Final renaming (doc), slight clean-up and refactoring.

ant/build.xml

@@ -26,6 +26,7 @@
 
   <!-- SET THE DIRECTORY PROPERTIES -->
   <property name="source.directory"               value="src" />
+	  <property name="ant.directory"               value="ant" />
   <property name="build.directory"                value="build" />
   <property name="distribution.directory"         value="dist" />
   <property name="resources.directory"            value="resources" />
@@ -33,6 +34,10 @@
   <property name="binary.distribution.directory"  value="${distribution.directory}/bin-dist" />
   <property name="javadoc.directory"              value="doc/api" />
   <property name="library.directory"              value="lib" />
+  <property name="debug.flag"					  value="true" />
+	  <property name="JE2Probs.directory"			  value="../JE2Probs" />				
+	  <property name="JE2ESModel.directory"			  value="../JE2ESModel" />				
+	  <property name="JE2Research.directory"			  value="../JE2Research" />				
 
   <!-- SET THE BINARY LIBRARIES PROPERTIES -->
   <property name="check.libraries.ant"            value="ant/check.xml" />
@@ -170,13 +175,15 @@
   <target name="compileAll" depends="usage, update.libraries" description="Update libraries and compile the project.">
     <antcall target="compile">
     </antcall>
+    <antcall target="compileProbs">
+    </antcall>
   </target>
 
   <target name="compileInfo" unless="silent">
     <echo message="ANT_HOME is set to = ${env.ANT_HOME}"/>
     <echo message="JAVA_HOME is set to = ${env.JAVA_HOME}"/>
     <echo message="You are using JDK version ${ant.java.version}"/>
-    <echo message="currently JDK version 1.3 is recomended!"/>
+    <echo message="currently JDK version 1.5 is recomended!"/>
     <echo message=""/>
     <echo message="use 'ant compileAll' - to compile all java sources (+ WSI)."/>
     <echo message="use 'ant compile'    - to compile only the java sources (faster)."/>
@@ -184,7 +191,7 @@
 
   <target name="compile" depends="usage, init, check, compileInfo" description="Compiles the project." >
   <!-- COMPILE PROJECT -->
-  <javac destdir="${build.directory}" optimize="on" deprecation="on" nowarn="on">
+  <javac destdir="${build.directory}" optimize="on" deprecation="on" nowarn="on" debug="${debug.flag}" >
      <src path="${source.directory}" />
      <exclude name="ant/**" />
      <exclude name="build/**" />
@@ -212,8 +219,30 @@
     <copy todir="${build.directory}/resources">
       <fileset dir="${resources.directory}" includes="**/*" />
    </copy>
+  	
+    <copy todir="${JE2Probs.directory}/${build.directory}/resources">
+      <fileset dir="${JE2Probs.directory}/${resources.directory}" includes="**/*" />
+   </copy>
+  	
+    <copy todir="${JE2ESModel.directory}/${build.directory}/resources">
+      <fileset dir="${JE2ESModel.directory}/${resources.directory}" includes="**/*" />
+   </copy>
+	
+    <copy todir="${JE2Research.directory}/${build.directory}/resources">
+      <fileset dir="${JE2Research.directory}/${resources.directory}" includes="**/*" />
+   </copy>
   </target>
 	
+<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+	        Compile JE2Probs
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+	<target name="compileProbs" depends="usage, init, compileInfo" description="Compiles the Probs project." >
+	  <!-- COMPILE PROBS PROJECT -->
+	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="compile">
+			<property name="silent" value="true"/>
+		</ant>
+	</target>
+	
 <!-- =================================================================== -->
 <!-- Jars all classes into one jar file                                  -->
 <!-- =================================================================== -->
@@ -265,7 +294,7 @@
     <mkdir dir="${bin.dist.dir}" />
     <mkdir dir="${bin.dist.dir}/${library.directory}" />
 <delete>
-      <fileset dir="${bin.dist.dir}/${library.directory}" includes="*EvA*jar" />
+      <fileset dir="${bin.dist.dir}/${library.directory}" includes="*EvA2Base*jar" />
 </delete>
 
 <jar jarfile="${bin.dist.dir}/${library.directory}/EvA2Base.jar"  basedir="${build.directory}" >

resources/lgpl-3.0.txt

@@ -0,0 +1,165 @@
+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions. 
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version. 
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

src/eva2/client/EvAClient.java

@@ -76,7 +76,7 @@ import wsi.ra.tool.BasicResourceLoader;
 public class EvAClient implements RemoteStateListener, Serializable {
 	public static final String EVA_PROPERTY_FILE = "resources/EvA2.props";
 	private static Properties EVA_PROPERTIES;
-	public static final String iconLocation = "resources/images/icon3.gif";
+	public static final String iconLocation = "resources/images/icon4.gif";
 	private static final String splashLocation = "resources/images/splashScreen2.png";
 	private static final String infoTitle = "EvA2 Information";
 	final int splashScreenTime = 1500;
@@ -478,6 +478,10 @@ public class EvAClient implements RemoteStateListener, Serializable {
 
 	}
 	
+	public static String getProductName() {
+		return m_ProductName;
+	}
+	
 	protected void logMessage(String msg) {
 		if (TRACE || m_LogPanel == null) System.out.println(msg);
 		if (m_LogPanel != null) m_LogPanel.logMessage(msg);

src/eva2/gui/PropertyFilePath.java

@@ -1,5 +1,7 @@
 package eva2.gui;
 
+import eva2.tools.ReflectPackage;
+
 /**
  * Created by IntelliJ IDEA.
  * User: streiche
@@ -13,7 +15,12 @@ public class PropertyFilePath implements java.io.Serializable {
     public String FilePath = "";
     public String FileExtension = "";
 
-    public PropertyFilePath(String s) {
+    /**
+     * Constructor setting the absolute path. F
+     * 
+     * @param s
+     */
+    private PropertyFilePath(String s) {
         this.setCompleteFilePath(s);
     }
     
@@ -23,6 +30,28 @@ public class PropertyFilePath implements java.io.Serializable {
         this.FileExtension  = d.FileExtension;
     }
 
+    /**
+     * Get an instance by an absolute path.
+     * 
+     * @param path
+     * @return
+     */
+    public static PropertyFilePath getFilePathAbsolute(String path) {
+    	return new PropertyFilePath(path);
+    }
+
+    /**
+     * Get an instance by a relative path.
+     * 
+     * @param relPath
+     * @return
+     */
+    public static PropertyFilePath getFilePathFromResource(String relPath) {
+    	String fName = ReflectPackage.getResourcePathFromCP(relPath);
+    	if (fName == null) return null;
+    	else return new PropertyFilePath(fName);
+    }
+
     public Object clone() {
         return (Object) new PropertyFilePath(this);
     }

src/eva2/server/go/operators/mutation/MutateESSuccessRule.java

@@ -26,6 +26,9 @@ public class MutateESSuccessRule extends MutateESStandard implements InterfaceMu
     protected double        m_SuccessRate         = 0.2;
     protected double        m_Alpha               = 1.2;
 
+    public MutateESSuccessRule() {
+    }
+    
     public MutateESSuccessRule(MutateESSuccessRule mutator) {
         this.m_MutationStepSize     = mutator.m_MutationStepSize;
         this.m_SuccessRate          = mutator.m_SuccessRate;

src/eva2/server/go/operators/paretofrontmetrics/MetricD1ApproxParetoFront.java

@@ -20,10 +20,7 @@ import eva2.server.go.tools.FileLoader;
  * To change this template use File | Settings | File Templates.
  */
 public class MetricD1ApproxParetoFront implements eva2.server.go.operators.paretofrontmetrics.InterfaceParetoFrontMetric, java.io.Serializable {
-
+    private PropertyFilePath    m_InputFilePath         = PropertyFilePath.getFilePathFromResource("resources/MOPReference/T1_250.txt");
-    private String              base                    = System.getProperty("user.dir");
-    private String              FS                      = System.getProperty("file.separator");
-    private PropertyFilePath    m_InputFilePath         = new PropertyFilePath(base+FS+"resources"+FS+"MOPReference"+FS+"T1_250.txt");
     private String[]            m_Titles;
     private double[][]          m_Reference;
 

src/eva2/server/go/operators/paretofrontmetrics/MetricD1TrueParetoFront.java

@@ -21,9 +21,9 @@ import eva2.server.go.tools.FileLoader;
  */
 public class MetricD1TrueParetoFront implements eva2.server.go.operators.paretofrontmetrics.InterfaceParetoFrontMetric, java.io.Serializable {
 
-    private String              base                    = System.getProperty("user.dir");
+//    private String              base                    = System.getProperty("user.dir");
-    private String              FS                      = System.getProperty("file.separator");
+//    private String              FS                      = System.getProperty("file.separator");
-    private PropertyFilePath    m_InputFilePath         = new PropertyFilePath(base+FS+"resources"+FS+"MOPReference"+FS+"T1_250.txt");
+    private PropertyFilePath    m_InputFilePath         = PropertyFilePath.getFilePathFromResource("resources/MOPReference/T1_250.txt");
     private String[]            m_Titles;
     private double[][]          m_Reference;
 

src/eva2/server/go/operators/paretofrontmetrics/MetricErrorRatio.java

@@ -24,10 +24,7 @@ import eva2.server.go.tools.FileLoader;
  * To change this template use File | Settings | File Templates.
  */
 public class MetricErrorRatio implements eva2.server.go.operators.paretofrontmetrics.InterfaceParetoFrontMetric, java.io.Serializable {
-
+    private PropertyFilePath    m_InputFilePath         = PropertyFilePath.getFilePathFromResource("resources/MOPReference/T1_250.txt");
-    private String              base                    = System.getProperty("user.dir");
-    private String              FS                      = System.getProperty("file.separator");
-    private PropertyFilePath    m_InputFilePath         = new PropertyFilePath(base+FS+"resources"+FS+"MOPReference"+FS+"T1_250.txt");
     private double              m_Epsilon               = 0.0001;
     private String[]            m_Titles;
     private double[][]          m_Reference;

src/eva2/server/go/operators/paretofrontmetrics/MetricMaximumParetoFrontError.java

@@ -19,10 +19,7 @@ import eva2.server.go.tools.FileLoader;
  * To change this template use File | Settings | File Templates.
  */
 public class MetricMaximumParetoFrontError implements eva2.server.go.operators.paretofrontmetrics.InterfaceParetoFrontMetric, java.io.Serializable {
-
+    private PropertyFilePath    m_InputFilePath         = PropertyFilePath.getFilePathFromResource("resources/MOPReference/T1_250.txt");
-    private String              base                    = System.getProperty("user.dir");
-    private String              FS                      = System.getProperty("file.separator");
-    private PropertyFilePath    m_InputFilePath         = new PropertyFilePath(base+FS+"resources"+FS+"MOPReference"+FS+"T1_250.txt");
     private String[]            m_Titles;
     private double[][]          m_Reference;
 

src/eva2/server/go/operators/paretofrontmetrics/MetricSWithReference.java

@@ -20,11 +20,8 @@ import eva2.server.go.tools.FileLoader;
  * To change this template use File | Settings | File Templates.
  */
 public class MetricSWithReference implements InterfaceParetoFrontMetric, java.io.Serializable {
-
     private double[][]          m_ObjectiveSpaceRange;
-    private String              base                    = System.getProperty("user.dir");
+    private PropertyFilePath    m_InputFilePath         = PropertyFilePath.getFilePathFromResource("resources/MOPReference/T1_250.txt");
-    private String              FS                      = System.getProperty("file.separator");
-    private PropertyFilePath    m_InputFilePath         = new PropertyFilePath(base+FS+"resources"+FS+"MOPReference"+FS+"T1_250.txt");
     private String[]            m_Titles;
     private double[][]          m_Reference;
     private double              m_ReferenceSMetric      = -1;
@@ -42,8 +39,6 @@ public class MetricSWithReference implements InterfaceParetoFrontMetric, java.io
             }
         }
         this.m_InputFilePath    = b.m_InputFilePath;
-        this.base               = System.getProperty("user.dir");
-        this.FS                 = System.getProperty("file.separator");
         if (b.m_Titles != null) {
             this.m_Titles = new String[b.m_Titles.length];
             System.arraycopy(b.m_Titles, 0, this.m_Titles, 0, this.m_Titles.length);

src/eva2/server/go/problems/AbstractProblemBinary.java

@@ -52,6 +52,16 @@ public abstract class AbstractProblemBinary extends AbstractOptimizationProblem
 	 */
 	public abstract int getProblemDimension();
 
+	/**
+	 * Initialize a single individual with index k in the
+	 * initPopulation cycle.
+	 * @param k
+	 * @param indy
+	 */
+    protected void initIndy(int k, AbstractEAIndividual indy) {
+    	indy.init(this);
+    }
+
 	@Override
 	public void initPopulation(Population population) {
         AbstractEAIndividual tmpIndy;
@@ -61,7 +71,7 @@ public abstract class AbstractProblemBinary extends AbstractOptimizationProblem
 
         for (int i = 0; i < population.getPopulationSize(); i++) {
             tmpIndy = (AbstractEAIndividual)((AbstractEAIndividual)this.m_Template).clone();
-            tmpIndy.init(this);
+            initIndy(i, tmpIndy);
             population.add(tmpIndy);
         }
         // population init must be last

src/eva2/server/go/problems/B1Problem.java

@@ -36,25 +36,6 @@ public class B1Problem extends AbstractProblemBinary implements java.io.Serializ
         return (Object) new B1Problem(this);
     }
 
-    /** This method inits a given population
-     * @param population    The populations that is to be inited
-     */
-    public void initPopulation(Population population) {
-        AbstractEAIndividual tmpIndy;
-
-        population.clear();
-
-        ((InterfaceDataTypeBinary)this.m_Template).setBinaryDataLength(this.m_ProblemDimension);
-        for (int i = 0; i < population.getPopulationSize(); i++) {
-            tmpIndy     = (AbstractEAIndividual)((AbstractEAIndividual)this.m_Template).clone();
-            tmpIndy.init(this);
-            population.add(tmpIndy);
-        }
-        // population init must be last
-        // it set's fitcalls and generation to zero
-        population.init();
-    }
-
     /** This is a simple method that evaluates a given Individual. The fitness
      * values of the individual will be set inside this method.
      * @param b         The BitSet that is to be evaluated.

src/eva2/server/go/problems/BKnapsackProblem.java

@@ -2,14 +2,13 @@ package eva2.server.go.problems;
 
 
 
-import java.util.*;
+import java.util.BitSet;
 
-import eva2.server.go.individuals.AbstractEAIndividual;
-import eva2.server.go.individuals.GAIndividualBinaryData;
-import eva2.server.go.individuals.InterfaceDataTypeBinary;
-import eva2.server.go.populations.Population;
-import eva2.server.go.strategies.InterfaceOptimizer;
 import wsi.ra.math.RNG;
+import eva2.server.go.individuals.AbstractEAIndividual;
+import eva2.server.go.individuals.InterfaceDataTypeBinary;
+import eva2.server.go.strategies.InterfaceOptimizer;
+import eva2.server.go.problems.AbstractProblemBinary;
 
 /**
  * Created by IntelliJ IDEA.
@@ -18,7 +17,7 @@ import wsi.ra.math.RNG;
  * Time: 15:12:46
  * To change this template use Options | File Templates.
  */
-public class BKnapsackProblem extends AbstractOptimizationProblem implements java.io.Serializable {
+public class BKnapsackProblem extends AbstractProblemBinary implements java.io.Serializable {
 
     private int                         m_Limit         = 5000;
     private double                      m_Punish        = 2.0;
@@ -128,12 +127,12 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
         {392,-386}};
 
     public BKnapsackProblem() {
-        this.m_Template         = new GAIndividualBinaryData();
+        super();
     }
+    
     public BKnapsackProblem(BKnapsackProblem b) {
         //AbstractOptimizationProblem
-        if (b.m_Template != null)
+    	cloneObjects(b);
-            this.m_Template         = (AbstractEAIndividual)((AbstractEAIndividual)b.m_Template).clone();
         // BKnapsackProblem
         this.m_Limit            = b.m_Limit;
         this.m_Punish           = b.m_Punish;
@@ -141,6 +140,10 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
         this.m_Lamarkism        = b.m_Lamarkism;
     }
 
+    public int getProblemDimension() {
+    	return items.length;
+    }
+    
     /** This method returns a deep clone of the problem.
      * @return  the clone
      */
@@ -154,32 +157,17 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
         // nothing to init here
     }
 
-    /** This method inits a given population
+    protected void initIndy(int k, AbstractEAIndividual indy) {
-     * @param population    The populations that is to be inited
+        indy.init(this);
-     */
+    	if (RNG.flipCoin(this.m_ProblemSpecificInit)) {
-    public void initPopulation(Population population) {
+    		BitSet tmpSet = new BitSet();
-        AbstractEAIndividual tmpIndy;
+    		tmpSet.clear();
 
-        population.clear();
+    		while (eval(tmpSet)[1] > 0) {
-
+    			tmpSet.set(RNG.randomInt(0,items.length-1));
-        ((InterfaceDataTypeBinary)this.m_Template).setBinaryDataLength(items.length);
+    		}
-        for (int i = 0; i < population.getPopulationSize(); i++) {
+    		((InterfaceDataTypeBinary)indy).SetBinaryDataLamarkian(tmpSet);
-            tmpIndy = (AbstractEAIndividual)((AbstractEAIndividual)this.m_Template).clone();
+    	}
-            tmpIndy.init(this);
-            if (RNG.flipCoin(this.m_ProblemSpecificInit)) {
-                BitSet tmpSet = new BitSet();
-                tmpSet.clear();
-
-                while (evaluate(tmpSet, items.length)[1] > 0) {
-                    tmpSet.set(RNG.randomInt(0,items.length-1));
-                }
-                ((InterfaceDataTypeBinary)tmpIndy).SetBinaryDataLamarkian(tmpSet);
-            }
-            population.add(tmpIndy);
-        }
-        // population init must be last
-        // it set's fitcalls and generation to zero
-        population.init();
     }
     
     /** This method evaluates a single individual and sets the fitness values
@@ -188,11 +176,9 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
     public void evaluate(AbstractEAIndividual individual) {
         BitSet          tmpBitSet;
         double[]        result;
-        InterfaceDataTypeBinary    tmpIndy;
 
-        tmpIndy     = (InterfaceDataTypeBinary) individual;
+        tmpBitSet   = ((InterfaceDataTypeBinary) individual).getBinaryData();
-        tmpBitSet   = tmpIndy.getBinaryData();
+        result = this.eval(tmpBitSet);
-        result = this.evaluate(tmpBitSet, tmpIndy.size());
         if (RNG.flipCoin(this.m_LocalSearch)) {
             // first remove surplus assets
             while (result[1] > 0) {
@@ -210,7 +196,7 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
                 }
                 // remove the weakest
                 tmpBitSet.clear(weakest);
-                result = this.evaluate(tmpBitSet, tmpIndy.size());
+                result = this.eval(tmpBitSet);
             }
             // now lets see if we can replace some guy with a more efficient one
             int weakest = tmpBitSet.nextSetBit(0);
@@ -228,7 +214,7 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
                 }
 
                 tmpBitSet.clear(weakest);
-                result = this.evaluate(tmpBitSet, tmpIndy.size());
+                result = this.eval(tmpBitSet);
                 int weight = 0;
                 for (int i = 0; i < items.length; i++) {
                     if (tmpBitSet.get(i)) weight  += items[i][0];
@@ -244,11 +230,11 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
                     }
                 }
                 if (stronger >= 0) tmpBitSet.set(stronger);
-                result = this.evaluate(tmpBitSet, tmpIndy.size());
+                result = this.eval(tmpBitSet);
             }
 
             if (this.m_Lamarkism) {
-                tmpIndy.SetBinaryDataLamarkian(tmpBitSet);
+            	((InterfaceDataTypeBinary) individual).SetBinaryDataLamarkian(tmpBitSet);
             }
         }
         result[0] += 5100;
@@ -261,9 +247,11 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
      * @param l         The length of the BitSet.
      * @return          Double[]
      */
-    public double[] evaluate(BitSet b, int l) {
+    public double[] eval(BitSet b) {
         double[]                result = new double[3];
 
+        int l = items.length; 
+        if (getProblemDimension() != l) System.err.println("Error in BKnapsack!");
         result[0] = 0;
         result[1] = 0; // the weight exceed
         result[2] = 0; // net worth
@@ -292,7 +280,7 @@ public class BKnapsackProblem extends AbstractOptimizationProblem implements jav
 
         tmpIndy     = (InterfaceDataTypeBinary) individual;
         tmpBitSet   = tmpIndy.getBinaryData();
-        report = this.evaluate(tmpBitSet, tmpIndy.size());
+        report = this.eval(tmpBitSet);
         result += individual.getStringRepresentation() + "\n";
         result += "Is worth: " + Math.abs(report[2]) + " and ";
         if (report[1] == 0) result += "does not exceed the weight limit!";

src/eva2/server/go/problems/MatlabProblem.java

@@ -13,7 +13,6 @@ import eva2.gui.BeanInspector;
 import eva2.server.go.individuals.AbstractEAIndividual;
 import eva2.server.go.individuals.ESIndividualDoubleData;
 import eva2.server.go.individuals.InterfaceDataTypeDouble;
-import eva2.server.go.operators.distancemetric.PhenotypeMetric;
 import eva2.server.go.operators.postprocess.InterfacePostProcessParams;
 import eva2.server.go.operators.postprocess.PostProcess;
 import eva2.server.go.operators.postprocess.PostProcessParams;
@@ -38,7 +37,7 @@ public class MatlabProblem extends AbstractProblemDouble implements InterfaceTex
 	
 	public static boolean hideFromGOE = true; 
 	
-	private F1Problem f1 = new F1Problem(); // TODO
+//	private F1Problem f1 = new F1Problem(); // TODO
 	
 //	transient private double[] currArray = null;
 //	private String mtCmd = null;
@@ -194,11 +193,11 @@ public class MatlabProblem extends AbstractProblemDouble implements InterfaceTex
 	public double[] eval(double[] x) {
 		log("evaluating " + BeanInspector.toString(x) + "\n");
 		double[] res = handler.requestEval(this, x);
-		double diff = PhenotypeMetric.euclidianDistance(res, f1.eval(x));
+//		double diff = PhenotypeMetric.euclidianDistance(res, f1.eval(x));
-		log("result: " + BeanInspector.toString(res) + " compared to " + BeanInspector.toString(f1.eval(x)) + "\n");
+//		log("result: " + BeanInspector.toString(res) + " compared to " + BeanInspector.toString(f1.eval(x)) + "\n");
-		if (diff != 0) {
+//		if (diff != 0) {
-			log("!!! diff is " + diff + "\n");
+//			log("!!! diff is " + diff + "\n");
-		}
+//		}
 		return res;
 		
 //		synchronized (this) {

src/eva2/server/go/problems/TF1Problem.java

@@ -299,7 +299,7 @@ public class TF1Problem extends AbstractMultiObjectiveOptimizationProblem implem
         int points = 500;
         String              base        = System.getProperty("user.dir");
         String              FS          = System.getProperty("file.separator");
-        PropertyFilePath    fileOutPath = new PropertyFilePath(base+FS+"resources"+FS+"MOPReference"+FS+"T1_"+points+".txt");
+        PropertyFilePath    fileOutPath = PropertyFilePath.getFilePathFromResource("resources/MOPReference"+FS+"T1_"+points+".txt");
         BufferedWriter      writer      = null;
         try {
             writer = new BufferedWriter(new FileWriter(fileOutPath.getCompleteFilePath()));

src/eva2/server/go/strategies/CHCAdaptiveSearchAlgorithm.java

@@ -7,7 +7,7 @@ import eva2.server.go.InterfacePopulationChangedEventListener;
 import eva2.server.go.individuals.AbstractEAIndividual;
 import eva2.server.go.individuals.InterfaceGAIndividual;
 import eva2.server.go.operators.selection.InterfaceSelection;
-import eva2.server.go.operators.selection.SelectBest;
+import eva2.server.go.operators.selection.SelectBestSingle;
 import eva2.server.go.operators.selection.SelectRandom;
 import eva2.server.go.populations.PBILPopulation;
 import eva2.server.go.populations.Population;
@@ -38,7 +38,7 @@ public class CHCAdaptiveSearchAlgorithm implements InterfaceOptimizer, java.io.S
     private Population                      m_Population        = new Population();
     private InterfaceOptimizationProblem    m_Problem           = new B1Problem();
     private InterfaceSelection              m_RecombSelectionOperator = new SelectRandom();
-    private InterfaceSelection              m_PopulSelectionOperator = new SelectBest();
+    private InterfaceSelection              m_PopulSelectionOperator = new SelectBestSingle();
 
     transient private String                m_Identifier = "";
     transient private InterfacePopulationChangedEventListener m_Listener;

src/eva2/server/go/strategies/ClusterBasedNichingEA.java

@@ -19,6 +19,7 @@ import eva2.server.go.operators.cluster.ClusteringDensityBased;
 import eva2.server.go.operators.cluster.InterfaceClustering;
 import eva2.server.go.operators.mutation.InterfaceMutation;
 import eva2.server.go.operators.mutation.MutateESGlobal;
+//import eva2.server.go.populations.Distraction;
 import eva2.server.go.populations.Population;
 import eva2.server.go.problems.B1Problem;
 import eva2.server.go.problems.Interface2DBorderProblem;
@@ -65,7 +66,7 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
     private int                             m_PopulationSize                = 50;
     private int								convergedCnt					= 0;
 
-    private static boolean                  TRACE     = true;
+    private static boolean                  TRACE     = false;
     private int                             m_ShowCycle = 100;
     transient private TopoPlot              m_Topology;
     private int                 			haltingWindow         			 = 15;
@@ -586,12 +587,10 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
             this.m_Population.addPopulation((Population)this.m_Species.get(i));
         }
         if (TRACE) System.out.println("Population size: " + this.m_Population.size());
-        if (TRACE) {
+//        if (TRACE) {
-//        	for (int i=0; i<m_Species.size(); i++) {
+//        	Distraction distr = new Distraction(5., 0, m_Species);
-//        		System.out.print("distraction center at " + BeanInspector.toString(m_Species.get(i).getDistractionCenter()));
+//        	if (m_Undifferentiated.size()>0) distr.calcDistractionFor(m_Undifferentiated.getBestEAIndividual());
-//        		System.out.println(", strength " + m_Species.get(i).getDistractionStrength());
+//        }
-//        	}
-        }
         this.firePropertyChangedEvent("NextGenerationPerformed");
     }
 

src/eva2/server/go/strategies/DifferentialEvolution.java

@@ -10,6 +10,7 @@ import eva2.server.go.problems.AbstractOptimizationProblem;
 import eva2.server.go.problems.F1Problem;
 import eva2.server.go.problems.InterfaceOptimizationProblem;
 import wsi.ra.math.RNG;
+import eva2.tools.EVAERROR;
 import eva2.tools.SelectedTag;
 import eva2.tools.Tag;
 
@@ -241,7 +242,7 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
                         indy1 = (InterfaceESIndividual)pop.get(RNG.randomInt(0, pop.size()-1));
                         indy2 = (InterfaceESIndividual)pop.get(RNG.randomInt(0, pop.size()-1));
                     } catch (java.lang.ClassCastException e) {
-                        System.out.println("Differential Evolution currently requires InterfaceESIndividual as basic data type!");
+                    	EVAERROR.errorMsgOnce("Differential Evolution currently requires InterfaceESIndividual as basic data type!");
                     }
                     xk = indy1.getDGenotype();
                     xl = indy2.getDGenotype();

src/eva2/server/go/strategies/IslandModelEA.java

@@ -21,7 +21,7 @@ import wsi.ra.jproxy.RMIServer;
 /** The one and only island model for parallelization. Since parallelization based
  * on the RMIProxyRemoteThread is on the one hand much slower than benchmark function
  * evaluation and on the other hand the GUI based distribution scheme is rather prone
- * to config errors (the correct ssh version is required, the JOpt.jar needs to be in
+ * to config errors (the correct ssh version is required, the jar needs to be in
  * the working dir and possible problem data must be on the servers to) an implicit
  * island-model has been implemented too to allow fast and reliabel computation.
  * This is still usefull, since it is less prone to premature convergence and also

src/eva2/server/go/strategies/Tribes.java

@@ -146,7 +146,7 @@ public class Tribes implements InterfaceOptimizer, java.io.Serializable {
 	public static int[] strategies = new int[10]; // Just for information
 	public static int[] status = new int[9]; // Just for information
 
-	public static boolean testBC = false;  // TODO project to JOpt
+	public static boolean testBC = false;  // TODO project to EvA2
 	public static int adaptOption = 2;
 	public static double blind=0;  // 0.5 //"Blind" move for very good particles, with a probability Tribes.blind
 	public static boolean repel=false; // If 1, use a "repelling" strategy (see moveExplorer() )
@@ -625,7 +625,7 @@ public class Tribes implements InterfaceOptimizer, java.io.Serializable {
 	/**
 	 * As TRIBES manages an own structured set of particles (the list of Tribes containing explorers
 	 * and memories), the setPopulation method is only telling Tribes the range
-	 * of the indiviuals in the beginning of the run, the indiviudals will be discarded.
+	 * of the indiviuals in the beginning of the run, the individuals will be discarded.
 	 */
 	public void setPopulation(Population pop) {
 		if (pop == null) return;

src/eva2/server/modules/GOParameters.java

@@ -2,11 +2,10 @@ package eva2.server.modules;
 
 import java.io.Serializable;
 
-import eva2.gui.BeanInspector;
 import eva2.server.go.InterfaceGOParameters;
-import eva2.server.go.InterfacePopulationChangedEventListener;
+import eva2.server.go.individuals.GAIndividualDoubleData;
 import eva2.server.go.operators.terminators.EvaluationTerminator;
-import eva2.server.go.problems.B1Problem;
+import eva2.server.go.problems.F1Problem;
 import eva2.server.go.strategies.GeneticAlgorithm;
 import eva2.tools.Serializer;
 
@@ -45,7 +44,8 @@ public class GOParameters extends AbstractGOParameters implements InterfaceGOPar
      *
      */
     public GOParameters() {
-    	super(new GeneticAlgorithm(), new B1Problem(), new EvaluationTerminator(1000));
+    	super(new GeneticAlgorithm(), new F1Problem(), new EvaluationTerminator(1000));
+    	((F1Problem)m_Problem).setEAIndividual(new GAIndividualDoubleData());
     }
 
     /**

src/eva2/server/modules/Processor.java

@@ -195,7 +195,7 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
         		this.goParams.getOptimizer().optimize();
         		// registerPopulationStateChanged *SHOULD* be fired by the optimizer or resp. the population
         		// as we are event listener
-//        		System.out.println(this.goParams.getOptimizer().getPopulation().getIndyList());
+        		//System.out.println(this.goParams.getOptimizer().getPopulation().getIndyList());
         	} while (isOptRunning() && !this.goParams.getTerminator().isTerminated(this.goParams.getOptimizer().getPopulation()));
         	runCounter++;
 

src/eva2/tools/ReflectPackage.java

@@ -3,15 +3,18 @@ package eva2.tools;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.jar.JarEntry;
 import java.util.jar.JarInputStream;
 
+import wsi.ra.tool.BasicResourceLoader;
+
 //import wsi.ra.tool.BasicResourceLoader;
 
 /**
@@ -238,75 +241,118 @@ public class ReflectPackage {
 			classPath = System.getProperty("java.class.path",".");
 			if (useFilteredClassPath) {
 				try {
-					String[] pathElements = getClassPathElements();
+					dynCP = getValidCPArray();
-					File f;
-					ArrayList<String> valids = new ArrayList<String>(pathElements.length);
-					for (int i=0; i<pathElements.length; i++) {
-//						System.err.println(pathElements[i]);
-						f = new File(pathElements[i]);
-//						if (f.canRead()) {valids.add(pathElements[i]);}
-						if (f.exists() && f.canRead()) {
-							valids.add(pathElements[i]);
-						}
-					}
-//					dynCP = valids.toArray(dynCP); // this causes Matlab to crash meanly.
-					dynCP = new String[valids.size()];
-					for (int i=0; i<valids.size(); i++) dynCP[i] = valids.get(i);
 				} catch (Exception e) {
 					System.err.println(e.getMessage());
 				}
 			} else dynCP = getClassPathElements();
 		}
 
-//		dynCP = System.getProperty("java.class.path",".").split(File.pathSeparator);
 		if (TRACE) System.out.println("classpath is " + classPath);
-//		System.err.println("no of path elements is " + dynCP.length);
+		for (int i=0; i<dynCP.length; i++) {
-//		if (usePathMap) {
+			if (TRACE) System.out.println("reading element "+dynCP[i]);
-//			System.err.println("Checking for " + pckg);
+			if (dynCP[i].endsWith(".jar")) {
-//			ArrayList<String> pathes = pathMap.get(pckg);
+				getClassesFromJarFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-//			System.err.println("stored objects: " + ((pathes != null) ? pathes.size() : 0));
+			} else {
-//			if (pathes == null) {
+				if (TRACE) System.out.println("reading from files: "+dynCP[i]+" "+pckg);
-//				pathes = new ArrayList<String>();
+				getClassesFromFilesFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-//				for (int i=0; i<dynCP.length; i++) {
-//					int added = 0;
-//					if (dynCP[i].endsWith(".jar")) {
-//						added = getClassesFromJarFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-//					} else {
-//						added = getClassesFromFilesFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-//					}
-//					if (added > 0) pathes.add(dynCP[i]);
-//				}
-//				pathMap.put(pckg, pathes);
-//			} else {
-//				for (int i=0; i<pathes.size(); i++) {
-//					System.err.println("reusing " + pathes.get(i));
-//					if (pathes.get(i).endsWith(".jar")) getClassesFromJarFltr(set, pathes.get(i), pckg, includeSubs, reqSuperCls);
-//					else getClassesFromFilesFltr(set, pathes.get(i), pckg, includeSubs, reqSuperCls);
-//				}
-//			}
-//		} else {
-			for (int i=0; i<dynCP.length; i++) {
-				if (TRACE) System.out.println("reading element "+dynCP[i]);
-				if (dynCP[i].endsWith(".jar")) {
-					getClassesFromJarFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-				} else {
-					if (TRACE) System.out.println("reading from files: "+dynCP[i]+" "+pckg);
-					getClassesFromFilesFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-				}
 			}
-//		}
+		}
 		Object[] clsArr = set.toArray();
 		if (bSort) {
 			Arrays.sort(clsArr, new ClassComparator());
 		}
 
 		List list;
-		 
-//		#1
 		list = Arrays.asList(clsArr);
 		return (Class[])list.toArray(new Class[list.size()]);
 	}
 
+	/**
+	 * Request a valid absolute resource path from a relative resource path
+	 * by searching the classpath entries. Returns null if the resource is not found.
+	 * @param res
+	 */
+	public static String getResourcePathFromCP(String res) {
+		String[] cpEntries = getClassPathElements();
+		URL url = ClassLoader.getSystemResource(res);
+		if (TRACE) System.out.println(res + ((url == null) ? " not" : " was") + " found by classloader.");
+		if (url != null) return url.getFile();
+		
+		File f;
+		String fNameSep;
+		if (res.startsWith(System.getProperty("file.separator"))) fNameSep = res;
+		else fNameSep = System.getProperty("file.separator")+res;
+
+		for (int i=0; i<cpEntries.length; i++) {
+			if (!cpEntries[i].endsWith(".jar")) { // its a fs directory (hopefully)
+				if (TRACE) System.out.println("reading element "+cpEntries[i]);
+				f = new File(cpEntries[i]+fNameSep);
+				if (TRACE) System.out.println(res + ((!f.exists()) ? " not" : " was") + " found in " + cpEntries[i]);
+				if (f.exists()) return f.getAbsolutePath();
+			}
+		}
+		return null;
+	}
+	
+	/**
+	 * Request a valid absolute resource path from a relative resource path
+	 * by searching the classpath entries. Returns null if the resource is not found.
+	 * @param res
+	 */
+	public static InputStream getResourceStreamFromCP(String res) {
+		
+		InputStream in = BasicResourceLoader.instance().getStreamFromResourceLocation(res);
+		if (TRACE) System.out.println(res + ((in == null) ? " not" : " was") + " found by classloader.");
+		if (in != null) return in;
+		
+		String[] cpEntries = getClassPathElements();
+		
+		File f;
+		String fNameSep;
+		if (res.startsWith(System.getProperty("file.separator"))) fNameSep = res;
+		else fNameSep = System.getProperty("file.separator")+res;
+
+		for (int i=0; i<cpEntries.length; i++) {
+			if (!cpEntries[i].endsWith(".jar")) { // its a fs directory (hopefully)
+				if (TRACE) System.out.println("reading element "+cpEntries[i]);
+				f = new File(cpEntries[i]+fNameSep);
+				if (TRACE) System.out.println(res + ((!f.exists()) ? " not" : " was") + " found in " + cpEntries[i]);
+				if (f.exists()) {
+					try {
+						return new FileInputStream(f);
+					} catch(Exception e) {
+						System.err.println("error reading file " + f.getAbsolutePath() + ": " + e.getMessage());
+					}
+				}
+			}
+		}
+		return null;
+	}
+	
+	public static ArrayList<String> getValidCPEntries() {
+		String[] pathElements = getClassPathElements();
+		File f;
+		ArrayList<String> valids = new ArrayList<String>(pathElements.length);
+		for (int i=0; i<pathElements.length; i++) {
+//						System.err.println(pathElements[i]);
+			f = new File(pathElements[i]);
+//						if (f.canRead()) {valids.add(pathElements[i]);}
+			if (f.exists() && f.canRead()) {
+				valids.add(pathElements[i]);
+			}
+		}
+		return valids;
+	}
+	
+	public static String[] getValidCPArray() {
+		ArrayList<String> valids = getValidCPEntries();
+//		vp = valids.toArray(dynCP); // this causes Matlab to crash meanly.
+		String[] vp = new String[valids.size()];
+		for (int i=0; i<valids.size(); i++) vp[i] = valids.get(i);
+		return vp;
+	}
+	
 	/**
 	 * Retrieve assignable classes of the given package from classpath.
 	 * 

src/wsi/ra/tool/BasicResourceLoader.java

@@ -302,8 +302,7 @@ public class BasicResourceLoader implements ResourceLoader
      * @param  rawResrcLoc  Description of the Parameter
      * @return                   the byte array of file.
      */
-    public byte[] getBytesFromResourceLocation(String rawResrcLoc)
+    public InputStream getStreamFromResourceLocation(String rawResrcLoc) {
-    {
         String resourceLocation = rawResrcLoc.replace('\\', '/');
 
         //System.out.println("Try to get: "+resourceLocation);
@@ -318,14 +317,14 @@ public class BasicResourceLoader implements ResourceLoader
         resourceLocation = resourceLocation.trim();
 
         // is a relative path defined ?
-        // this can only be possible, if this is a file resource loacation
+        // this can only be possible, if this is a file resource location
         if (resourceLocation.startsWith("..") ||
                 resourceLocation.startsWith("/") ||
                 resourceLocation.startsWith("\\") ||
                 ((resourceLocation.length() > 1) &&
                     (resourceLocation.charAt(1) == ':')))
         {
-            return getBytesFromFile(resourceLocation);
+            return getStreamFromFile(resourceLocation);
         }
 
         InputStream in = ClassLoader.getSystemResourceAsStream(resourceLocation);
@@ -346,10 +345,23 @@ public class BasicResourceLoader implements ResourceLoader
         {
             logger.debug("Stream opened for " + resourceLocation);
         }
+        return in;
+    }
     
-        byte[] bytes = getBytesFromStream(in);
+    /**
+     *  Gets the byte data from a file at the given resource location.
+     *
+     * @param  rawResrcLoc  Description of the Parameter
+     * @return                   the byte array of file.
+     */
+    public byte[] getBytesFromResourceLocation(String rawResrcLoc)
+    {
+        InputStream in = getStreamFromResourceLocation(rawResrcLoc);
 
-        return bytes;
+        if (in == null) {
+        	return null;
+        }
+        return getBytesFromStream(in);
     }
 
     /**
@@ -442,7 +454,7 @@ public class BasicResourceLoader implements ResourceLoader
      * @param  fileName  Description of the Parameter
      * @return           the byte array of the file.
      */
-    private byte[] getBytesFromFile(String fileName)
+    private FileInputStream getStreamFromFile(String fileName)
     {
         if (fileName.startsWith("/cygdrive/"))
         {
@@ -462,6 +474,7 @@ public class BasicResourceLoader implements ResourceLoader
         try
         {
             fis = new FileInputStream(file);
+            return fis;
         }
         catch (Exception e)
         {
@@ -470,11 +483,25 @@ public class BasicResourceLoader implements ResourceLoader
             return null;
         }
 
+    }
+    
+    /**
+     *  Gets the byte data from a file.
+     *
+     * @param  fileName  Description of the Parameter
+     * @return           the byte array of the file.
+     */
+    private byte[] getBytesFromFile(String fileName) {
+    	FileInputStream fis = getStreamFromFile(fileName);
+    	if (fis == null) {
+    		System.err.println("couldnt get file input stream!");
+    		return null;
+    	}
         BufferedInputStream bis = new BufferedInputStream(fis);
 
         // only files with <65536 bytes are allowed
         //if( file.length() > 65536 ) System.out.println("Resource files should be smaller than 65536 bytes...");
-        int size = (int) file.length();
+        int size = (int) new File(fileName).length();
         byte[] b = new byte[size];
         int rb = 0;
         int chunk = 0;