Further code cleanup

refs #2
- Removed old comments
- Fixed typos
- Removed unused code

src/eva2/EvAInfo.java

@@ -45,8 +45,6 @@ public class EvAInfo {
     public static final String infoTitle = productName + " Information";
     public static final String copyrightYear = "2010-2014";
 
-    ////////////// Property handling...
-
     private static Properties evaProperties;
 
     static {
@@ -102,8 +100,4 @@ public class EvAInfo {
     public static String propDefaultModule() {
         return getProperty("DefaultModule");
     }
-
-    public static String propShowModules() {
-        return getProperty("ShowModules");
-    }
 }

src/eva2/gui/BeanInspector.java

@@ -19,8 +19,6 @@ import java.util.logging.Logger;
 /**
  * Some miscellaneous functions to help with Beans, reflection, conversion and
  * generic display.
- *
- * @author mkron, Holger Ulmer, Felix Streichert, Hannes Planatscher
  */
 public class BeanInspector {
     private static final Logger LOGGER = Logger.getLogger(BeanInspector.class.getName());
@@ -164,13 +162,11 @@ public class BeanInspector {
             }
             int len = Array.getLength(obj);
             for (int i = 0; i < len; i++) {
-//				sbuf.append(toString(Array.get(obj, i)));
                 if (withNewlines) {
                     sbuf.append('\n');
                 }
                 sbuf.append(toString(Array.get(obj, i), delim, tight, indentStr, indentDepth, withNewlines));
                 if (i < len - 1) {
-//					sbuf.append(delim);
                     if (!tight) {
                         sbuf.append(" ");
                     }
@@ -216,7 +212,6 @@ public class BeanInspector {
         for (int ii = 0; ii < methods.length; ii++) { // check if the object has its own toString method, in this case use it
             if ((methods[ii].getName().equals("toString") /*|| (methods[ii].getName().equals("getStringRepresentation"))*/) && (methods[ii].getParameterTypes().length == 0)) {
                 Object[] args = new Object[0];
-                //args[0] = obj;
                 try {
                     String ret = (String) methods[ii].invoke(obj, args);
                     return makeIndent(indentStr, indentDepth) + ret;
@@ -292,8 +287,6 @@ public class BeanInspector {
         System.out.println("----");
         System.out.println(BeanInspector.toString(new Population(), ';', false, ">", 1, false));
         System.out.println(BeanInspector.toString(new GeneticAlgorithm(), ';', false, ">", 1, false));
-        //		System.out.println(BeanInspector.toString(new Population(), ',', false, "\t"));
-//		System.out.println(BeanInspector.toString(new GeneticAlgorithm(), ',', false, "\t"));
     }
 
     /**
@@ -308,7 +301,6 @@ public class BeanInspector {
     public static Pair<String[], Object[]> getPublicPropertiesOf(Object target, boolean requireSetter, boolean showHidden) {
         BeanInfo Info = null;
         PropertyDescriptor[] Properties = null;
-//		MethodDescriptor[] Methods = null;
         try {
             Info = Introspector.getBeanInfo(target.getClass());
             Properties = Info.getPropertyDescriptors();
@@ -322,21 +314,15 @@ public class BeanInspector {
         Object[] valArray = new Object[Properties.length];
         for (int i = 0; i < Properties.length; i++) {
             if ((Properties[i].isHidden() && !showHidden) || Properties[i].isExpert()) {
-//				System.err.println(Properties[i].getDisplayName() + " is " + ( (Properties[i].isExpert())? "expert": "hidden"));
                 continue;
             }
             String name = Properties[i].getDisplayName();
-            //System.out.println("name = "+name );
-            //Class type = Properties[i].getPropertyType();
-            //System.out.println("type = "+type.getName() );
             Method getter = Properties[i].getReadMethod();
             Method setter = Properties[i].getWriteMethod();
             // Only display read/write properties.
             if (getter == null || (setter == null && requireSetter)) {
                 continue;
             }
-            //System.out.println("name = "+name );
-            //System.out.println("type = "+type.getName() );
             Object args[] = {};
 
             try {
@@ -375,7 +361,6 @@ public class BeanInspector {
         // then the properties
         BeanInfo Info = null;
         PropertyDescriptor[] Properties = null;
-//		MethodDescriptor[] Methods = null;
         try {
             Info = Introspector.getBeanInfo(obj.getClass());
             Properties = Info.getPropertyDescriptors();
@@ -390,17 +375,12 @@ public class BeanInspector {
                 continue;
             }
             String name = Properties[i].getDisplayName();
-            //System.out.println("name = "+name );
-//			Class type = Properties[i].getPropertyType();
-            //System.out.println("type = "+type.getName() );
             Method getter = Properties[i].getReadMethod();
             Method setter = Properties[i].getWriteMethod();
             // Only display read/write properties.
             if (getter == null || setter == null) {
                 continue;
             }
-            //System.out.println("name = "+name );
-            //System.out.println("type = "+type.getName() );
             Object args[] = {};
             try {
                 Object value = getter.invoke(obj, args);
@@ -753,11 +733,11 @@ public class BeanInspector {
         if (val instanceof Integer) {
             return ((Integer) val).doubleValue();
         } else if (val instanceof Double) {
-            return ((Double) val).doubleValue();
+            return (Double) val;
         } else if (val instanceof Boolean) {
             return (((Boolean) val) ? 1. : 0.);
         } else if (val instanceof Character) {
-            return ((Character) val).charValue();
+            return (Character) val;
         } else if (val instanceof Byte) {
             return ((Byte) val).doubleValue();
         } else if (val instanceof Short) {
@@ -816,21 +796,21 @@ public class BeanInspector {
             return d;
         }
         if ((destType == Integer.class) || (destType == int.class)) {
-            return new Integer(d.intValue());
+            return d.intValue();
         } else if ((destType == Boolean.class) || (destType == boolean.class)) {
             return (d != 0) ? Boolean.TRUE : Boolean.FALSE;
         } else if ((destType == Byte.class) || (destType == byte.class)) {
-            return new Byte(d.byteValue());
+            return d.byteValue();
         } else if ((destType == Short.class) || (destType == short.class)) {
-            return new Short(d.shortValue());
+            return d.shortValue();
         } else if ((destType == Long.class) || (destType == long.class)) {
-            return new Long(d.longValue());
+            return d.longValue();
         } else if ((destType == Float.class) || (destType == float.class)) {
-            return new Float(d.floatValue());
+            return d.floatValue();
         } else { // this makes hardly sense...
             System.err.println("warning: converting from double to character or void...");
             if ((destType == Character.class) || (destType == char.class)) {
-                return new Character(d.toString().charAt(0));
+                return d.toString().charAt(0);
             } else {
                 return 0;
             }
@@ -891,7 +871,6 @@ public class BeanInspector {
      * @return
      */
     public static Object decodeType(Class<?> destType, Object value) {
-//		System.err.println("desttype: " + destType.toString() + ", val: " + value.getClass().toString());
         if (destType.isAssignableFrom(value.getClass())) {
             // value is already of destType or assignable (subclass), so just return it
             return value;
@@ -974,14 +953,10 @@ public class BeanInspector {
             return false;
         }
         PropertyDescriptor[] properties = bi.getPropertyDescriptors();
-//		Method getter = null;
         Method setter = null;
         Class<?> type = null;
-//		System.err.println("looking at " + toString(obj));
         for (int i = 0; i < properties.length; i++) {
             if (properties[i].getDisplayName().equals(mem)) {
-//				System.err.println("looking at " + properties[i].getDisplayName());
-//				getter  = properties[i].getReadMethod();
                 setter = properties[i].getWriteMethod();
                 type = properties[i].getPropertyType();
                 break;
@@ -989,7 +964,6 @@ public class BeanInspector {
         }
         if (setter != null) {
             try {
-//				System.out.println("setting value...");
                 Object[] args = new Object[]{decodeType(type, val)};
                 if (args[0] != null) {
                     setter.invoke(obj, args);

src/eva2/gui/ExtDesktopManager.java

@@ -1,14 +1,4 @@
 package eva2.gui;
-/*
- * Title:        EvA2
- * Description:
- * Copyright:    Copyright (c) 2003
- * Company:      University of Tuebingen, Computer Architecture
- * @author Holger Ulmer, Felix Streichert, Hannes Planatscher
- * @version:  $Revision: 10 $
- *            $Date: 2006-01-18 11:02:22 +0100 (Wed, 18 Jan 2006) $
- *            $Author: streiche $
- */
 
 import javax.swing.*;
 import java.awt.*;

src/eva2/gui/JExtDesktopPane.java

@@ -1,9 +1,4 @@
 package eva2.gui;
-/*
- * Title: EvA2 Description: Copyright: Copyright (c) 2003 Company: University of Tuebingen, Computer
- * Architecture @author Holger Ulmer, Felix Streichert, Hannes Planatscher @version: $Revision: 10 $
- * $Date: 2006-01-18 11:02:22 +0100 (Wed, 18 Jan 2006) $ $Author: streiche $
- */
 
 import eva2.gui.editor.ComponentFilter;
 
@@ -11,6 +6,7 @@ import javax.swing.*;
 import java.awt.*;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
 import java.awt.event.KeyEvent;
 import java.beans.PropertyVetoException;
 import java.util.Vector;
@@ -55,32 +51,35 @@ public class JExtDesktopPane extends JDesktopPane {
             }
         };
 
-        windowMenu.add(actWindowTileVert = new ExtAction("Tile &Vertically", "Tiles all windows vertically",
+        actWindowTileVert = new ExtAction("Tile &Vertically", "Tiles all windows vertically",
-                KeyStroke.getKeyStroke(KeyEvent.VK_COMMA, Event.CTRL_MASK)) {
+                KeyStroke.getKeyStroke(KeyEvent.VK_COMMA, InputEvent.CTRL_MASK)) {
 
             @Override
             public void actionPerformed(final ActionEvent event) {
                 tileWindows(SwingConstants.HORIZONTAL);
             }
-        });
+        };
+        windowMenu.add(actWindowTileVert);
 
-        windowMenu.add(actWindowTileHorz = new ExtAction("Tile &Horizontally", "Tiles all windows horizontically",
+        actWindowTileHorz = new ExtAction("Tile &Horizontally", "Tiles all windows horizontically",
-                KeyStroke.getKeyStroke(KeyEvent.VK_PERIOD, Event.CTRL_MASK)) {
+                KeyStroke.getKeyStroke(KeyEvent.VK_PERIOD, InputEvent.CTRL_MASK)) {
 
             @Override
             public void actionPerformed(final ActionEvent event) {
                 tileWindows(SwingConstants.VERTICAL);
             }
-        });
+        };
+        windowMenu.add(actWindowTileHorz);
 
-        windowMenu.add(actWindowOverlap = new ExtAction("&Cascade Windows", "Cascades all visible windows",
+        actWindowOverlap = new ExtAction("&Cascade Windows", "Cascades all visible windows",
-                KeyStroke.getKeyStroke(KeyEvent.VK_M, Event.CTRL_MASK)) {
+                KeyStroke.getKeyStroke(KeyEvent.VK_M, InputEvent.CTRL_MASK)) {
 
             @Override
             public void actionPerformed(final ActionEvent event) {
                 overlapWindows();
             }
-        });
+        };
+        windowMenu.add(actWindowOverlap);
 
         windowMenu.addSeparator();
         desktopManager.WINDOW_LIST_START = 4;
@@ -232,7 +231,7 @@ public class JExtDesktopPane extends JDesktopPane {
                 } else {
                     f.setSelected(true);
                 }
-            } catch (PropertyVetoException exc) {
+            } catch (PropertyVetoException ignore) {
             }
         }
     }
@@ -240,18 +239,17 @@ public class JExtDesktopPane extends JDesktopPane {
     @Override
     public void addImpl(Component comp, Object constraints, int index) {
         super.addImpl(comp, constraints, index);
-        //System.out.println("JExtDesktopPane.addImpl");
         if (comp instanceof JInternalFrame) {
             JInternalFrame docFrame = (JInternalFrame) comp;
             int frameIndex = windowMenu.getItemCount() - desktopManager.WINDOW_LIST_START + 1;
             if (docFrame.getClientProperty(ExtDesktopManager.INDEX) != null) {
                 return;
             }
-            docFrame.putClientProperty(ExtDesktopManager.INDEX, new Integer(frameIndex));
+            docFrame.putClientProperty(ExtDesktopManager.INDEX, frameIndex);
             JMenuItem m = new JMenuItem((frameIndex < 10 ? frameIndex + " " : "") + docFrame.getTitle());
             if (frameIndex < 10) {
                 m.setMnemonic((char) (0x30 + frameIndex));
-                m.setAccelerator(KeyStroke.getKeyStroke(0x30 + frameIndex, Event.ALT_MASK));
+                m.setAccelerator(KeyStroke.getKeyStroke(0x30 + frameIndex, InputEvent.ALT_MASK));
             }
             m.setToolTipText("Shows the window " + docFrame.getTitle());
             m.putClientProperty(ExtDesktopManager.FRAME, docFrame);

src/eva2/gui/JTextoutputFrame.java

@@ -5,10 +5,7 @@ import eva2.optimization.tools.FileTools;
 import javax.swing.*;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
-import javax.swing.text.AbstractDocument;
+import javax.swing.text.*;
-import javax.swing.text.AttributeSet;
-import javax.swing.text.BadLocationException;
-import javax.swing.text.DocumentFilter;
 import java.awt.*;
 import java.awt.event.*;
 import java.io.Serializable;

src/eva2/gui/Main.java

@@ -367,7 +367,7 @@ public class Main extends JFrame implements OptimizationStateListener {
 
             createActions();
 
-            setSize(800, 600);
+            setSize(1024, 800);
             Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
             setLocation((screenSize.width - this.getWidth()) / 2, (int) ((screenSize.height - this.getHeight()) / 2.5));
 
@@ -533,8 +533,8 @@ public class Main extends JFrame implements OptimizationStateListener {
             System.setProperty("com.apple.mrj.application.live-resize", "true");
             try {
                 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
-            } catch (ClassNotFoundException | InstantiationException | IllegalAccessException | UnsupportedLookAndFeelException e) {
+            } catch (ClassNotFoundException | InstantiationException | IllegalAccessException | UnsupportedLookAndFeelException ex) {
-                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+                LOGGER.log(Level.INFO, "Could not set Look&Feel", ex);
             }
         } else {
             /* Set Look and Feel */

src/eva2/gui/PropertySheetPanel.java

@@ -170,7 +170,7 @@ public class PropertySheetPanel extends JPanel implements PropertyChangeListener
         propertyTable.setRowHeight(20);
         propertyTable.setDragEnabled(false);
         propertyTable.putClientProperty("terminateEditOnFocusLost", Boolean.TRUE);
-        propertyTable.setIntercellSpacing(new Dimension(8, 0));
+        //propertyTable.setIntercellSpacing(new Dimension(8, 0));
 
         // Close any child windows at this point
         removeAll();

src/eva2/optimization/individuals/AbstractEAIndividualComparator.java

@@ -93,12 +93,12 @@ public class AbstractEAIndividualComparator implements Comparator<Object>, Seria
      *
      * @param indyDataKey
      * @param fitnessCriterion
-     * @param priorizeConstraints
+     * @param preferFeasible
      * @see #AbstractEAIndividualComparator(int)
      * @see #AbstractEAIndividualComparator(String)
      */
-    public AbstractEAIndividualComparator(String indDataKey, int fitnessCriterion, boolean preferFeasible) {
+    public AbstractEAIndividualComparator(String indyDataKey, int fitnessCriterion, boolean preferFeasible) {
-        this.indyDataKey = indDataKey;
+        this.indyDataKey = indyDataKey;
         this.fitCriterion = fitnessCriterion;
         this.preferFeasible = preferFeasible;
     }

src/eva2/optimization/modules/Processor.java

@@ -235,7 +235,7 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
 
             this.optimizationParameters.getProblem().initializeProblem();
             this.optimizationParameters.getOptimizer().setProblem(this.optimizationParameters.getProblem());
-            this.optimizationParameters.getTerminator().init(this.optimizationParameters.getProblem());
+            this.optimizationParameters.getTerminator().initialize(this.optimizationParameters.getProblem());
             maybeInitParamCtrl(optimizationParameters);
             if (this.createInitialPopulations) {
                 this.optimizationParameters.getOptimizer().initialize();

src/eva2/optimization/operator/crossover/NoCrossover.java

@@ -42,7 +42,7 @@ public class NoCrossover implements InterfaceCrossover, java.io.Serializable {
         for (int i = 0; i < partners.size(); i++) {
             result[i + 1] = (AbstractEAIndividual) ((AbstractEAIndividual) partners.get(i)).clone();
         }
-        //in case the crossover was successfull lets give the mutation operators a chance to mate the strategy parameters
+        //in case the crossover was successful lets give the mutation operators a chance to mate the strategy parameters
         for (int i = 0; i < result.length; i++) {
             result[i].getMutationOperator().crossoverOnStrategyParameters(indy1, partners);
         }

src/eva2/optimization/operator/migration/InterfaceMigration.java

@@ -10,11 +10,6 @@ import eva2.optimization.strategies.InterfaceOptimizer;
  * MOXMigration typically stands for multi-criterial migration.
  * For multi-criterial optimization the migration scheme
  * also may give the subdividing scheme.
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 15.09.2004
- * Time: 14:45:15
- * To change this template use File | Settings | File Templates.
  */
 public interface InterfaceMigration {
 
@@ -27,7 +22,7 @@ public interface InterfaceMigration {
      * Typically i'll need some initialization method for
      * every bit of code i write....
      */
-    public void initMigration(InterfaceOptimizer[] islands);
+    public void initializeMigration(InterfaceOptimizer[] islands);
 
     /**
      * The migrate method can be called asychnronously or

src/eva2/optimization/operator/migration/MOBestMigration.java

@@ -27,7 +27,7 @@ public class MOBestMigration implements InterfaceMigration, java.io.Serializable
      * every bit of code i write....
      */
     @Override
-    public void initMigration(InterfaceOptimizer[] islands) {
+    public void initializeMigration(InterfaceOptimizer[] islands) {
         // pff at a later stage i could initialize a topology here
     }
 

src/eva2/optimization/operator/migration/MOClusteringSeparation.java

@@ -65,7 +65,7 @@ public class MOClusteringSeparation implements InterfaceMigration, java.io.Seria
      * every bit of code i write....
      */
     @Override
-    public void initMigration(InterfaceOptimizer[] islands) {
+    public void initializeMigration(InterfaceOptimizer[] islands) {
         // pff at a later stage i could initialize a topology here
         if (this.reuseC) {
             this.kMeans.resetC();

src/eva2/optimization/operator/migration/MOConeSeparation.java

@@ -61,7 +61,7 @@ public class MOConeSeparation implements InterfaceMigration, java.io.Serializabl
      * every bit of code i write....
      */
     @Override
-    public void initMigration(InterfaceOptimizer[] islands) {
+    public void initializeMigration(InterfaceOptimizer[] islands) {
         // pff at a later stage i could initialize a topology here
     }
 

src/eva2/optimization/operator/migration/MOXMeansSeparation.java

@@ -64,7 +64,7 @@ public class MOXMeansSeparation implements InterfaceMigration, java.io.Serializa
      * every bit of code i write....
      */
     @Override
-    public void initMigration(InterfaceOptimizer[] islands) {
+    public void initializeMigration(InterfaceOptimizer[] islands) {
         // pff at a later stage i could initialize a topology here
     }
 

src/eva2/optimization/operator/migration/SOBestMigration.java

@@ -27,7 +27,7 @@ public class SOBestMigration implements InterfaceMigration, java.io.Serializable
      * every bit of code i write....
      */
     @Override
-    public void initMigration(InterfaceOptimizer[] islands) {
+    public void initializeMigration(InterfaceOptimizer[] islands) {
         // pff at a later stage i could initialize a topology here
     }
 

src/eva2/optimization/operator/migration/SOMONoMigration.java

@@ -20,7 +20,7 @@ public class SOMONoMigration implements InterfaceMigration, java.io.Serializable
      * every bit of code i write....
      */
     @Override
-    public void initMigration(InterfaceOptimizer[] islands) {
+    public void initializeMigration(InterfaceOptimizer[] islands) {
 
     }
 

src/eva2/optimization/operator/moso/InterfaceMOSOConverter.java

@@ -8,11 +8,6 @@ import eva2.optimization.population.Population;
  * a single double values, thus allowing weight aggregation, goal programming and
  * so on. To allow logging the original double[] values are stored in the userData
  * using the key "MOFitness".
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 05.03.2004
- * Time: 10:44:14
- * To change this template use File | Settings | File Templates.
  */
 public interface InterfaceMOSOConverter {
 
@@ -43,11 +38,6 @@ public interface InterfaceMOSOConverter {
      */
     public void setOutputDimension(int dim);
 
-//    /** This method allows the problem to set the names of the output variables
-//     * @param dim       Output names
-//     */
-//    public void setOutputNames(String[] dim);
-
     /**
      * This method processes a single individual
      *

src/eva2/optimization/operator/postprocess/PostProcess.java

@@ -683,7 +683,7 @@ public class PostProcess {
         Pair<Integer, Boolean> stepsAbortedFlag = null;
         for (int i = 0; i < candidates.size(); i++) { // improve each single sub pop
             subPop = nmPops.get(i);
-            term.init(prob);
+            term.initialize(prob);
 
             switch (method) {
                 case nelderMead:

src/eva2/optimization/operator/selection/InterfaceSelection.java

@@ -12,11 +12,6 @@ import eva2.optimization.population.Population;
  * not implemented. All selection method should obey Deb's constraint
  * handling principle, first select feasible, only if all are infeasible
  * select the individuals with the smallest constraint violation.
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 18.03.2003
- * Time: 11:24:22
- * To change this template use Options | File Templates.
  */
 public interface InterfaceSelection {
 
@@ -51,12 +46,12 @@ public interface InterfaceSelection {
     /**
      * This method allows you to select >size< partners for a given Individual
      *
-     * @param dad              The already seleceted parent
+     * @param dad               The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
-     * @param size             The number of partners needed.
+     * @param size              The number of partners needed.
      * @return The selected partners.
      */
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size);
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size);
 
     /**
      * Toggle the use of obeying the constraint violation principle

src/eva2/optimization/operator/selection/SelectAll.java

@@ -77,13 +77,13 @@ public class SelectAll implements InterfaceSelection, java.io.Serializable {
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectBestIndividuals.java

@@ -160,17 +160,15 @@ public class SelectBestIndividuals implements InterfaceSelection, java.io.Serial
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
-/**********************************************************************************************************************
+
- * These are for GUI
- */
     /**
      * This method returns a global info string
      *

src/eva2/optimization/operator/selection/SelectEPTournaments.java

@@ -158,13 +158,13 @@ public class SelectEPTournaments implements InterfaceSelection, java.io.Serializ
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectMOMAIIDominanceCounter.java

@@ -105,13 +105,13 @@ public class SelectMOMAIIDominanceCounter implements InterfaceSelection, java.io
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectMOMaxiMin.java

@@ -73,13 +73,13 @@ public class SelectMOMaxiMin implements InterfaceSelection, java.io.Serializable
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectMONSGAIICrowedTournament.java

@@ -143,13 +143,13 @@ public class SelectMONSGAIICrowedTournament implements InterfaceSelection, java.
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectMONonDominated.java

@@ -97,13 +97,13 @@ public class SelectMONonDominated implements InterfaceSelection, java.io.Seriali
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
     /**

src/eva2/optimization/operator/selection/SelectMOPESA.java

@@ -90,13 +90,13 @@ public class SelectMOPESA implements InterfaceSelection, java.io.Serializable {
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectMOPESAII.java

@@ -126,13 +126,13 @@ public class SelectMOPESAII implements InterfaceSelection, java.io.Serializable
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectMOSPEAII.java

@@ -113,13 +113,13 @@ public class SelectMOSPEAII implements InterfaceSelection, java.io.Serializable
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectParticleWheel.java

@@ -133,13 +133,13 @@ public class SelectParticleWheel implements InterfaceSelection, java.io.Serializ
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
 /**********************************************************************************************************************

src/eva2/optimization/operator/selection/SelectRandom.java

@@ -96,18 +96,15 @@ public class SelectRandom implements InterfaceSelection, java.io.Serializable {
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already selected parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/optimization/operator/selection/SelectTournament.java

@@ -9,11 +9,6 @@ import eva2.tools.math.RNG;
  * also scaling invariant.
  * In case of multiple fitness values the selection
  * critria is selected randomly for each selection event.
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 01.04.2003
- * Time: 16:17:26
- * To change this template use Options | File Templates.
  */
 public class SelectTournament implements InterfaceSelection, java.io.Serializable {
 
@@ -112,18 +107,15 @@ public class SelectTournament implements InterfaceSelection, java.io.Serializabl
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/optimization/operator/selection/SelectXProbRouletteWheel.java

@@ -146,13 +146,13 @@ public class SelectXProbRouletteWheel implements InterfaceSelection, java.io.Ser
      * This method allows you to select partners for a given Individual
      *
      * @param dad              The already seleceted parent
-     * @param avaiablePartners The mating pool.
+     * @param availablePartners The mating pool.
      * @param size             The number of partners needed.
      * @return The selected partners.
      */
     @Override
-    public Population findPartnerFor(AbstractEAIndividual dad, Population avaiablePartners, int size) {
+    public Population findPartnerFor(AbstractEAIndividual dad, Population availablePartners, int size) {
-        return this.selectFrom(avaiablePartners, size);
+        return this.selectFrom(availablePartners, size);
     }
 
     /**

src/eva2/optimization/operator/terminators/CombinedTerminator.java

@@ -38,12 +38,12 @@ public class CombinedTerminator implements InterfaceTerminator, Serializable {
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         if (t1 != null) {
-            t1.init(prob);
+            t1.initialize(prob);
         }
         if (t2 != null) {
-            t2.init(prob);
+            t2.initialize(prob);
         }
         msg = "Not terminated.";
     }

src/eva2/optimization/operator/terminators/EvaluationTerminator.java

@@ -4,6 +4,7 @@ import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.optimization.population.PopulationInterface;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.util.annotation.Description;
+import eva2.util.annotation.Parameter;
 
 import java.io.Serializable;
 
@@ -20,13 +21,14 @@ public class EvaluationTerminator implements InterfaceTerminator,
     /**
      * Number of fitness calls on the problem which is optimized.
      */
+    @Parameter(name = "Max. Fitness Calls", description = "Number of calls to fitness function.")
     protected int maxFitnessCalls = 1000;
 
     public EvaluationTerminator() {
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         msg = "Not terminated.";
     }
 
@@ -74,14 +76,4 @@ public class EvaluationTerminator implements InterfaceTerminator,
         //System.out.println("getFitnessCalls"+maxFitnessCalls);
         return maxFitnessCalls;
     }
-
-    /**
-     * Returns the tip text for this property
-     *
-     * @return tip text for this property
-     */
-    public String fitnessCallsTipText() {
-        return "number of calls to fitness function.";
-    }
-
 }

src/eva2/optimization/operator/terminators/FitnessValueTerminator.java

@@ -23,7 +23,7 @@ public class FitnessValueTerminator implements InterfaceTerminator,
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         msg = "Not terminated.";
     }
 

src/eva2/optimization/operator/terminators/GenerationTerminator.java

@@ -20,7 +20,7 @@ public class GenerationTerminator implements InterfaceTerminator, Serializable {
     private String msg = "";
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         msg = "Not terminated.";
     }
 

src/eva2/optimization/operator/terminators/HistoryConvergenceTerminator.java

@@ -42,7 +42,7 @@ public class HistoryConvergenceTerminator implements InterfaceTerminator, Serial
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         msg = "Not terminated.";
     }
 

src/eva2/optimization/operator/terminators/InterfaceTerminator.java

@@ -6,8 +6,6 @@ import eva2.problems.InterfaceOptimizationProblem;
 
 /**
  * Interface for a termination criterion.
- *
- * @author mkron, streiche
  */
 public interface InterfaceTerminator {
     /**
@@ -25,5 +23,5 @@ public interface InterfaceTerminator {
 
     public String lastTerminationMessage();
 
-    public void init(InterfaceOptimizationProblem prob);
+    public void initialize(InterfaceOptimizationProblem prob);
 }

src/eva2/optimization/operator/terminators/KnownOptimaFoundTerminator.java

@@ -29,7 +29,7 @@ public class KnownOptimaFoundTerminator implements InterfaceTerminator, Serializ
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         if (prob != null) {
             if (prob instanceof InterfaceMultimodalProblemKnown) {
                 mProblem = (InterfaceMultimodalProblemKnown) prob;

src/eva2/optimization/operator/terminators/ParetoMetricTerminator.java

@@ -43,8 +43,8 @@ public class ParetoMetricTerminator extends PopulationMeasureTerminator implemen
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
-        super.init(prob);
+        super.initialize(prob);
         if (prob instanceof AbstractMultiObjectiveOptimizationProblem) {
             moProb = (AbstractMultiObjectiveOptimizationProblem) prob;
         } else {

src/eva2/optimization/operator/terminators/PhenotypeConvergenceTerminator.java

@@ -28,8 +28,8 @@ public class PhenotypeConvergenceTerminator extends PopulationMeasureTerminator
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
-        super.init(prob);
+        super.initialize(prob);
 //		oldPhenNorm  = 0;
         oldIndy = null;
     }

src/eva2/optimization/operator/terminators/PopulationMeasureTerminator.java

@@ -76,7 +76,7 @@ public abstract class PopulationMeasureTerminator implements InterfaceTerminator
     }
 
     @Override
-    public void init(InterfaceOptimizationProblem prob) {
+    public void initialize(InterfaceOptimizationProblem prob) {
         firstTime = true;
         msg = "Not terminated.";
 //		oldFit = null;

src/eva2/optimization/population/Population.java

@@ -1031,7 +1031,7 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
      * @return The index of the best (worst) individual.
      */
     public int getIndexOfBestOrWorstIndividual(boolean bBest, Comparator<Object> comparator) {
-        ArrayList<?> sorted = sortBy(comparator);
+        ArrayList<?> sorted = getSorted(comparator);
         if (bBest) {
             return indexOf(sorted.get(0));
         } else {

src/eva2/optimization/stat/EvAStatisticalEvaluation.java

@@ -12,8 +12,6 @@ import java.util.List;
 /**
  * Do some statistical tests on a set of job results. Note that the plausibility (comparability of the
  * jobs) is not tested here.
- *
- * @author mkron
  */
 public class EvAStatisticalEvaluation {
 
@@ -230,9 +228,6 @@ public class EvAStatisticalEvaluation {
         if (dat1 != null && dat2 != null) {
             t = Mathematics.tTestEqSizeEqVar(dat1, dat2);
         }
-//		MannWhitneyTest mwt = new MannWhitneyTest(job1.getDoubleDataColumn(field), job2.getDoubleDataColumn(field));
-//		double t = mwt.getSP();
-//		t = roundTo2DecimalPlaces(t);
         return "" + t;
     }
 
@@ -243,7 +238,6 @@ public class EvAStatisticalEvaluation {
         if (dat1 != null && dat2 != null) {
             t = Mathematics.tTestUnEqSizeEqVar(dat1, dat2);
         }
-//		t = roundTo2DecimalPlaces(t);
         return "" + t;
     }
 
@@ -254,7 +248,6 @@ public class EvAStatisticalEvaluation {
         if (dat1 != null && dat2 != null) {
             t = Mathematics.tTestUnEqSizeUnEqVar(dat1, dat2);
         }
-//		t = roundTo2DecimalPlaces(t);
         return "" + t;
     }
 
@@ -266,8 +259,6 @@ public class EvAStatisticalEvaluation {
             Object obj = ReflectPackage.instantiateWithParams("jsc.independentsamples.MannWhitneyTest", new Object[]{dat1, dat2}, null);
             if (obj != null) {
                 Object sp = BeanInspector.callIfAvailable(obj, "getSP", new Object[]{});
-//				System.out.println(BeanInspector.niceToString(obj));
-//				System.out.println("SP val is " + sp);
                 t = (Double) sp;
             } else {
                 System.err.println("For the MannWhitney test, the JSC package is required on the class path!");

src/eva2/optimization/stat/GenericStatistics.java

@@ -162,16 +162,16 @@ public class GenericStatistics implements Serializable {
                     String desc = fields[i].toString(); //System.out.println("desc "+desc);
                     int istransient = desc.indexOf("transient");
 
-                    Object FieldValue = null;
+                    Object fieldValue = null;
                     if (istransient == -1 || fields[i].getName().equals("elementData")) {  // the elementdatahack
                         fields[i].setAccessible(true);
                         try {
-                            FieldValue = fields[i].get(target);
+                            fieldValue = fields[i].get(target);
-                            if (FieldValue instanceof Double) {
+                            if (fieldValue instanceof Double) {
-                                data[index] = ((Double) FieldValue).doubleValue();
+                                data[index] = (Double) fieldValue;
                             }
-                            if (FieldValue instanceof Integer) {
+                            if (fieldValue instanceof Integer) {
-                                data[index] = ((Integer) FieldValue).doubleValue();
+                                data[index] = ((Integer) fieldValue).doubleValue();
                             }
                             index++;
                         } catch (Exception ex) {

src/eva2/optimization/stat/GraphSelectionEnum.java

@@ -35,14 +35,6 @@ public enum GraphSelectionEnum {
         }
     }
 
-    //	public static boolean doPlotCurrentBest(StringSelection sel) {
-//		return sel.isSelected(GraphSelectionEnum.currentBest.ordinal());
-//	}
-//	
-//	public static boolean doPlotRunBest(StringSelection sel) {
-//		return sel.isSelected(GraphSelectionEnum.runBest.ordinal());
-//	}
-//	
     public static boolean doPlotWorst(StringSelection sel) {
         return sel.isSelected(GraphSelectionEnum.currentWorst.ordinal());
     }
@@ -51,14 +43,6 @@ public enum GraphSelectionEnum {
         return sel.isSelected(GraphSelectionEnum.meanFit.ordinal());
     }
 
-    //	public static boolean doPlotCurrentBestFeasible(StringSelection sel) {
-//		return sel.isSelected(GraphSelectionEnum.currentBestFeasible.ordinal()); 
-//	}
-//	
-//	public static boolean doPlotRunBestFeasible(StringSelection sel) {
-//		return sel.isSelected(GraphSelectionEnum.runBestFeasible.ordinal()); 
-//	}
-//	
     public static boolean doPlotAvgEucDist(StringSelection sel) {
         return sel.isSelected(GraphSelectionEnum.avgEucPopDistance.ordinal());
     }

src/eva2/optimization/stat/OptimizationJob.java

@@ -13,8 +13,6 @@ import java.util.List;
  * framework should guarantee that the job is removed as a statistics listener.
  * <p/>
  * A job contains data fields of a multi-run experiment and header strings describing the data.
- *
- * @author mkron
  */
 public class OptimizationJob implements Serializable, InterfaceStatisticsListener {
 

src/eva2/optimization/stat/StatisticsWithGUI.java

@@ -32,7 +32,6 @@ public class StatisticsWithGUI extends AbstractStatistics implements Serializabl
     private Graph[][] fitnessGraph;
     private Graph[][] statGraph;
     private String graphInfoString;
-    protected int plotCounter;
     private JTextoutputFrameInterface proxyPrinter;
     /*
      * List of descriptor strings and optional indices. strictly its redundant
@@ -135,7 +134,6 @@ public class StatisticsWithGUI extends AbstractStatistics implements Serializabl
         for (int i = 0; i < fitnessGraph.length; i++) {
             fitnessGraph[i] = new Graph[graphCount];
             for (int j = 0; j < fitnessGraph[i].length; j++) {
-//				String[] d = (String[]) description.get(i);
                 // this is where the column string for ascii export is created! Uah!
                 fitnessGraph[i][j] =
                         fitnessFrame[i].getNewGraph(graphDesc.get(j).head + "_"
@@ -166,12 +164,6 @@ public class StatisticsWithGUI extends AbstractStatistics implements Serializabl
             return;
         }
         boolean isValidGraph = fitnessFrame[graph].isValid();
-        if (!isValidGraph) {
-            // this happens if the user closed the plot window.
-            // if the plots are reinitialized immediately, the user might get angry, so wait (till next opt start)
-//			EVAERROR.WARNING("fitness graph is invalid, trying to reinitialize...");
-//			initPlots(getDescription());
-        }
         if (isValidGraph) {
             fitnessGraph[graph][subGraph].setConnectedPoint(x, y);
         }
@@ -242,6 +234,5 @@ public class StatisticsWithGUI extends AbstractStatistics implements Serializabl
                 index++;
             }
         }
-//		}
     }
 }

src/eva2/optimization/strategies/EvolutionStrategyIPOP.java

@@ -131,7 +131,7 @@ public class EvolutionStrategyIPOP extends EvolutionStrategies implements Interf
         // update the stagnation time in the terminator
         if (!isStagnationTimeUserDef() && (fitConvTerm != null)) {
             fitConvTerm.setStagnationTime(calcDefaultStagnationTime());
-            fitConvTerm.init(getProblem());
+            fitConvTerm.initialize(getProblem());
         }
         bestList.add(best);
         best = null;

src/eva2/optimization/strategies/IslandModelEA.java

@@ -116,7 +116,7 @@ public class IslandModelEA implements InterfacePopulationChangedEventListener, I
              }*/
         }
 
-        this.migration.initMigration(this.islands);
+        this.migration.initializeMigration(this.islands);
         Population pop;
         this.population.incrGeneration(); // the island-initialization has increased the island-pop generations.
 
@@ -183,7 +183,7 @@ public class IslandModelEA implements InterfacePopulationChangedEventListener, I
              }*/
         }
 
-        this.migration.initMigration(this.islands);
+        this.migration.initializeMigration(this.islands);
         Population pop;
         for (int i = 0; i < this.islands.length; i++) {
             pop = (Population) this.islands[i].getPopulation().clone();

src/eva2/optimization/tools/AbstractObjectEditor.java

@@ -33,10 +33,6 @@ public abstract class AbstractObjectEditor implements PropertyEditor, java.beans
     public GeneralGenericObjectEditorPanel objectEditorPanel;
     public Hashtable editorTable = new Hashtable();
 
-    /**
-     * ****************************** java.beans.PropertyChangeListener ************************
-     */
-
     @Override
     public void addPropertyChangeListener(PropertyChangeListener l) {
         if (propertyChangeSupport == null) {

src/eva2/optimization/tools/FileTools.java

@@ -9,13 +9,7 @@ import java.awt.*;
 import java.io.*;
 import java.util.ArrayList;
 
-
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 09.06.2005
- * Time: 13:01:18
- * To change this template use File | Settings | File Templates.
  */
 public class FileTools {
 

src/eva2/tools/BasicResourceLoader.java

@@ -359,31 +359,6 @@ public class BasicResourceLoader implements ResourceLoader {
         return in;
     }
 
-//    public InputStream getStreamFromClassPath(String resourceLocation) {
-//    	String[] dynCP = ReflectPackage.getValidCPArray(); 
-//    	Vector<String> found = new Vector<String>();
-//		for (int i=0; i<dynCP.length; i++) {
-//			System.out.println("reading element "+dynCP[i]);
-//			if (dynCP[i].endsWith(".jar")) {
-//				// those should be found somewhere else
-////				getClassesFromJarFltr(set, dynCP[i], pckg, includeSubs, reqSuperCls);
-//			} else {
-//				String absRes = dynCP[i];
-//				if (!absRes.endsWith("/")) absRes += "/";
-//				absRes += resourceLocation;
-//				System.out.println("reading from files: "+dynCP[i]);
-//				InputStream in = getStreamFromFile(absRes);
-//				if (in != null) found.add(absRes);
-//			}
-//		}
-//		if (found.size() == 0) return null;
-//		if (found.size()>1) {
-//			System.err.println("Warning, more than one instance of " + resourceLocation + " were found, returning first of:");
-//			for (int i=0; i<found.size(); i++) System.err.println(found.get(i));
-//		}
-//		return getStreamFromFile(found.get(0));
-//    }
-
     /**
      * Gets the byte data from a file at the given resource location.
      *
@@ -626,6 +601,4 @@ public class BasicResourceLoader implements ResourceLoader {
         }
         return userProps;
     }
-
-
 }

src/eva2/tools/EVAERROR.java

@@ -3,29 +3,19 @@ package eva2.tools;
 import java.util.HashMap;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-/**
- * Title:        EvA2
- * Description:
- * Copyright:    Copyright (c) 2003
- * Company:      University of Tuebingen, Computer Architecture
- * @author Holger Ulmer, Felix Streichert, Hannes Planatscher
- * @version: $Revision: 245 $
- *            $Date: 2007-11-08 17:24:53 +0100 (Thu, 08 Nov 2007) $
- *            $Author: mkron $
- */
 
 /**
  *
  */
 public class EVAERROR {
-    private static final Logger logger = Logger.getLogger(EVAERROR.class.getName());
+    private static final Logger LOGGER = Logger.getLogger(EVAERROR.class.getName());
     private static transient HashMap<String, Boolean> errorMap = null;
 
     /**
      *
      */
     public static void EXIT(String message) {
-        logger.log(Level.SEVERE, message);
+        LOGGER.log(Level.SEVERE, message);
         System.exit(-1);
     }
 
@@ -33,7 +23,7 @@ public class EVAERROR {
      *
      */
     public static void EXIT(String message, Exception ex) {
-        logger.log(Level.SEVERE, message, ex);
+        LOGGER.log(Level.SEVERE, message, ex);
         System.exit(-1);
     }
 
@@ -41,7 +31,7 @@ public class EVAERROR {
      *
      */
     public static void WARNING(String message) {
-        logger.log(Level.WARNING, message);
+        LOGGER.log(Level.WARNING, message);
     }
 
     /**
@@ -56,7 +46,7 @@ public class EVAERROR {
         }
 
         if (!errorMap.containsKey(message)) {
-            logger.log(Level.SEVERE, message);
+            LOGGER.log(Level.SEVERE, message);
             errorMap.put(message, true);
         }
     }

src/eva2/tools/MultirunRefiner.java

@@ -18,15 +18,6 @@ import java.util.Vector;
 
 /**
  * MultirunRefiner
- * Description:     This is a small programm .
- * Copyright:       Copyright (c) 2001
- * Company:         University of Tuebingen, Computer Architecture
- *
- * @author Felix Streichert
- * @version: $Revision: 10 $
- * $Date: 2006-01-18 11:02:22 +0100 (Wed, 18 Jan 2006) $
- * $Author: streiche $
- * @since JDK 1.3.0_02
  */
 
 public class MultirunRefiner {

src/eva2/tools/ResourceLoader.java

@@ -29,14 +29,8 @@ package eva2.tools;
 
 /**
  * TODO description.
- *
- * @.author wegnerj
- * @.license GPL
- * @.cvsversion $Revision: 1.8 $, $Date: 2005/02/17 16:48:44 $
  */
 public interface ResourceLoader {
-    //~ Methods ////////////////////////////////////////////////////////////////
-
     /**
      * Gets the byte data from a file at the given resource location.
      *
@@ -44,8 +38,4 @@ public interface ResourceLoader {
      * @return the byte array of file.
      */
     byte[] getBytesFromResourceLocation(String rawResrcLoc);
-}
+}
-
-///////////////////////////////////////////////////////////////////////////////
-//END OF FILE.
-///////////////////////////////////////////////////////////////////////////////

src/eva2/tools/StringTools.java

@@ -9,8 +9,6 @@ import java.util.regex.Pattern;
 /**
  * Utility class to provide simplification functions
  * for working with Strings.
- *
- * @author Fabian Becker, Marcel Kronfeld
  */
 public final class StringTools {
 
@@ -103,13 +101,6 @@ public final class StringTools {
         return -1;
     }
 
-//    public static void main(String[] args) {
-//    	System.out.println(toHTML("Hallo-asdfsadfsafdsadfo, dies ist ein doller test text!", 15));
-//    	System.out.println(toHTML("Set the interval of data output for intermediate verbosity (in generations).", 15));
-//    	System.out.println(toHTML("Set the interval of data output for intermediate verbosity (in generations).", 25));
-//    	System.out.println(toHTML("Set the interval of data output for intermediate verbosity (in generations).", 30));
-//    }
-
     /**
      * Parse an array of Strings as an argument list. Take the argument list, a set of keys together
      * with their arities. Returns for each key a value depending on arity and whether it was found.

src/eva2/tools/TXTFileFilter.java

@@ -8,17 +8,7 @@ package eva2.tools;
 
 import javax.swing.filechooser.FileFilter;
 
-/**
+/**A simple File Filter for *.txt files.
- * TXTFileFilter
- * Description:     A simple File Filter for *.txt files.
- * Copyright:       Copyright (c) 2001
- * Company:         University of Tuebingen, Computer Architecture
- *
- * @author Felix Streichert
- * @version: $Revision: 10 $
- * $Date: 2006-01-18 11:02:22 +0100 (Wed, 18 Jan 2006) $
- * $Author: streiche $
- * @since JDK 1.3.0_02
  */
 
 public class TXTFileFilter extends FileFilter {

src/eva2/tools/URLGetter.java

@@ -5,16 +5,6 @@ import java.io.InputStreamReader;
 import java.net.URL;
 import java.net.URLConnection;
 
-/**
- * <p>Title: EvA2</p>
- * <p>Description: </p>
- * <p>Copyright: Copyright (c) 2003</p>
- * <p>Company: </p>
- *
- * @author not attributable
- * @version 1.0
- */
-
 public class URLGetter {
     public URLGetter() {
 

src/eva2/tools/diagram/ColorBarCalculator.java

@@ -12,25 +12,12 @@
 
 package eva2.tools.diagram;
 
-/*============================================================================
- * IMPORTS
- *============================================================================*/
-
 import java.awt.*;
 
-
-/*============================================================================
- * CLASS DECLARATION
- *============================================================================*/
-
 /**
  * Calculates the color values for a legend-style color bar.
  */
 public class ColorBarCalculator {
-  /*--------------------------------------------------------------------------
-   * static public final member variables
-   *--------------------------------------------------------------------------*/
-
     static public final int BLUE_TO_RED = 0;
     static public final int GREY_SCALE = 1;
     static public final int BLUE_SCALE = 2;
@@ -38,25 +25,13 @@ public class ColorBarCalculator {
     // GREY_SCALE returns luminance values in [0.1;0.9], GREY_EXTENDED_SCALE in [0.0;1.0]
     static public final int GREY_EXTENDED_SCALE = 4;
 
-  /*--------------------------------------------------------------------------
-   * private member variables
-   *--------------------------------------------------------------------------*/
-
     private int color_scale = BLUE_TO_RED;
     private boolean inverseScale = false;
 
-  /*--------------------------------------------------------------------------
-   * constructor
-   *--------------------------------------------------------------------------*/
-
     public ColorBarCalculator(int color_scale) {
         this.color_scale = color_scale;
     }
 
-  /*--------------------------------------------------------------------------
-   * public methods
-   *--------------------------------------------------------------------------*/
-
     public void setColorScale(int color_scale) {
         this.color_scale = color_scale;
     }
@@ -122,10 +97,6 @@ public class ColorBarCalculator {
         return inverseScale;
     }
 
-  /*--------------------------------------------------------------------------
-   * static public methods
-   *--------------------------------------------------------------------------*/
-
     /**
      * Returns color for the given float-value, which must be in the range from 0 to 1.
      * Warning: Creates new color object, better use the method 'getRGB' if possible.
@@ -141,9 +112,4 @@ public class ColorBarCalculator {
         float hue = value * (value + value * 0.8F) / 2.65F - 1F;
         return Color.HSBtoRGB(hue, 0.6F, 1F);
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/
-

src/eva2/tools/math/Jama/EigenvalueDecomposition.java

@@ -22,10 +22,6 @@ import eva2.tools.math.Jama.util.Maths;
 
 public class EigenvalueDecomposition implements java.io.Serializable {
 
-/* ------------------------
-   Class variables
- * ------------------------ */
-
     /**
      * Row and column dimension (square matrix).
      *

src/eva2/tools/math/Jama/LUDecomposition.java

@@ -17,10 +17,6 @@ package eva2.tools.math.Jama;
 
 public class LUDecomposition implements java.io.Serializable {
 
-/* ------------------------
-   Class variables
- * ------------------------ */
-
     /**
      * Array for internal storage of decomposition.
      *

src/eva2/tools/math/Jama/Matrix.java

@@ -68,10 +68,6 @@ public class Matrix implements Cloneable, Serializable {
      */
     private static final long serialVersionUID = 3672826349694248499L;
 
-  /* ------------------------
-     Class variables
-   * ------------------------ */
-
     /**
      * Array for internal storage of elements.
      *
@@ -87,10 +83,6 @@ public class Matrix implements Cloneable, Serializable {
      */
     private int m, n;
 
-/* ------------------------
-   Constructors
- * ------------------------ */
-
     /**
      * Construct an m-by-n matrix of zeros.
      *
@@ -213,11 +205,6 @@ public class Matrix implements Cloneable, Serializable {
         return Ret;
     }
 
-
-/* ------------------------
-   Public Methods
- * ------------------------ */
-
     /**
      * Construct a matrix from a copy of a 2-D array.
      *
@@ -309,9 +296,6 @@ public class Matrix implements Cloneable, Serializable {
         double[][] C = new double[m][n];
         for (int i = 0; i < m; i++) {
             System.arraycopy(A[i], 0, C[i], 0, n);
-//         for (int j = 0; j < n; j++) {
-//            C[i][j] = A[i][j];
-//         }
         }
         return C;
     }
@@ -1396,11 +1380,6 @@ public class Matrix implements Cloneable, Serializable {
         return new Matrix(A);
     }
 
-
-/* ------------------------
-   Private Methods
- * ------------------------ */
-
     /**
      * Check if size(A) == size(B) *
      */

src/eva2/tools/print/PagePrinter.java

@@ -12,20 +12,12 @@
 
 package eva2.tools.print;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import javax.swing.*;
 import java.awt.*;
 import java.awt.image.BufferedImage;
 import java.awt.print.PageFormat;
 import java.awt.print.Printable;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 public class PagePrinter {
     Component c;
     Graphics g;
@@ -150,8 +142,4 @@ public class PagePrinter {
         }
         return Printable.PAGE_EXISTS;
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/