Code cleanup, comments, javadoc fixes.

src/eva2/EvAInfo.java

@@ -77,8 +77,7 @@ public class EvAInfo {
     }
 
     public static String getProperty(String key) {
-        String myVal = evaProperties.getProperty(key);
+        return evaProperties.getProperty(key);
-        return myVal;
     }
 
     public static Properties getProperties() {
@@ -98,7 +97,6 @@ public class EvAInfo {
     }
 
     public static String propDefaultModule() {
-        String defaultModule = getProperty("DefaultModule");
+        return getProperty("DefaultModule");
-        return defaultModule;
     }
 }

src/eva2/cli/OptimizationBuilder.java

@@ -120,7 +120,7 @@ public final class OptimizationBuilder {
             Class<?>[] params = new Class[0];
             try {
                 Constructor constructor = clazz.getConstructor(params);
-                instance = (T)constructor.newInstance(new Object[]{});
+                instance = (T)constructor.newInstance();
             } catch (NoSuchMethodException | InvocationTargetException | InstantiationException | IllegalAccessException ex) {
                 ex.printStackTrace();
             }

src/eva2/gui/ExtDesktopManager.java

@@ -2,6 +2,7 @@ package eva2.gui;
 
 import javax.swing.*;
 import java.awt.*;
+import java.awt.event.InputEvent;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -50,11 +51,11 @@ public class ExtDesktopManager extends DefaultDesktopManager {
         for (i = index; i < Math.min(WINDOW_LIST_START + 9, desktop.getWindowMenu().getItemCount()); i++) {
             JMenuItem m = desktop.getWindowMenu().getItem(i);
             JInternalFrame frame = (JInternalFrame) m.getClientProperty(FRAME);
-            frame.putClientProperty(INDEX, ((Integer) frame.getClientProperty(INDEX)).intValue() - 1);
+            frame.putClientProperty(INDEX, (Integer) frame.getClientProperty(INDEX) - 1);
             int winIndex = i - WINDOW_LIST_START + 1;
             m.setText((winIndex) + " " + frame.getTitle());
             m.setMnemonic((char) (0x30 + winIndex));
-            m.setAccelerator(KeyStroke.getKeyStroke(0x30 + winIndex, Event.ALT_MASK));
+            m.setAccelerator(KeyStroke.getKeyStroke(0x30 + winIndex, InputEvent.ALT_MASK));
         }
 
         if (internalFrame.isSelected()) {

src/eva2/gui/JEFrame.java

@@ -4,8 +4,8 @@ import javax.swing.*;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.InternalFrameListener;
-import java.awt.*;
 import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
 import java.awt.event.KeyEvent;
 
 public class JEFrame extends JInternalFrame {
@@ -62,7 +62,7 @@ public class JEFrame extends JInternalFrame {
             }
         });
         this.getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
-                KeyStroke.getKeyStroke(KeyEvent.VK_F, Event.CTRL_MASK),
+                KeyStroke.getKeyStroke(KeyEvent.VK_F, InputEvent.CTRL_MASK),
                 "ctrlFpressed"
         );
         this.getRootPane().getActionMap().put(
@@ -75,7 +75,7 @@ public class JEFrame extends JInternalFrame {
                 }
         );
         this.getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
-                KeyStroke.getKeyStroke(KeyEvent.VK_O, Event.CTRL_MASK),
+                KeyStroke.getKeyStroke(KeyEvent.VK_O, InputEvent.CTRL_MASK),
                 "ctrlOpressed"
         );
         this.getRootPane().getActionMap().put(
@@ -91,7 +91,7 @@ public class JEFrame extends JInternalFrame {
                 }
         );
         this.getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
-                KeyStroke.getKeyStroke(KeyEvent.VK_LESS, Event.CTRL_MASK),
+                KeyStroke.getKeyStroke(KeyEvent.VK_LESS, InputEvent.CTRL_MASK),
                 "ctrlSmallerpressed"
         );
         final JEFrame self = this;

src/eva2/gui/JExtToolBar.java

@@ -42,7 +42,7 @@ public class JExtToolBar extends JToolBar {
         if (k != null) {
             int modifiers = k.getModifiers();
             if (modifiers > 0) {
-                result.append(KeyEvent.getKeyModifiersText(modifiers) + "+");
+                result.append(KeyEvent.getKeyModifiersText(modifiers)).append("+");
             }
             result.append(KeyEvent.getKeyText(k.getKeyCode()));
         }

src/eva2/gui/JTextEditorInternalFrame.java

@@ -10,8 +10,8 @@ import javax.swing.text.Keymap;
 import javax.swing.undo.CannotRedoException;
 import javax.swing.undo.CannotUndoException;
 import javax.swing.undo.UndoManager;
-import java.awt.*;
 import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
 import java.awt.event.KeyEvent;
 import java.io.*;
 import java.util.Hashtable;
@@ -26,7 +26,7 @@ public class JTextEditorInternalFrame extends JDocFrame {
     private class UndoAction extends ExtAction {
         public UndoAction() {
             super("R<EFBFBD>ckg<EFBFBD>ngig", new ImageIcon("images/EditUndo.gif"), "Macht die letzte Aktion r<>ckg<6B>ngig",
-                    KeyStroke.getKeyStroke(KeyEvent.VK_Z, Event.CTRL_MASK));
+                    KeyStroke.getKeyStroke(KeyEvent.VK_Z, InputEvent.CTRL_MASK));
             setEnabled(false);
         }
 
@@ -57,7 +57,7 @@ public class JTextEditorInternalFrame extends JDocFrame {
     ///////////////////////////////////////////
     private class RedoAction extends ExtAction {
         public RedoAction() {
-            super("Wiederholen", "Wiederholt die letzte Aktion", KeyStroke.getKeyStroke(KeyEvent.VK_Z, Event.CTRL_MASK | Event.SHIFT_MASK));
+            super("Wiederholen", "Wiederholt die letzte Aktion", KeyStroke.getKeyStroke(KeyEvent.VK_Z, InputEvent.CTRL_MASK | InputEvent.SHIFT_MASK));
             setEnabled(false);
         }
 

src/eva2/gui/editor/FilePathEditor.java

@@ -160,14 +160,14 @@ public class FilePathEditor extends JPanel implements PropertyEditor {
     ActionListener fileChooserAction = new ActionListener() {
         @Override
         public void actionPerformed(ActionEvent event) {
-            if (event.getActionCommand() == "ApproveSelection") {
+            if (event.getActionCommand().equals("ApproveSelection")) {
                 filePath.setCompleteFilePath(fileChooser.getSelectedFile().getAbsolutePath());
                 propertyChangeSupport.firePropertyChange("", filePath, null);
                 Window w = (Window) fileChooser.getTopLevelAncestor();
                 w.dispose();
                 panel = null;
             }
-            if (event.getActionCommand() == "CancelSelection") {
+            if (event.getActionCommand().equals("CancelSelection")) {
                 filePath.setCompleteFilePath(fileChooser.getSelectedFile().getAbsolutePath());
                 propertyChangeSupport.firePropertyChange("", filePath, null);
                 Window w = (Window) fileChooser.getTopLevelAncestor();

src/eva2/gui/editor/GenericObjectEditor.java

@@ -48,8 +48,7 @@ public class GenericObjectEditor implements PropertyEditor {
                     }
                     classes.add(current);
                 } catch (ClassNotFoundException ex) {
-                    LOGGER.log(Level.WARNING,
+                    LOGGER.log(Level.WARNING, String.format("Requesting className: %1$s, Couldn't load: %2$s", className, current), ex);
-                            String.format("Requesting className: %1$s, Couldn't load: %2%s", className, current), ex);
                 }
             }
             return classes;

src/eva2/gui/plot/DPointSetMultiIcon.java

@@ -192,15 +192,7 @@ public class DPointSetMultiIcon extends DComponent {
     }
 
     public int getSize() {
-        int size = Math.min(xMI.getSize(), yMI.getSize());
+        return Math.min(xMI.getSize(), yMI.getSize());
-
-        //    int size = x.getSize();
-        //    if( size != y.getSize() ) throw
-        //      new ArrayStoreException(
-        //        "The number of x-values is not equal to the number of y-values.\n"
-        //        +"The size of the DPointSet isn<73>t clear."
-        //      );
-        return size;
     }
 
     /**

src/eva2/optimization/individuals/AbstractEAIndividual.java

@@ -1162,7 +1162,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
      * Try to convert the individuals position to double[] and return it.
      * Returns null if there is no conversion available.
      *
-     * @param indy
      * @return double valued position of an individual or null
      */
     public double[] getDoublePosition() {

src/eva2/optimization/individuals/EAIndividualComparator.java

@@ -73,7 +73,7 @@ public class EAIndividualComparator implements Comparator<Object>, Serializable
     public boolean equals(Object other) {
         if (other instanceof EAIndividualComparator) {
             EAIndividualComparator o = (EAIndividualComparator) other;
-            if ((indyDataKey == o.indyDataKey) || (indyDataKey != null && (indyDataKey.equals(o.indyDataKey)))) {
+            if ((indyDataKey.equals(o.indyDataKey)) || (indyDataKey != null && (indyDataKey.equals(o.indyDataKey)))) {
                 if ((fitCriterion == o.fitCriterion) && (preferFeasible == o.preferFeasible)) {
                     return true;
                 }

src/eva2/optimization/individuals/IndividualInterface.java

@@ -31,7 +31,7 @@ public interface IndividualInterface {
      * Check whether the instance is dominating the given other individual and return
      * true in this case.
      *
-     * @param other a second individual of the same type
+     * @param fitness other a second individual of the same type
      * @return true if the instance dominates the other individual, else false
      */
     boolean isDominant(double[] fitness);

src/eva2/optimization/individuals/codings/gp/AbstractGPNode.java

@@ -350,9 +350,7 @@ public abstract class AbstractGPNode implements InterfaceProgram, java.io.Serial
             try {
                 node = (AbstractGPNode) c.newInstance();
                 ret = ret + " (" + node.getOpIdentifier() + "," + node.getArity() + ")";
-            } catch (InstantiationException e) {
+            } catch (InstantiationException | IllegalAccessException e) {
-                e.printStackTrace();
-            } catch (IllegalAccessException e) {
                 e.printStackTrace();
             }
         }

src/eva2/optimization/mocco/MOCCOChooseReferenceSolution.java

@@ -100,7 +100,7 @@ public class MOCCOChooseReferenceSolution extends MOCCOPhase implements Interfac
                 gbc.gridx = 2;
                 gbc.gridy = i + 1;
                 gbc.weightx = 1;
-                textA = new JTextField("" + (Double) referenceSolution.getData(obj[i].getIdentName()));
+                textA = new JTextField("" + referenceSolution.getData(obj[i].getIdentName()));
                 textA.setEditable(false);
                 tmpP.add(textA, gbc);
 

src/eva2/optimization/mocco/MOCCOParameterizeGDF.java

@@ -265,7 +265,7 @@ public class MOCCOParameterizeGDF extends MOCCOPhase implements InterfaceProcess
 
         double[] result = new double[tmpA.size()];
         for (int i = 0; i < result.length; i++) {
-            result[i] = ((Double) tmpA.get(i)).doubleValue();
+            result[i] = (Double) tmpA.get(i);
         }
         return result;
     }

src/eva2/optimization/mocco/MOCCOParameterizeSTEP.java

@@ -127,7 +127,7 @@ public class MOCCOParameterizeSTEP extends MOCCOPhase implements InterfaceProces
             }
             gbc.gridx = 2;
             gbc.gridy = i + 1;
-            this.refSolTextField[i] = new JTextField("" + (Double) refSolution.getData(obj[i].getIdentName()));
+            this.refSolTextField[i] = new JTextField("" + refSolution.getData(obj[i].getIdentName()));
             this.refSolTextField[i].setEditable(false);
             panelSTEP.add(this.refSolTextField[i], gbc);
             gbc.gridx = 3;
@@ -336,7 +336,7 @@ public class MOCCOParameterizeSTEP extends MOCCOPhase implements InterfaceProces
 
         double[] result = new double[tmpA.size()];
         for (int i = 0; i < result.length; i++) {
-            result[i] = ((Double) tmpA.get(i)).doubleValue();
+            result[i] = (Double) tmpA.get(i);
         }
         return result;
     }

src/eva2/optimization/modules/Processor.java

@@ -183,13 +183,12 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
                 errMsg = "check console output for error messages.";
             }
             errMsg = "Exception in Processor: " + errMsg;
-            e.printStackTrace();
             LOGGER.log(Level.SEVERE, errMsg, e);
+            e.printStackTrace();
             try {
                 JOptionPane.showMessageDialog(null, StringTools.wrapLine(errMsg, 60, 0.2), "Error in Optimization", JOptionPane.ERROR_MESSAGE);
             } catch (Exception | Error ignored) {
             }
-            //statistics.stopOptimizationPerformed(false);
             setOptimizationRunning(false); // normal finish
             if (optimizationStateListener != null) {
                 optimizationStateListener.performedStop(); // is only needed in client server mode

src/eva2/optimization/operator/archiving/ArchivingPESAII.java

@@ -157,9 +157,9 @@ public class ArchivingPESAII extends AbstractArchiving implements java.io.Serial
                     }
                 }
                 // now i got all the boogies of the same grid element
-                // lets assign them thier squeeze factor
+                // lets assign them their squeeze factor
                 for (int j = 0; j < coll.size(); j++) {
-                    result[((Integer) coll.get(j))] = coll.size();
+                    result[(int) coll.get(j)] = coll.size();
                     tmpIndy = pop.get(((Integer) coll.get(j)).intValue());
                     tmpIndy.putData("SqueezeFactor", coll.size());
                     tmpIndy.putData("GridBox", curGrid);

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

@@ -34,7 +34,7 @@ public class AdaptiveCrossoverEAMixer extends CrossoverEAMixer implements Interf
     /**
      * Create a mutation mixer with equal weights of the given mutation operators.
      *
-     * @param mutators
+     * @param crossovers
      */
     public AdaptiveCrossoverEAMixer(InterfaceCrossover... crossovers) {
         this.crossoverMixer = new PropertyCrossoverMixer(crossovers);

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

@@ -138,7 +138,7 @@ public class CrossoverESUNDX implements InterfaceCrossover, java.io.Serializable
 
         for (int i = 0; i < parents.length; i++) {
             tmpVec = Mathematics.vvSub(parents[i], mean);
-            if (Mathematics.isValidVec(tmpVec)) {
+            if (Mathematics.isValidVector(tmpVec)) {
                 if (result.size() == 0) {
                     result.add(tmpVec);
                 } else {
@@ -149,7 +149,7 @@ public class CrossoverESUNDX implements InterfaceCrossover, java.io.Serializable
                         toro = Mathematics.svMult(tmpD, toro);
                         tmpVec = Mathematics.vvSub(tmpVec, toro);
                     }
-                    if (Mathematics.isValidVec(tmpVec)) {
+                    if (Mathematics.isValidVector(tmpVec)) {
                         result.add(tmpVec);
                     }
                 }
@@ -171,7 +171,7 @@ public class CrossoverESUNDX implements InterfaceCrossover, java.io.Serializable
 
         while (completeList.size() < mean.length) {
             tmpVec = RNG.gaussianVector(mean.length, 1., true);
-            if (Mathematics.isValidVec(tmpVec)) {
+            if (Mathematics.isValidVector(tmpVec)) {
                 // apply the infamous Gram-Schmidt
                 for (int j = 0; j < completeList.size(); j++) {
                     toro = (double[]) completeList.get(j);
@@ -179,7 +179,7 @@ public class CrossoverESUNDX implements InterfaceCrossover, java.io.Serializable
                     toro = Mathematics.svMult(tmpD, toro);
                     tmpVec = Mathematics.vvSub(tmpVec, toro);
                 }
-                if (Mathematics.isValidVec(tmpVec)) {
+                if (Mathematics.isValidVector(tmpVec)) {
                     Mathematics.normVect(tmpVec, tmpVec);
                     tmpVec = Mathematics.svMult(Mathematics.vvMult(theOther, tmpVec), tmpVec);
                     result.add(tmpVec);

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

@@ -67,12 +67,10 @@ public class CrossoverOBGAPMX implements InterfaceCrossover, java.io.Serializabl
 
             ((InterfaceOBGAIndividual) result[0]).setOBGenotype(pperm1);
             ((InterfaceOBGAIndividual) result[1]).setOBGenotype(pperm2);
-            //((InterfaceDataTypePermutation) result[0]).SetPermutationDataLamarckian(pperm1);
-            //((InterfaceDataTypePermutation) result[1]).SetPermutationDataLamarckian(pperm2);
         }
-        //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++) {
+        for (AbstractEAIndividual indy : result) {
-            result[i].getMutationOperator().crossoverOnStrategyParameters(indy1, partners);
+            indy.getMutationOperator().crossoverOnStrategyParameters(indy1, partners);
         }
 
 

src/eva2/optimization/operator/mutation/MutateGIOrdinal.java

@@ -81,7 +81,7 @@ public class MutateGIOrdinal implements InterfaceMutation, java.io.Serializable
                 mutInd = RNG.randomInt(0, x.length - 1);
                 mutate = RNG.gaussianDouble(this.stepSize);
                 // ToDo: WTF?
-                mutate *= (range[mutInd][1] - range[mutInd][1]);
+                mutate *= (0);
                 mut = (int) Math.round(mutate);
                 if (mut == 0) {
                     if (RNG.flipCoin(0.5)) {

src/eva2/optimization/operator/mutation/MutateGITranslocate.java

@@ -103,7 +103,7 @@ public class MutateGITranslocate implements InterfaceMutation, java.io.Serializa
             int[] tmp = new int[x.length];
             int[] without = new int[x.length - length];
             int[] insert = new int[length];
-            System.arraycopy(x, 0 + from, insert, 0, length);
+            System.arraycopy(x, from, insert, 0, length);
             for (int i = 0; i < without.length; i++) {
                 if (i < from) {
                     without[i] = x[i];
@@ -112,7 +112,7 @@ public class MutateGITranslocate implements InterfaceMutation, java.io.Serializa
                 }
             }
             System.arraycopy(without, 0, tmp, 0, to);
-            System.arraycopy(insert, to - to, tmp, to, to + length - to);
+            System.arraycopy(insert, 0, tmp, to, to + length - to);
             System.arraycopy(without, to + length - length, tmp, to + length, x.length - (to + length));
 //    		System.out.println(""+from+"/"+to+"/"+length);
 //    		this.printInt("After  ", tmp);

src/eva2/optimization/statistics/AbstractStatistics.java

@@ -601,9 +601,9 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
                 printedIteration++;
                 meanData = data.get(i - 1);
                 sbuf.append(i);
-                for (int k = 0; k < meanData.length; k++) {
+                for (Double value : meanData) {
                     sbuf.append(delim);
-                    sbuf.append(BeanInspector.toString(meanData[k]));
+                    sbuf.append(BeanInspector.toString(value));
                 }
                 sbuf.append("\n");
             }
@@ -777,7 +777,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
      * @see #getSimpleOutputHeader()
      */
     protected Object[] getSimpleOutputValues() {
-        GraphSelectionEnum[] selEnumVals = null;
+        GraphSelectionEnum[] selEnumVals;
         selEnumVals = GraphSelectionEnum.values();
         Object[] ret = new Object[1 + selEnumVals.length];
         ret[0] = functionCalls;
@@ -1121,8 +1121,8 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
      * Returns true if the given iteration is a verbose one according to StatsParameter - meaning
      * that full iteration data should be plotted.
      *
-     * @param iteration
+     * @param iteration Iteration number
-     * @return
+     * @return true if current iteration is verbose
      */
     private boolean printLineByVerbosity(int iteration) {
         return (statisticsParameter.getOutputVerbosity() == InterfaceStatisticsParameters.OutputVerbosity.ALL)
@@ -1177,8 +1177,8 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
     /**
      * Compare two individual interfaces and return true if the second one is dominant.
      *
-     * @param indy1
+     * @param indy1 First individual
-     * @param indy2
+     * @param indy2 Second individual
      * @return true if the second individual is dominant, else false
      */
     public static boolean secondIsBetter(IndividualInterface indy1, IndividualInterface indy2) {
@@ -1191,7 +1191,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
         if (indy1 instanceof AbstractEAIndividual) {
             return ((AbstractEAIndividual) indy2).isDominatingDebConstraints((AbstractEAIndividual) indy1);
         }
-        return (indy2.isDominant(indy1));
+        return indy2.isDominant(indy1);
     }
 
     @Override

src/eva2/optimization/statistics/StatisticalEvaluation.java

@@ -345,9 +345,7 @@ public class StatisticalEvaluation {
         for (OptimizationJob j : jobList) {
             if (lSoFar == null) {
                 lSoFar = new LinkedList<>();
-                for (String f : j.getFieldHeaders()) {
+                Collections.addAll(lSoFar, j.getFieldHeaders());
-                    lSoFar.add(f);
-                }
             } else {
                 for (String f : lSoFar) {
                     if (j.getFieldIndex(f) >= 0) {

src/eva2/optimization/strategies/NichePSO.java

@@ -29,6 +29,7 @@ import eva2.problems.*;
 import eva2.tools.chart2d.*;
 import eva2.util.annotation.Description;
 import eva2.util.annotation.Hidden;
+import eva2.util.annotation.Parameter;
 
 import java.io.*;
 import java.text.SimpleDateFormat;
@@ -435,7 +436,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
      * Schedule new particles to be added to this swarm, rndly inited over the
      * search space by the problem
      *
-     * @param size            number of particles to be created
      * @param particleIndices set of indices that should be used for the added
      *                        particles, if null new indices are created
      */
@@ -2016,15 +2016,15 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
 
     /**
      * Set parameters as to Brits, Engelbrecht & Bergh: A Niching Particle Swarm
-     * Optimizer. SEAL 2002. Exeption: the swarm size is 100 by default, because
+     * Optimizer. SEAL 2002. Exception: the swarm size is 100 by default, because
      * 30 (of the orig. paper) seems way too low.
      *
-     * @param an       already existing NichePSO instance or null to create a new one
+     * @param npso  an already existing NichePSO instance or null to create a new one
      * @param problem
      * @param randSeed
      * @param evalCnt
      * @return
-     * @see #stdNPSO(AbstractOptimizer, long, int)
+     * @see #stdNPSO(eva2.problems.AbstractOptimizationProblem, long, int)
      */
     public static OptimizationParameters stdNPSO(NichePSO npso, AbstractOptimizationProblem problem, long randSeed, int evalCnt) {
         if (npso == null) {
@@ -2074,7 +2074,7 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
      * @param randSeed
      * @param evalCnt
      * @return
-     * @see #stdNPSO(AbstractOptimizer, long, int)
+     * @see #stdNPSO(eva2.problems.AbstractOptimizationProblem, long, int)
      */
     public static OptimizationParameters starNPSO(NichePSO npso, AbstractOptimizationProblem problem, long randSeed, int evalCnt) {
         starNPSO(npso, evalCnt);
@@ -2087,7 +2087,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
         }
         int popSize = 200;
         npso.setMainSwarmSize(popSize);
-//		double avgRange = Mathematics.getAvgRange(((InterfaceDataTypeDouble)problem.getIndividualTemplate()).getDoubleRange());
 
         // set strategies
         npso.setDeactivationStrategy(new StandardDeactivationStrategy());
@@ -2101,14 +2100,10 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
         npso.getMainSwarm().setAlgoType(ParticleSwarmOptimization.PSOType.Inertness);
         npso.setMainSwarmAlgoType(ParticleSwarmOptimization.PSOType.Inertness);
         npso.getMainSwarm().setPhi1(1.2);
-//		npso.SetMainSwarmPhi2(0); // by default no communication in the mainswarm
         npso.setMainSwarmTopologyTag(0); // this doesnt have any effect due to no communication
         npso.setMainSwarmTopologyRange(0);
         npso.mainSwarmAlgoType = ParticleSwarmOptimization.PSOType.Inertness;
         npso.getMainSwarm().setParameterControl(new ParamAdaption[]{getDefaultInertnessAdaption()});
-//		npso.setMainSwarmInertness(new LinearParameterAging(0.7, 0.2, evalCnt/popSize));
-//		npso.getMainSwarm().setSpeedLimit(avgRange/2.);
-//		npso.getMainSwarm().setCheckSpeedLimit(true);
 
         // parameters for the subswarms
         npso.getSubswarmOptimizerTemplate().setGcpso(true);
@@ -2116,8 +2111,6 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
         npso.getSubswarmOptimizerTemplate().setAlgoType(ParticleSwarmOptimization.PSOType.Constriction);
 
         npso.getSubswarmOptimizerTemplate().setConstriction(2.05, 2.05);
-//		npso.getSubswarmOptimizerTemplate().setInertnessAging(new NoParameterAging(npso.getSubswarmOptimizerTemplate().getInertnessOrChi()));
-//		System.out.println(BeanInspector.niceToString(npso));
         return npso;
     }
 
@@ -2128,13 +2121,15 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
 
     @Override
     public String[] getAdditionalDataInfo() {
-        return new String[]{"Size of the main swarm of explorers",
+        return new String[]{
-                "Number of sub-swarms currently active",
+            "Size of the main swarm of explorers",
-                "Average sub-swarm size",
+            "Number of sub-swarms currently active",
-                "The number of stored potential local optima",
+            "Average sub-swarm size",
-                "The median correlation of stored solutions",
+            "The number of stored potential local optima",
-                "The mean distance of stored solutions",
+            "The median correlation of stored solutions",
-                "Current inertness of the main swarm"};
+            "The mean distance of stored solutions",
+            "Current inertness of the main swarm"
+        };
     }
 
     @Override
@@ -2179,11 +2174,8 @@ public class NichePSO extends AbstractOptimizer implements InterfaceAdditionalPo
         return paramControl.getSingleAdapters();
     }
 
+    @Parameter(description = "You may define dynamic paramter control strategies using the parameter name.")
     public void setParameterControl(ParamAdaption[] paramControl) {
         this.paramControl.setSingleAdapters(paramControl);
     }
-
-    public String parameterControlTipText() {
-        return "You may define dynamic paramter control strategies using the parameter name.";
-    }
 }

src/eva2/optimization/strategies/ParticleSwarmOptimization.java

@@ -942,19 +942,11 @@ public class ParticleSwarmOptimization extends AbstractOptimizer implements java
                             }
                         }
                     }
-                    // this was the binary variant
-//				k = (2*sortedIndex+1);
-//				if (k < pop.size()) {
-//					compareAndSet(localBestFitness, localBestPosition, (AbstractEAIndividual)sortedPop[k], useHistoric);
-//					k++;
-//					if (k < pop.size()) compareAndSet(localBestFitness, localBestPosition, (AbstractEAIndividual)sortedPop[k], useHistoric);
-//				}
                 }
                 break;
             case hpso: // Hierarchical PSO
                 if (index >= 0) {
                     k = getParentIndex(topologyRange, index, pop.size());
-//				compareAndSet(localBestFitness, localBestPosition, (AbstractEAIndividual)pop.get(k), useHistoric);
                     indy = pop.get(k);
                     System.arraycopy(indy.getData(partBestFitKey), 0, localBestFitness, 0, localBestFitness.length);
                     System.arraycopy(indy.getData(partBestPosKey), 0, localBestPosition, 0, localBestPosition.length);
@@ -1488,7 +1480,7 @@ public class ParticleSwarmOptimization extends AbstractOptimizer implements java
                 AbstractEAIndividual indy = pop.getEAIndividual(i);
                 if (indy == null) {
                     System.err.println("Error in PSO.setPopulation!");
-                } else if (!indy.hasData(this.partTypeKey)) {
+                } else if (!indy.hasData(partTypeKey)) {
                     initIndividualDefaults(indy, initialVelocity);
                     initIndividualMemory(indy);
                     indy.putData(indexKey, i);

src/eva2/problems/AbstractDynTransProblem.java

@@ -42,7 +42,7 @@ public abstract class AbstractDynTransProblem extends AbstractSynchronousOptimiz
      * Evaluate the function at the individuals position using an arbitrary translation which may be dynamically changing.
      *
      * @param individual the individual to be evaluated
-     * @param t          timestamp of the evaluation
+     * @param time       timestamp of the evaluation
      */
     @Override
     public void evaluateAt(AbstractEAIndividual individual, double time) {

src/eva2/problems/AbstractMultiModalProblemKnown.java

@@ -284,7 +284,7 @@ public abstract class AbstractMultiModalProblemKnown extends AbstractProblemDoub
      * based on the full list of known optima. Assumes that both realOpts and population have fitness
      * values assigned as in a maximization problem. This is the standard formulation of MPR.
      *
-     * @param mmProb
+     * @param realOpts
      * @param pop
      * @param epsilon
      * @return

src/eva2/problems/AbstractProblemBinary.java

@@ -49,8 +49,8 @@ public abstract class AbstractProblemBinary extends AbstractOptimizationProblem
      * Evaluate a BitSet representing a possible solution. This is the target
      * function implementation.
      *
-     * @param x a BitSet representing a possible
+     * @param bs a BitSet representing a possible solution
-     * @return
+     * @return Fitness
      */
     public abstract double[] evaluate(BitSet bs);
 

src/eva2/problems/B1Problem.java

@@ -44,7 +44,6 @@ public class B1Problem extends AbstractProblemBinary implements java.io.Serializ
      * values of the individual will be set inside this method.
      *
      * @param b The BitSet that is to be evaluated.
-     * @param l The length of the BitSet.
      * @return Double[]
      */
     @Override
@@ -63,7 +62,7 @@ public class B1Problem extends AbstractProblemBinary implements java.io.Serializ
 
     /**
      * This method allows you to output a string that describes a found solution
-     * in a way that is most suiteable for a given problem.
+     * in a way that is most suitable for a given problem.
      *
      * @param individual The individual that is to be shown.
      * @return The description.

src/eva2/problems/BKnapsackProblem.java

@@ -262,7 +262,6 @@ public class BKnapsackProblem extends AbstractProblemBinary implements java.io.S
      * values of the individual will be set inside this method.
      *
      * @param b The BitSet that is to be evaluated.
-     * @param l The length of the BitSet.
      * @return Double[]
      */
     @Override

src/eva2/tools/BasicResourceLoader.java

@@ -529,7 +529,7 @@ public class BasicResourceLoader implements ResourceLoader {
     /**
      * Gets the byte data from a file.
      *
-     * @param fileName Description of the Parameter
+     * @param stream Stream to read from
      * @return the byte array of the file.
      */
     private byte[] getBytesFromStream(InputStream stream) {

src/eva2/tools/MultirunRefiner.java

@@ -288,7 +288,7 @@ public class MultirunRefiner {
      */
     public static String refineToText(ArrayList<double[]> result) {
         double[] mean;
-        StringBuffer sbuf = new StringBuffer("Event\tBest\tMean\tWorst\n");
+        StringBuilder sbuf = new StringBuilder("Event\tBest\tMean\tWorst\n");
 
         for (int i = 0; i < result.size(); i++) {
             mean = result.get(i);

src/eva2/tools/math/BayNet.java

@@ -215,7 +215,7 @@ public final class BayNet {
      * @param j edge to this node
      */
     public void addEdge(Integer i, Integer j) {
-        if (i != j) {
+        if (!i.equals(j)) {
             if (!this.network[i][j]) {
                 this.network[i][j] = true;
                 this.rootNodes.remove(j);
@@ -253,7 +253,8 @@ public final class BayNet {
     /**
      * find the next value where all the parents are already set
      *
-     * @param data
+     * @param probabilities
+     * @param nodes
      * @return
      */
     private int findNext(double[] probabilities, List<BayNode> nodes) {
@@ -358,7 +359,6 @@ public final class BayNet {
      * calculate the next probability
      *
      * @param data          the already calculated data
-     * @param probabilities the already calculated probabilities
      * @param toCalculate   the Nodes that have yet to be calculated
      * @param next          the node for which to calculate the probability
      * @return the new probabilities array
@@ -463,10 +463,9 @@ public final class BayNet {
     /**
      * check if the given Network is acyclic
      *
-     * @param net the Network
+     * @return true if the net is acyclic
-     * @return is the net acyclic
      */
-    public boolean isACyclic() {
+    public boolean isAcyclic() {
         List<Pair<Integer, Integer>> deletedEdges = new LinkedList<>();
         List<BayNode> nodes = getRootNodes();
         boolean res = false;

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

@@ -37,16 +37,16 @@ public class CholeskyDecomposition implements java.io.Serializable {
     /**
      * Cholesky algorithm for symmetric and positive definite matrix.
      *
-     * @param A Square, symmetric matrix.
+     * @param arg A square, symmetric matrix.
      * @return Structure to access L and isspd flag.
      */
 
-    public CholeskyDecomposition(Matrix Arg) {
+    public CholeskyDecomposition(Matrix matrix) {
         // Initialize.
-        double[][] A = Arg.getArray();
+        double[][] A = matrix.getArray();
-        n = Arg.getRowDimension();
+        n = matrix.getRowDimension();
         L = new double[n][n];
-        isspd = (Arg.getColumnDimension() == n);
+        isspd = (matrix.getColumnDimension() == n);
         // Main loop.
         for (int j = 0; j < n; j++) {
             double[] Lrowj = L[j];

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

@@ -274,7 +274,6 @@ public class Matrix implements Cloneable, Serializable {
     /**
      * Return the diagonal array for a matrix.
      *
-     * @param M
      * @return
      */
     public double[] diag() {
@@ -290,7 +289,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return Two-dimensional array copy of matrix elements.
      */
-
     public double[][] getArrayCopy() {
         double[][] C = new double[m][n];
         for (int i = 0; i < m; i++) {
@@ -304,7 +302,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return Matrix elements packed in a one-dimensional array by columns.
      */
-
     public double[] getColumnPackedCopy() {
         double[] vals = new double[m * n];
         for (int i = 0; i < m; i++) {
@@ -337,11 +334,10 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return Matrix elements packed in a one-dimensional array by rows.
      */
-
     public double[] getRowPackedCopy() {
         double[] vals = new double[m * n];
         for (int i = 0; i < m; i++) {
-            System.arraycopy(A[i], 0, vals, i * n + 0, n);
+            System.arraycopy(A[i], 0, vals, i * n, n);
         }
         return vals;
     }
@@ -351,7 +347,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return m, the number of rows.
      */
-
     public int getRowDimension() {
         return m;
     }
@@ -361,7 +356,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return n, the number of columns.
      */
-
     public int getColumnDimension() {
         return n;
     }
@@ -374,7 +368,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return A(i, j)
      * @throws ArrayIndexOutOfBoundsException
      */
-
     public double get(int i, int j) {
         return A[i][j];
     }
@@ -394,7 +387,7 @@ public class Matrix implements Cloneable, Serializable {
         double[][] B = X.getArray();
         try {
             for (int i = i0; i <= i1; i++) {
-                System.arraycopy(A[i], j0, B[i - i0], j0 - j0, j1 + 1 - j0);
+                System.arraycopy(A[i], j0, B[i - i0], 0, j1 + 1 - j0);
             }
         } catch (ArrayIndexOutOfBoundsException e) {
             throw new ArrayIndexOutOfBoundsException("Submatrix indices");
@@ -410,7 +403,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return A(r(:), c(:))
      * @throws ArrayIndexOutOfBoundsException Submatrix indices
      */
-
     public Matrix getMatrix(int[] r, int[] c) {
         Matrix X = new Matrix(r.length, c.length);
         double[][] B = X.getArray();
@@ -455,8 +447,8 @@ public class Matrix implements Cloneable, Serializable {
      * Get a submatrix.
      *
      * @param r  Array of row indices.
-     * @param i0 Initial column index
+     * @param j0 Initial column index
-     * @param i1 Final column index
+     * @param j1 Final column index
      * @return A(r(:), j0:j1)
      * @throws ArrayIndexOutOfBoundsException Submatrix indices
      */
@@ -466,7 +458,7 @@ public class Matrix implements Cloneable, Serializable {
         double[][] B = X.getArray();
         try {
             for (int i = 0; i < r.length; i++) {
-                System.arraycopy(A[r[i]], j0, B[i], j0 - j0, j1 + 1 - j0);
+                System.arraycopy(A[r[i]], j0, B[i], 0, j1 + 1 - j0);
             }
         } catch (ArrayIndexOutOfBoundsException e) {
             throw new ArrayIndexOutOfBoundsException("Submatrix indices");
@@ -802,7 +794,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B another matrix
      * @return A.*B
      */
-
     public Matrix arrayTimes(Matrix B) {
         checkMatrixDimensions(B);
         Matrix X = new Matrix(m, n);
@@ -821,7 +812,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B another matrix
      * @return A.*B
      */
-
     public Matrix arrayTimesEquals(Matrix B) {
         checkMatrixDimensions(B);
         for (int i = 0; i < m; i++) {
@@ -838,7 +828,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B another matrix
      * @return A./B
      */
-
     public Matrix arrayRightDivide(Matrix B) {
         checkMatrixDimensions(B);
         Matrix X = new Matrix(m, n);
@@ -857,7 +846,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B another matrix
      * @return A./B
      */
-
     public Matrix arrayRightDivideEquals(Matrix B) {
         checkMatrixDimensions(B);
         for (int i = 0; i < m; i++) {
@@ -874,7 +862,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B another matrix
      * @return A.\B
      */
-
     public Matrix arrayLeftDivide(Matrix B) {
         checkMatrixDimensions(B);
         Matrix X = new Matrix(m, n);
@@ -893,7 +880,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B another matrix
      * @return A.\B
      */
-
     public Matrix arrayLeftDivideEquals(Matrix B) {
         checkMatrixDimensions(B);
         for (int i = 0; i < m; i++) {
@@ -910,7 +896,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param s scalar
      * @return s*A
      */
-
     public Matrix times(double s) {
         Matrix X = new Matrix(m, n);
         double[][] C = X.getArray();
@@ -983,7 +968,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param s scalar
      * @return replace A by s*A
      */
-
     public Matrix timesEquals(double s) {
         for (int i = 0; i < m; i++) {
             for (int j = 0; j < n; j++) {
@@ -1000,7 +984,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return Matrix product, A * B
      * @throws IllegalArgumentException Matrix inner dimensions must agree.
      */
-
     public Matrix times(Matrix B) {
         if (B.m != n) {
             throw new IllegalArgumentException("Matrix inner dimensions must agree.");
@@ -1048,7 +1031,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return LUDecomposition
      * @see LUDecomposition
      */
-
     public LUDecomposition lu() {
         return new LUDecomposition(this);
     }
@@ -1059,7 +1041,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return QRDecomposition
      * @see QRDecomposition
      */
-
     public QRDecomposition qr() {
         return new QRDecomposition(this);
     }
@@ -1070,7 +1051,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return CholeskyDecomposition
      * @see CholeskyDecomposition
      */
-
     public CholeskyDecomposition chol() {
         return new CholeskyDecomposition(this);
     }
@@ -1081,7 +1061,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return SingularValueDecomposition
      * @see SingularValueDecomposition
      */
-
     public SingularValueDecomposition svd() {
         return new SingularValueDecomposition(this);
     }
@@ -1092,7 +1071,6 @@ public class Matrix implements Cloneable, Serializable {
      * @return EigenvalueDecomposition
      * @see EigenvalueDecomposition
      */
-
     public EigenvalueDecomposition eig() {
         return new EigenvalueDecomposition(this);
     }
@@ -1103,7 +1081,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B right hand side
      * @return solution if A is square, least squares solution otherwise
      */
-
     public Matrix solve(Matrix B) {
         //System.out.print("m="+m+"n"+n);
         return (m == n ? (new LUDecomposition(this)).solve(B) :
@@ -1116,7 +1093,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param B right hand side
      * @return solution if A is square, least squares solution otherwise.
      */
-
     public Matrix solveTranspose(Matrix B) {
         return transpose().solve(B.transpose());
     }
@@ -1126,7 +1102,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return inverse(A) if A is square, pseudoinverse otherwise.
      */
-
     public Matrix inverse() {
         return solve(identity(m, m));
     }
@@ -1136,7 +1111,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return determinant
      */
-
     public double det() {
         return new LUDecomposition(this).det();
     }
@@ -1146,7 +1120,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return effective numerical rank, obtained from SVD.
      */
-
     public int rank() {
         return new SingularValueDecomposition(this).rank();
     }
@@ -1156,7 +1129,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return ratio of largest to smallest singular value.
      */
-
     public double cond() {
         return new SingularValueDecomposition(this).cond();
     }
@@ -1166,7 +1138,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @return sum of the diagonal elements.
      */
-
     public double trace() {
         double t = 0;
         for (int i = 0; i < Math.min(m, n); i++) {
@@ -1182,7 +1153,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param n Number of colums.
      * @return An m-by-n matrix with uniformly distributed random elements.
      */
-
     public static Matrix random(int m, int n) {
         Matrix A = new Matrix(m, n);
         double[][] X = A.getArray();
@@ -1201,7 +1171,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param n Number of colums.
      * @return An m-by-n matrix with ones on the diagonal and zeros elsewhere.
      */
-
     public static Matrix identity(int m, int n) {
         Matrix A = new Matrix(m, n);
         double[][] X = A.getArray();
@@ -1242,7 +1211,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param w Column width.
      * @param d Number of digits after the decimal.
      */
-
     public void print(int w, int d) {
         print(new PrintWriter(System.out, true), w, d);
     }
@@ -1255,7 +1223,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param w      Column width.
      * @param d      Number of digits after the decimal.
      */
-
     public void print(PrintWriter output, int w, int d) {
         DecimalFormat format = new DecimalFormat();
         format.setDecimalFormatSymbols(new DecimalFormatSymbols(Locale.US));
@@ -1277,7 +1244,6 @@ public class Matrix implements Cloneable, Serializable {
      * @param width  Field width for each column.
      * @see java.text.DecimalFormat#setDecimalFormatSymbols
      */
-
     public void print(NumberFormat format, int width) {
         print(new PrintWriter(System.out, true), format, width);
     }
@@ -1325,7 +1291,6 @@ public class Matrix implements Cloneable, Serializable {
      *
      * @param input the input stream.
      */
-
     public static Matrix read(BufferedReader input) throws java.io.IOException {
         StreamTokenizer tokenizer = new StreamTokenizer(input);
 
@@ -1382,7 +1347,6 @@ public class Matrix implements Cloneable, Serializable {
     /**
      * Check if size(A) == size(B) *
      */
-
     private void checkMatrixDimensions(Matrix B) {
         if (B.m != m || B.n != n) {
             System.out.println("B.m" + B.m);
@@ -1397,7 +1361,7 @@ public class Matrix implements Cloneable, Serializable {
      * Subtract a line from the indicated line of this matrix in place.
      *
      * @param rowIndex
-     * @param B
+     * @param v
      */
     public void rowSubtract(int rowIndex, double[] v) {
         if ((v.length != n) || (rowIndex < 0) || (rowIndex >= m)) {

src/eva2/tools/math/Mathematics.java

@@ -454,7 +454,7 @@ public final class Mathematics {
      */
     public static boolean isValidVec(double[][] d) {
         for (int i = 0; i < d.length; i++) {
-            if (!isValidVec(d[i])) {
+            if (!isValidVector(d[i])) {
                 return false;
             }
         }
@@ -468,7 +468,7 @@ public final class Mathematics {
      * @param d
      * @return
      */
-    public static boolean isValidVec(double[] d) {
+    public static boolean isValidVector(double[] d) {
         double sum = 0;
         for (int i = 0; i < d.length; i++) {
             if (Double.isNaN(d[i])) {
@@ -479,7 +479,7 @@ public final class Mathematics {
         if (Double.isNaN(sum)) {
             return false;
         }
-        return Math.abs(sum) >= 0.000000000000000001;
+        return Math.abs(sum) >= 10E-18;
     }
 
     /**

src/eva2/tools/math/interpolation/AbstractDataSet.java

@@ -58,7 +58,7 @@ public abstract class AbstractDataSet {
     /**
      * Modifies the X data.
      *
-     * @param the data modifier
+     * @param modifier the data modifier
      */
     public void modifyXData(AbstractDataModifier modifier) {
         modifier.modifyX(xDoubleData);
@@ -67,7 +67,7 @@ public abstract class AbstractDataSet {
     /**
      * Modifies the Y data.
      *
-     * @param the data modifier
+     * @param modifier the data modifier
      */
     public void modifyYData(AbstractDataModifier modifier) {
         modifier.modifyY(yDoubleData);
@@ -76,7 +76,7 @@ public abstract class AbstractDataSet {
     /**
      * Modifies the data.
      *
-     * @param the data modifier
+     * @param modifier the data modifier
      */
     public void modifyData(AbstractDataModifier modifier) {
         modifier.modify(xDoubleData, yDoubleData);