out.println(i + "\t" + dist[i]);
+    }
+
+    private void makeTempDir() throws jplag.ExitException {
+        print(null, "Creating temporary dir.\n");
+        File f = new File("temp");
+        if (!f.exists()) {
+            if (!f.mkdirs()) {
+                throw new jplag.ExitException("Cannot create temporary directory!");
+            }
+        }
+        if (!f.isDirectory()) {
+            throw new ExitException("'temp' is not a directory!");
+        }
+        if (!f.canWrite()) {
+            throw new ExitException("Cannot write directory: 'temp'");
+        }
+    }
+
+    private void myWrite(String str) {
+        if (writer != null) {
+            try {
+                writer.write(str);
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        } else
+            System.out.print(str);
+    }
+
+    // PARSE
+    /*
+     * Compiles all "submissions"
+     */
+    private void parseAll() throws jplag.ExitException {
+        if (submissions == null) {
+            System.out.println("  Nothing to parse!");
+            return;
+        }
+        // lets go:)
+        int count = 0;
+        int totalcount = submissions.size();
+        options.setState(Options.PARSING);
+        options.setProgress(0);
+        long msec = System.currentTimeMillis();
+        Iterator<Submission> iter = submissions.iterator();
+
+        if (options.externalSearch)
+            makeTempDir();
+        int invalid = 0;
+        while (iter.hasNext()) {
+            boolean ok = true;
+            boolean removed = false;
+            Submission subm = iter.next();
+            print(null, "------ Parsing submission: " + subm.name + "\n");
+            currentSubmissionName = subm.name;
+            options.setProgress(count * 100 / totalcount);
+            if (!(ok = subm.parse()))
+                errors++;
+
+            if (options.exp && options.filter != null)
+                subm.struct = options.filter.filter(subm.struct); // EXPERIMENT
+            count++;
+            if (subm.struct != null && subm.size() < options.min_token_match) {
+                print(null, "Submission contains fewer tokens than minimum match " + "length allows!\n");
+                subm.struct = null;
+                invalid++;
+                removed = true;
+            }
+            if (options.externalSearch) {
+                if (subm.struct != null) {
+                    this.gSTiling.create_hashes(subm.struct, options.min_token_match, false);
+                    subm.struct.save(new File("temp", subm.dir.getName() + subm.name));
+                    subm.struct = null;
+                }
+            }
+            if (!options.externalSearch && subm.struct == null) {
+                invalidSubmissionNames = (invalidSubmissionNames == null) ? subm.name : invalidSubmissionNames + " - " + subm.name;
+                iter.remove();
+            }
+            if (ok && !removed)
+                print(null, "OK\n");
+            else
+                print(null, "ERROR -> Submission removed\n");
+        }
+
+        options.setProgress(100);
+        print("\n" + (count - errors - invalid) + " submissions parsed successfully!\n" + errors + " parser error"
+                + (errors != 1 ? "s!\n" : "!\n"), null);
+        if (invalid != 0) {
+            print(null, invalid
+                    + ((invalid == 1) ? " submission is not valid because it contains" : " submissions are not valid because they contain")
+                    + " fewer tokens\nthan minimum match length allows.\n");
+        }
+        long time = System.currentTimeMillis() - msec;
+        print("\n\n", "\nTotal time for parsing: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
+                + ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n"
+                + "Time per parsed submission: " + (count > 0 ? (time / count) : "n/a") + " msec\n\n");
+    }
+
+    private void parseBasecodeSubmission() throws jplag.ExitException {
+        Submission subm = basecodeSubmission;
+        if (subm == null) {
+            options.useBasecode = false;
+            return;
+        }
+        long msec = System.currentTimeMillis();
+        print("----- Parsing basecode submission: " + subm.name + "\n", null);
+
+        // lets go:
+        if (options.externalSearch)
+            makeTempDir();
+
+        if (!subm.parse())
+            throwBadBasecodeSubmission();
+
+        if (options.exp && options.filter != null)
+            subm.struct = options.filter.filter(subm.struct); // EXPERIMENT
+
+        if (subm.struct != null && subm.size() < options.min_token_match)
+            throw new ExitException("Basecode submission contains fewer tokens " + "than minimum match length allows!\n");
+
+        if (options.useBasecode)
+            gSTiling.create_hashes(subm.struct, options.min_token_match, true);
+        if (options.externalSearch) {
+            if (subm.struct != null) {
+                gSTiling.create_hashes(subm.struct, options.min_token_match, false);
+                subm.struct.save(new File("temp", subm.dir.getName() + subm.name));
+                subm.struct = null;
+            }
+        }
+
+        print("\nBasecode submission parsed!\n", null);
+        long time = System.currentTimeMillis() - msec;
+        print("\n", "\nTime for parsing Basecode: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
+                + ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n");
+    }
+
+    // Excluded files:
+
+    /*
+     * If an exclusion file is given, it is read in and all stings are saved in
+     * the set "excluded".
+     */
+    private void readExclusionFile() {
+        if (options.exclude_file == null)
+            return;
+        excluded = new HashSet<String>();
+
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(options.exclude_file));
+            String line;
+            while ((line = in.readLine()) != null) {
+                excluded.add(line.trim());
+            }
+            in.close();
+        } catch (FileNotFoundException e) {
+            System.out.println("Exclusion file not found: " + options.exclude_file);
+        } catch (IOException e) {
+        }
+        print(null, "Excluded files:\n");
+        if (options.verbose_long) {
+            Iterator<String> iter = excluded.iterator();
+            while (iter.hasNext()) {
+                print(null, "  " + iter.next() + "\n");
+            }
+        }
+    }
+
+    /*
+     * If an include file is given, read it in and store all the strings in
+     * "included".
+     */
+    private void readIncludeFile() {
+        if (options.include_file == null)
+            return;
+        included = new Vector<String>();
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(options.include_file));
+            String line;
+            while ((line = in.readLine()) != null) {
+                included.addElement(line.trim());
+            }
+            in.close();
+        } catch (FileNotFoundException e) {
+            System.out.println("Include file not found: " + options.include_file);
+        } catch (IOException e) {
+        }
+        print(null, "Included dirs:\n");
+        if (options.verbose_long) {
+            Enumeration<String> enum1 = included.elements();
+            while (enum1.hasMoreElements())
+                print(null, "  " + enum1.nextElement() + "\n");
+        }
+    }
+
+    private void registerMatch(AllMatches match, int[] dist, SortedVector<AllMatches> avgmatches, SortedVector<AllMatches> maxmatches,
+                               SortedVector<AllMatches> minmatches, int a, int b) {
+        float avgpercent = match.percent();
+        float maxpercent = match.percentMaxAB();
+        float minpercent = match.percentMinAB();
+
+        dist[((((int) avgpercent) / 10) == 10) ? 9 : (((int) avgpercent) / 10)]++;
+        if (!options.store_percent) {
+            if ((avgmatches.size() < options.store_matches || avgpercent > avgmatches.lastElement().percent()) && avgpercent > 0) {
+                avgmatches.insert(match);
+                if (avgmatches.size() > options.store_matches)
+                    avgmatches.removeElementAt(options.store_matches);
+            }
+            if (maxmatches != null && (maxmatches.size() < options.store_matches || maxpercent > maxmatches.lastElement().percent())
+                    && maxpercent > 0) {
+                maxmatches.insert(match);
+                if (maxmatches.size() > options.store_matches)
+                    maxmatches.removeElementAt(options.store_matches);
+            }
+            if (minmatches != null && (minmatches.size() < options.store_matches || minpercent > minmatches.lastElement().percent())
+                    && minpercent > 0) {
+                minmatches.insert(match);
+                if (minmatches.size() > options.store_matches)
+                    minmatches.removeElementAt(options.store_matches);
+            }
+        } else { // store_percent
+            if (avgpercent > options.store_matches) {
+                avgmatches.insert(match);
+                if (avgmatches.size() > Options.MAX_RESULT_PAIRS)
+                    avgmatches.removeElementAt(Options.MAX_RESULT_PAIRS);
+            }
+
+            if (maxmatches != null && maxpercent > options.store_matches) {
+                maxmatches.insert(match);
+                if (maxmatches.size() > Options.MAX_RESULT_PAIRS)
+                    maxmatches.removeElementAt(Options.MAX_RESULT_PAIRS);
+            }
+
+            if (minmatches != null && minpercent > options.store_matches) {
+                minmatches.insert(match);
+                if (minmatches.size() > Options.MAX_RESULT_PAIRS)
+                    minmatches.removeElementAt(Options.MAX_RESULT_PAIRS);
+            }
+        }
+        if (options.clustering)
+            options.similarity.setSimilarity(a, b, avgpercent);
+    }
+
+    private String toUTF8(String str) {
+        byte[] utf8 = null;
+        try {
+            utf8 = str.getBytes("UTF-8");
+        } catch (UnsupportedEncodingException e) {
+        }
+        return new String(utf8);
+    }
+
+    /** *************************** */
+    /* THE MAIN PROCEDURE */
+
+    /**
+     * **************************
+     */
+    public void run() throws jplag.ExitException {
+        if (options.output_file != null) {
+            try {
+                writer = new FileWriter(new File(options.output_file));
+                writer.write(name_long + "\n");
+                writer.write(dateTimeFormat.format(new Date()) + "\n\n");
+            } catch (IOException ex) {
+                System.out.println("Unable to open or write to log file: " + options.output_file);
+                throw new ExitException("Unable to create log file!");
+            }
+        } else
+            print(null, name_long + "\n\n");
+        print(null, "Language: " + options.language.name() + "\n\n");
+        if (options.original_dir == null)
+            print(null, "Root-dir: " + options.root_dir + "\n"); // server
+        // this file contains all files names which are excluded
+        readExclusionFile();
+        if (options.include_file == null) {
+            createSubmissions();
+            System.out.println(submissions.size() + " submissions");
+        } else
+            createSubmissionsExp();
+
+        if (!options.skipParse) {
+            try {
+                parseAll();
+                System.gc();
+                parseBasecodeSubmission();
+            } catch (OutOfMemoryError e) {
+                submissions = null;
+                System.gc();
+                System.out.println("[" + new Date() + "] OutOfMemoryError " + "during parsing of submission \"" + currentSubmissionName
+                        + "\"");
+                throw new ExitException("Out of memory during parsing of submission \"" + currentSubmissionName + "\"");
+            } catch (ExitException e) {
+                throw e;
+            } catch (Throwable e) {
+                System.out.println("[" + new Date() + "] Unknown exception " + "during parsing of submission \"" + currentSubmissionName
+                        + "\"");
+                e.printStackTrace();
+                throw new ExitException("Unknown exception during parsing of " + "submission \"" + currentSubmissionName + "\"");
+            }
+        } else
+            print("Skipping parsing...\n", null);
+
+        if (validSubmissions() < 2) {
+            throwNotEnoughSubmissions();
+        }
+        errorVector = null; // errorVector is not needed anymore
+
+        if (options.clustering) {
+            clusters = new Clusters(this);
+            options.similarity = new SimilarityMatrix(submissions.size());
+        }
+        System.gc();
+        if (options.exp) { // EXPERIMENT
+            expCompare();
+        } else if (options.externalSearch) {
+            try {
+                externalCompare();
+            } catch (OutOfMemoryError e) {
+                e.printStackTrace();
+            }
+        } else {
+            if (options.compare > 0)
+                specialCompare(); // compare every submission to x others
+            else {
+                switch (options.comparisonMode) {
+                    case Options.COMPMODE_NORMAL:
+                        compare();
+                        break;
+
+                    case Options.COMPMODE_REVISION:
+                        revisionCompare();
+                        break;
+
+                    default:
+                        throw new ExitException("Illegal comparison mode: \"" + options.comparisonMode + "\"");
+                }
+            }
+        }
+        closeWriter();
+
+        String str = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>";
+        str += "<jplag_infos>\n";
+        str += "<infos \n";
+
+        String sp = "\"";
+        str += " title = " + sp + toUTF8(options.getTitle()) + sp;
+        str += " source = " + sp + (get_original_dir() != null ? toUTF8(get_original_dir()) : "") + sp;
+        str += " n_of_programs = " + sp + submissions.size() + sp;
+        str += " errors = " + sp + get_language().errorsCount() + sp;
+        str += " path_to_files = " + sp + toUTF8((options.sub_dir != null) ? options.sub_dir : "") + sp;
+        str += " basecode_dir = " + sp + toUTF8((options.basecode != null) ? options.basecode : "") + sp;
+        str += " read_subdirs = " + sp + this.options.read_subdirs + sp;
+        str += " clustertype = " + sp + this.options.getClusterTyp() + sp;
+        str += " store_matches = " + sp + this.options.store_matches + ((this.options.store_percent) ? "%" : "") + sp;
+        String suf = "";
+        for (int s = 0; s < this.options.suffixes.length; s++)
+            suf += "," + this.options.suffixes[s];
+        str += " suffixes = " + sp + suf.substring(1) + sp;
+        str += " language_name = " + sp + this.options.languageName + sp;
+        str += " comparison_mode = " + sp + this.options.comparisonMode + sp;
+        str += " country_tag = " + sp + this.options.getCountryTag() + sp;
+        str += " min_token = " + sp + this.options.min_token_match + sp;
+        str += " date = " + sp + System.currentTimeMillis() + sp;
+
+        str += "/>\n";
+        str += "</jplag_infos>";
+
+        try {
+            FileWriter fw = new FileWriter(new File(this.options.result_dir + File.separator + "result.xml"));
+            fw.write(str);
+            fw.close();
+        } catch (IOException ex) {
+            System.out.println("Unable to create result.xml");
+        }
+    }
+
+    public void set_result_dir(String result_dir) {
+        this.options.result_dir = result_dir;
+    }
+
+    /*
+     * Now the special comparison:
+     */
+    private void specialCompare() throws jplag.ExitException {
+        File root = new File(options.result_dir);
+        HTMLFile f = this.report.openHTMLFile(root, "index.html");
+        this.report.copyFixedFiles(root);
+
+        this.report.writeIndexBegin(f, "Special Search Results"); // start HTML
+        f.println("<P><A NAME=\"matches\"><H4>Matches:</H4><P>");
+
+        int size = submissions.size();
+        int matchIndex = 0;
+
+        print("Comparing: ", validSubmissions() + " submissions");
+        print("\n(Writing results at the same time.)\n", null);
+
+        options.setState(Options.COMPARING);
+        options.setProgress(0);
+        int totalcomps = size * size;
+        int i, j, anz = 0, count = 0;
+        AllMatches match;
+        Submission s1, s2;
+        long msec = System.currentTimeMillis();
+        for (i = 0; i < (size - 1); i++) {
+            // Result vector
+            SortedVector<AllMatches> matches = new SortedVector<AllMatches>(new AllMatches.AvgComparator());
+
+            s1 = submissions.elementAt(i);
+            if (s1.struct == null) {
+                count += (size - 1);
+                continue;
+            }
+            for (j = 0; j < size; j++) {
+                s2 = submissions.elementAt(j);
+                if ((i == j) || (s2.struct == null)) {
+                    count++;
+                    continue;
+                }
+
+                match = this.gSTiling.compare(s1, s2);
+                anz++;
+
+                float percent = match.percent();
+
+                if ((matches.size() < options.compare || matches.size() == 0 || match.moreThan(matches.lastElement().percent()))
+                        && match.moreThan(0)) {
+                    matches.insert(match);
+                    if (matches.size() > options.compare)
+                        matches.removeElementAt(options.compare);
+                }
+
+                if (options.clustering)
+                    options.similarity.setSimilarity(i, j, percent);
+
+                count++;
+                options.setProgress(count * 100 / totalcomps);
+            }
+
+            // now output matches:
+            f.println("<TABLE CELLPADDING=3 CELLSPACING=2>");
+            boolean once = true;
+            for (Iterator<AllMatches> iter = matches.iterator(); iter.hasNext(); ) {
+                match = iter.next();
+                if (once) {
+                    f.println("<TR><TD BGCOLOR=" + this.report.color(match.percent(), 128, 192, 128, 192, 255, 255) + ">" + s1.name
+                            + "<TD WIDTH=\"10\">-&gt;");
+                    once = false;
+                }
+
+                int other = (match.subName(0).equals(s1.name) ? 1 : 0);
+                f.println(" <TD BGCOLOR=" + this.report.color(match.percent(), 128, 192, 128, 192, 255, 255)
+                        + " ALIGN=center><A HREF=\"match" + matchIndex + ".html\">" + match.subName(other) + "</A><BR><FONT COLOR=\""
+                        + this.report.color(match.percent(), 0, 255, 0, 0, 0, 0) + "\"><B>(" + match.roundedPercent() + "%)</B></FONT>");
+                this.report.writeMatch(root, matchIndex++, match);
+            }
+            f.println("</TR>");
+        }
+        f.println("</TABLE><P>\n");
+        f.println("<!---->");
+        this.report.writeIndexEnd(f);
+        f.close();
+
+        options.setProgress(100);
+        long time = System.currentTimeMillis() - msec;
+        print("\n", "Total time: " + ((time / 3600000 > 0) ? (time / 3600000) + " h " : "")
+                + ((time / 60000 > 0) ? ((time / 60000) % 60000) + " min " : "") + (time / 1000 % 60) + " sec\n" + "Time per comparison: "
+                + (time / anz) + " msec\n");
+
+    }
+
+    // DEBUG !!!
+    public void token_distribution() {
+        int[] count = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+                0, 0, 0}; // to
+        // count
+        // the
+        // distribution
+
+        Enumeration<Submission> enum1 = submissions.elements();
+
+        while (enum1.hasMoreElements()) {
+            Structure struct = enum1.nextElement().struct;
+            if (struct != null)
+                for (int i = struct.size() - 1; i >= 0; i--)
+                    count[struct.tokens[i].type]++;
+        }
+
+        int tot = 0;
+        for (int i = 0; i < 0; i++) { // !!!!!!!!!!!!!!!
+            int c = count[i];
+            tot += c;
+            // System.out.println(Token.type2string(i)+"\t"+c);
+        }
+        System.out.println((tot > 999 ? "" : (tot > 99 ? " " : (tot > 9 ? "  " : "   "))) + tot);
+    }
+
+    public boolean use_clustering() {
+        return this.options.clustering;
+    }
+
+    public boolean use_debugParser() {
+        return this.options.debugParser;
+    }
+
+    public boolean use_diff_report() {
+        return this.options.diff_report;
+    }
+
+    public boolean use_externalSearch() {
+        return this.options.externalSearch;
+    }
+
+    public boolean use_verbose_details() {
+        return this.options.verbose_details;
+    }
+
+    public boolean use_verbose_long() {
+        return this.options.verbose_long;
+    }
+
+    public boolean use_verbose_parser() {
+        return this.options.verbose_parser;
+    }
+
+    public boolean use_verbose_quiet() {
+        return this.options.verbose_quiet;
+    }
+
+    public boolean useBasecode() {
+        return this.options.useBasecode;
+    }
+
+    // RESULT
+
+    /*
+     * Erst wird die Existenz des Ergebnis-Verzeichnisses sichergestellt, dann
+     * wird die Erstellung der Dateien durch die Klasse "Report" erledigt.
+     */
+    private void writeResults(int[] dist, SortedVector<AllMatches> avgmatches, SortedVector<AllMatches> maxmatches,
+                              SortedVector<AllMatches> minmatches, Cluster clustering) throws jplag.ExitException {
+        options.setState(Options.GENERATING_RESULT_FILES);
+        options.setProgress(0);
+        if (options.original_dir == null)
+            print("Writing results to: " + options.result_dir + "\n", null);
+        File f = new File(options.result_dir);
+        if (!f.exists())
+            if (!f.mkdirs()) {
+                throw new jplag.ExitException("Cannot create directory!");
+            }
+        if (!f.isDirectory()) {
+            throw new jplag.ExitException(options.result_dir + " is not a directory!");
+        }
+        if (!f.canWrite()) {
+            throw new jplag.ExitException("Cannot write directory: " + options.result_dir);
+        }
+
+        this.report.write(f, dist, avgmatches, maxmatches, minmatches, clustering, options);
+
+        if (options.externalSearch)
+            writeTextResult(f, avgmatches);
+    }
+
+    private void writeTextResult(File dir, SortedVector<AllMatches> matches) {
+        Iterator<AllMatches> iter = matches.iterator();
+
+        print("Writing special 'matches.txt' file\n", null);
+
+        try {
+            File f = new File(dir, "matches.txt");
+            PrintWriter writer = new PrintWriter(new FileWriter(f));
+
+            while (iter.hasNext()) {
+                AllMatches match = iter.next();
+
+                String file1, file2, tmp;
+                file1 = match.subA.name;
+                file2 = match.subB.name;
+
+                if (file1.compareTo(file2) > 0) {
+                    tmp = file2;
+                    file2 = file1;
+                    file1 = tmp;
+                }
+
+                writer.println(file1 + "\t" + file2 + "\t" + match.percent());
+            }
+            writer.close();
+        } catch (IOException e) {
+            print("IOException while writing file\n", null);
+        }
+    }
 }

jplag/src/main/java/jplag/Report.java

@@ -98,14 +98,14 @@ public class Report implements TokenConstants {
 	public void writeHTMLHeader(HTMLFile file, String title) {
 		file.println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">");
 		file.println("<HTML><HEAD><TITLE>" + title + "</TITLE>");
-		file.println("<META http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\">");
+		file.println("<META http-equiv=\"Content-Type\" content=\"text/html; charset=UTF-8\">");
 		file.println("</HEAD>");
 	}
 
 	public void writeHTMLHeaderWithScript(HTMLFile file, String title) {
 		file.println("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">");
 		file.println("<HTML>\n<HEAD>\n <TITLE>" + title + "</TITLE>");
-		file.println("<META http-equiv=\"Content-Type\" content=\"text/html; charset=iso-8859-1\">");
+		file.println("<META http-equiv=\"Content-Type\" content=\"text/html; charset=UTF-8\">");
 		file.println("  <script type=\"text/javascript\">\n  <!--");
 		file.println("   function ZweiFrames(URL1,F1,URL2,F2)\n   {");
 		file.println("    parent.frames[F1].location.href=URL1;");

jplag/src/main/java/jplag/Submission.java

@@ -8,6 +8,7 @@ import java.io.FileOutputStream;
 import java.io.FileReader;
 import java.io.FilenameFilter;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.net.URL;
 import java.text.DecimalFormat;
 import java.util.Vector;
@@ -81,7 +82,7 @@ public class Submission implements Comparable<Submission> {
 			return;
 		if (readSubDirs) {
 			String[] dirs = aktDir.list();
-			if (subDir != "")
+			if (!subDir.equals(""))
 				for (int i = 0; i < dirs.length; i++)
 					lookupDir(dir, subDir + File.separator + dirs[i]);
 			else
@@ -214,7 +215,10 @@ public class Submission implements Comparable<Submission> {
 		for (int i = 0; i < files.length; i++) {
 			text.removeAllElements();
 			try {
-				BufferedReader in = new BufferedReader(new FileReader(new File(dir, files[i])));
+				/* file encoding = "UTF-8" */
+				FileInputStream fileInputStream = new FileInputStream(new File(dir, files[i]));
+				InputStreamReader inputStreamReader = new InputStreamReader(fileInputStream, "UTF-8");
+				BufferedReader in = new BufferedReader(inputStreamReader);
 				while ((help = in.readLine()) != null) {
 					help = help.replaceAll("&", "&amp;");
 					help = help.replaceAll("<", "&lt;");
@@ -223,6 +227,8 @@ public class Submission implements Comparable<Submission> {
 					text.addElement(help);
 				}
 				in.close();
+				inputStreamReader.close();
+				fileInputStream.close();
 			} catch (FileNotFoundException e) {
 				System.out.println("File not found: " + ((new File(dir, files[i])).toString()));
 			} catch (IOException e) {

jplag/src/main/resources/jplag/data/help-de.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Wie man die Ergebnisse liest</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">
@@ -11,19 +11,19 @@
 
 <p>Das Fenster ist in vier Teile unterteilt:
 
-<p>Die beiden unteren Teile enthalten die Programme, wobei ähnliche Abschnitte
+<p>Die beiden unteren Teile enthalten die Programme, wobei ähnliche Abschnitte
 mit der selben Farbe markiert sind und durch <img src="forward.gif"
-alt="Vorwärts"> oder <img src="back.gif" alt="Rückwärts"> auf die jeweilige
+alt="Vorwärts"> oder <img src="back.gif" alt="Rückwärts"> auf die jeweilige
 Stelle im anderen Programm verwiesen wird. Klickt man auf diese Bilder,
 springen die anderen Ansichten zu den entsprechenden Stellen.<br>
-Wurde zu einem Block kein ähnlicher Abschnitt im anderen Programm gefunden, so
+Wurde zu einem Block kein ähnlicher Abschnitt im anderen Programm gefunden, so
 wird dieser Block schwarz dargestellt. 
 
-<p>Der linke obere Teil zeigt die prozentuale Ähnlichkeit zwischen den beiden
+<p>Der linke obere Teil zeigt die prozentuale Ähnlichkeit zwischen den beiden
 Programmen und bietet Verweise zur Index-Seite und zu dieser Hilfe-Seite an.
 
-<p>Zuletzt enthält der rechte obere Teil eine Tabelle aller Abschnitte, zu denen
-ähnliche Abschnitte gefunden wurden. Dabei hat die Tabelle folgendes Format:
+<p>Zuletzt enthält der rechte obere Teil eine Tabelle aller Abschnitte, zu denen
+ähnliche Abschnitte gefunden wurden. Dabei hat die Tabelle folgendes Format:
 
 <p><TABLE BORDER="1" CELLSPACING="0" BGCOLOR="#d0d0d0">
 <TR><TH><TH>Programm_1 (??%)<TH>Programm_2 (??%)<TH>Meta-Zeichen
@@ -36,7 +36,7 @@ Programmen und bietet Verweise zur Index-Seite und zu dieser Hilfe-Seite an.
 </TABLE>
 
 <p>Jede Zeile gibt einen Bereich von Dateizeilen an, die als gleich zu
-betrachten sind, zusammen mit der Größe der Abschnitte in Meta-Zeichen.
+betrachten sind, zusammen mit der Größe der Abschnitte in Meta-Zeichen.
 Die Dateinamen sind wiederum Verweise auf die entsprechenden
 Stellen in beiden Programmen, die in der Farbe des kleinen Rechtecks dargestellt
 werden.

jplag/src/main/resources/jplag/data/help-en.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>How to read the results</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-es.html

@@ -1,33 +1,33 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<HTML><HEAD><TITLE>Cómo leer los resultados</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<HTML><HEAD><TITLE>Cómo leer los resultados</TITLE>
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">
 
 <center><IMG SRC="logo.gif" ALT="JPlag" BORDER="0"></center>
 
-<h1>Cómo leer los resultados</h1>
+<h1>Cómo leer los resultados</h1>
 
 <p>La ventana se encuentra dividida en cuatro marcos:
 
 <p>Los dos marcos grandes en el fondo contienen las solicitudes en las
- cuales los parrafos similares están marcados con el mismo color. El texto 
-negro significa que no se encontró ninguna parte que coincidiese con la 
-otra solicitud. Además, cada parrafo tiene asociado <img src="forward.gif" alt="Adelante"> o
-<img src="back.gif" alt="Atrás">. Pulsar sobre estos iconos lleva el foco en el 
+ cuales los parrafos similares están marcados con el mismo color. El texto 
+negro significa que no se encontró ninguna parte que coincidiese con la 
+otra solicitud. Además, cada parrafo tiene asociado <img src="forward.gif" alt="Adelante"> o
+<img src="back.gif" alt="Atrás">. Pulsar sobre estos iconos lleva el foco en el 
 otro marco del programa al pasaje que coincida realiza un scroll en la tabla
-a lo alto de la otra posición.
+a lo alto de la otra posición.
 
 <p>El marco izquierdo en la parte superior muestra el porcentaje de la 
 semejanza entre los dos programas y proporciona links al inicio 
-y a la página estás leyendo ahora.
+y a la página estás leyendo ahora.
 
 <p>El marco de la derecha contiene una tabla de todos los pasajes que
 coinciden. La tabla tiene el siguiente formato:
 
 <p><TABLE BORDER="1" CELLSPACING="0" BGCOLOR="#d0d0d0">
-<TR><TH><TH>Solicitud1 (??%)<TH>Solicitud2 (??%)<TH>Símbolos
+<TR><TH><TH>Solicitud1 (??%)<TH>Solicitud2 (??%)<TH>Símbolos
 <TR><TD BGCOLOR="#c00000"><FONT COLOR="#c00000">-</FONT><TD>
 <A HREF="">archivo1 (1-8)</a><TD><A HREF="">archivo2 (1-10)</A>
 <TD ALIGN=center><FONT COLOR="#b00000">23</FONT>
@@ -36,13 +36,13 @@ coinciden. La tabla tiene el siguiente formato:
 <TD ALIGN=center><FONT COLOR="#600000">11</FONT>
 </TABLE>
 
-<p>Cada línea proporciona un rango de números de línea del archivo1 y 
-el archivo2 que son consideradas iguales, junto con el tamaño del 
-pasaje en símbolos.
+<p>Cada línea proporciona un rango de números de línea del archivo1 y 
+el archivo2 que son consideradas iguales, junto con el tamaño del 
+pasaje en símbolos.
 
 Los nombres de archivos son hyperlinks al parrafo apropiado en ambos programas.
 
-El parrafo tiene el color del rectángulo pequeño en el borde izquierdo de la fila.
+El parrafo tiene el color del rectángulo pequeño en el borde izquierdo de la fila.
 
 <p><a href="index.html">INDICE</a>
 <p>

jplag/src/main/resources/jplag/data/help-fr.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>How to read the results</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-pt.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>How to read the results</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-ptbr.html

@@ -3,7 +3,7 @@
 <head>
   <title>Como ler os resultados</title>
   <meta http-equiv="Content-Type"
- content="text/html; charset=iso-8859-1">
+ content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#ffffff" link="#000088" text="#000000" vlink="#000000">
 <center><img src="logo.gif" alt="JPlag" border="0"></center>
@@ -14,19 +14,19 @@
 trechos similares est&atilde;o marcados com a mesma cor. Texto preto
 significa que n&atilde;o foi encontrado algum trecho equivalente em
 outro arquivo submetido.<br>
-&nbsp; Todo trecho com alguma equivalência encontrada
+&nbsp; Todo trecho com alguma equivalência encontrada
 tem um <img src="forward.gif" alt="Forward">
 ou
 <img src="back.gif" alt="Backward"> associado. Clicando nesses icones, o 
-foco vai para outro bloco com o trecho equivalente já na posição apropriada.
+foco vai para outro bloco com o trecho equivalente já na posição apropriada.
 </p>
 <p>O bloco da esquerda mostra a porcentagem de similaridade entre
-dois programas e possui links para a página inicial e para o código  
-que você estava vendo.
+dois programas e possui links para a página inicial e para o código  
+que você estava vendo.
 
 </p>
 <p>
-O bloco da direita contém uma tabela de todos os trechos equivalentes encontrados.
+O bloco da direita contém uma tabela de todos os trechos equivalentes encontrados.
 A tabela tem o seguinte formato:
 </p>
 <p>
@@ -35,9 +35,9 @@ A tabela tem o seguinte formato:
     <tr>
       <th><br>
       </th>
-      <th>Submissão1 (??%)</th>
-      <th>Submissão2 (??%)</th>
-      <th>Marcação
+      <th>Submissão1 (??%)</th>
+      <th>Submissão2 (??%)</th>
+      <th>Marcação
       </th>
     </tr>
     <tr>
@@ -59,11 +59,11 @@ A tabela tem o seguinte formato:
   </tbody>
 </table>
 </p>
-<p> Cada coluna mostra uma sequência de números de linhas do arquivo1 e arquivo 2 que
-são consideradas equivalentes, juntamente com o tamanho do trecho em
-marcações. Os nomes dos arquivos são um hiperlink para o trecho apropriado em 
+<p> Cada coluna mostra uma sequência de números de linhas do arquivo1 e arquivo 2 que
+são consideradas equivalentes, juntamente com o tamanho do trecho em
+marcações. Os nomes dos arquivos são um hiperlink para o trecho apropriado em 
 ambos os programas.
-O trecho tem a cor de um pequeno retângulo na fronteira esquerda da coluna.
+O trecho tem a cor de um pequeno retângulo na fronteira esquerda da coluna.
 </p>
 <p><a href="index.html">INDEX</a>
 </p>

jplag/src/main/resources/jplag/data/help-sim-de.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Match ranking</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-sim-en.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Match ranking</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-sim-es.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Ranking de Coincidencias</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">
@@ -11,23 +11,23 @@
 
 <p>JPlag compara los programas intentando cubrir uno de los programas 
 con secuencias (preferiblemente grandes) del otro programa. La cobertura 
-de un programa se define como la proporción del código de fuente frente 
-al tamaño total del código de fuente.</p>
+de un programa se define como la proporción del código de fuente frente 
+al tamaño total del código de fuente.</p>
 
 <h4>Rango de coincidencias por semejanza media</h4>
 
 <p>La semejanza media se define como la media de la cobertura de 
 ambos programas.<br/>
 
-Esta es la semejanza por defecto que funciona en la mayoría de los casos: Las 
+Esta es la semejanza por defecto que funciona en la mayoría de los casos: Las 
 coincidencias con una alta semajanza media indica que esos programas funcionan 
 de una forma muy similar.</b>
 
-<h4>Rango de coincidencias por semjanza máxima</h4>
+<h4>Rango de coincidencias por semjanza máxima</h4>
 
-<p>La semejanza máxima se define como la mayor de ambas coberturas del programa.<br/>
-Este ranking es especialmente útil en programas que son muy diferentes en tamaño. Esto 
-se puede manifestar cuando se introducen grandes porciones de código dentro de uno de ellos 
+<p>La semejanza máxima se define como la mayor de ambas coberturas del programa.<br/>
+Este ranking es especialmente útil en programas que son muy diferentes en tamaño. Esto 
+se puede manifestar cuando se introducen grandes porciones de código dentro de uno de ellos 
 para que no se distinga respecto al programa plagiado.</p>
 
 <p><a href="index.html">INDEX</a></p>

jplag/src/main/resources/jplag/data/help-sim-fr.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Match ranking</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-sim-pt.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Match ranking</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">

jplag/src/main/resources/jplag/data/help-sim-ptbr.html

@@ -1,33 +1,33 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <HTML><HEAD><TITLE>Match ranking</TITLE>
-<META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 </HEAD>
 
 <BODY BGCOLOR="#ffffff" LINK="#000088" VLINK="#000000" TEXT="#000000">
 
 <center><IMG SRC="logo.gif" ALT="JPlag" BORDER="0"></center>
 
-<h1>Ranking de Equivalências</h1>
+<h1>Ranking de Equivalências</h1>
 
 <p> JPlag compara programas tentando cobrir um dos programas com trechos 
 (preferencialmente grandes) de outros programs. A cobertura de um programa
-é definida como a razão do código fonte coberto com seu tamanho total.
+é definida como a razão do código fonte coberto com seu tamanho total.
 </p>
 
-<h4>Ranking de equivalências pela similaridade média</h4>
+<h4>Ranking de equivalências pela similaridade média</h4>
 
-<p>A similaridade média é definida como a média das coberturas de ambos os programas.<br/>
-Essa é a similaridade padrão que funciona na maioria dos casos: Equivalências com
+<p>A similaridade média é definida como a média das coberturas de ambos os programas.<br/>
+Essa é a similaridade padrão que funciona na maioria dos casos: Equivalências com
 uma similaridade alta indica que os programas funcionam de uma maneira muito
 semelhante.</b>
 
-<h4>Ranking de equivalências pela similaridade máxima</h4>
+<h4>Ranking de equivalências pela similaridade máxima</h4>
 
-<p>A similaridade máxima é definida como a máxima similaridade da cobertura 
+<p>A similaridade máxima é definida como a máxima similaridade da cobertura 
 de ambos os programas.<br/>
-Esse ranking é especialmente útil quando programas são muito distintos 
-em tamanho. Isso pode acontecer quando partes inúteis de código são inseridas com o intuito
-de enganar um programa que busca plágios.</p>
+Esse ranking é especialmente útil quando programas são muito distintos 
+em tamanho. Isso pode acontecer quando partes inúteis de código são inseridas com o intuito
+de enganar um programa que busca plágios.</p>
 
 <p><a href="index.html">INDEX</a></p>
 <p/>