More general cleanup.

refs #2

src/eva2/optimization/individuals/AbstractEAIndividual.java

@@ -185,9 +185,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
                 return false;
             }
 
-            // Age will not be used
-            //if (this.age != indy.age) return false;
-
             // checking on mutation/crossover probabilities
             if (this.mutationProbability != indy.mutationProbability) {
                 return false;
@@ -203,7 +200,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
             if (!this.crossoverOperator.equals(indy.crossoverOperator)) {
                 return false;
             }
-//            System.err.println("Check whether this is semantically meant by equality!!! (AbstractEAIndividual.equals())");
             return true;
         } else {
             return false;
@@ -235,10 +231,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
         return "AbstractEAIndividual";
     }
 
-//    public String getIndividualName() {
-//        return this.name;
-//    }
-
     /**
      * This method is used when a new offspring is created the increment the
      * name.
@@ -276,28 +268,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
      */
     public abstract boolean equalGenotypes(AbstractEAIndividual individual);
 
-//    /** Every object should have it's equals method, but who to programm it.
-//     * Currently i will limit myself to check the class and the fitness
-//     * values.
-//     * @param obj
-//     * @return True if the objects are equal.
-//     */
-//    public boolean equals(Object obj) {
-//        if (obj instanceof AbstractEAIndividual) {
-//            AbstractEAIndividual indy = (AbstractEAIndividual)obj;
-//            if (this.fitness.length != indy.fitness.length) return false;
-////            for (int i = 0; i < this.fitness.length; i++) if (this.fitness[i] != indy.fitness[i]) return false;
-////            for (int i = 0; i < this.fitness.length; i++)
-////                if (new Double(this.fitness[i]).compareTo(new Double(indy.fitness[i])) != 0) return false;
-//            for (int i = 0; i < this.fitness.length; i++) {
-//                if (Math.abs(this.fitness[i]- indy.fitness[i]) > 0.00000001) return false;
-//            }
-//            return true;
-//        } else {
-//            return false;
-//        }
-//    }
-
     /**
      * This method will allow a default initialisation of the individual
      *
@@ -305,7 +275,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
      */
     public void init(InterfaceOptimizationProblem opt) {
         initializationOperator.initialize(this, opt);
-//        this.defaultInit(opt);
         this.mutationOperator.init(this, opt);
         this.crossoverOperator.init(this, opt);
     }
@@ -411,7 +380,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
             sb.append("[ ");
             for (int i = 0; i < parentTree.length; i++) {
                 sb.append(parentTree[i].getHeritageTree(depth - 1));
-//					if ((i+1) < parentTree.length) sb.append(", ");
             }
             sb.append("] ");
         }
@@ -779,7 +747,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
         } else {
             return (constrViolComp > 0);
         }
-//        return isDominatingFitnessNotEqual(getFitness(), indy.getFitness());
     }
 
     /**
@@ -1087,8 +1054,6 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
         } else if (individual instanceof InterfaceDataTypeDouble) {
             double[] d = ((InterfaceDataTypeDouble) individual).getDoubleData();
             for (int i = 0; i < d.length; i++) {
-//                sb.append(d[i]);
-//                if ((i+1) < d.length) sb.append(separator);
                 fm.format("% .3f", d[i]);
                 if ((i + 1) < d.length) {
                     sb.append(separator);

src/eva2/optimization/individuals/InterfaceDataTypeDouble.java

@@ -4,11 +4,6 @@ package eva2.optimization.individuals;
  * This interface gives access to a double phenotype and except
  * for problemspecific operators should only be used by the
  * optimization problem.
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 24.03.2003
- * Time: 10:57:39
- * To change this template use Options | File Templates.
  */
 public interface InterfaceDataTypeDouble {
 

src/eva2/optimization/individuals/OBGAIndividualPermutationData.java

@@ -90,10 +90,6 @@ public class OBGAIndividualPermutationData extends AbstractEAIndividual implemen
         }
     }
 
-    /************************************************************************************
-     * AbstractEAIndividual methods
-     */
-
     /**
      * This method will initialize the individual with a given value for the
      * phenotype.
@@ -203,11 +199,11 @@ public class OBGAIndividualPermutationData extends AbstractEAIndividual implemen
             perm[p] = new int[this.genotype[p].length];
             ArrayList pot = new ArrayList();
             for (int i = 0; i < this.sizePermutation()[p]; i++) {
-                pot.add(new Integer(firstindex[p] + i));
+                pot.add(firstindex[p] + i);
             }
             int i = 0;
             while (!pot.isEmpty()) {
-                perm[p][i] = ((Integer) (pot.remove(RNG.randomInt(0, pot.size() - 1)))).intValue();
+                perm[p][i] = (Integer) (pot.remove(RNG.randomInt(0, pot.size() - 1)));
                 i++;
             }
         }

src/eva2/optimization/strategies/DifferentialEvolution.java

@@ -296,10 +296,11 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
     /**
      * This method will generate one new individual from the given population
      *
-     * @param pop The current population
+     * @param population    The current population
+     * @param parentIndex
      * @return AbstractEAIndividual
      */
-    public AbstractEAIndividual generateNewIndividual(Population pop, int parentIndex) {
+    public AbstractEAIndividual generateNewIndividual(Population population, int parentIndex) {
         AbstractEAIndividual indy;
         InterfaceDataTypeDouble esIndy;
 
@@ -309,11 +310,11 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
             parents = null;
         }
         try {
-            // select one random indy as starting individual. its a parent in any case.
+            // select one random indy as starting individual. It's a parent in any case.
             if (parentIndex < 0) {
-                parentIndex = RNG.randomInt(0, pop.size() - 1);
+                parentIndex = RNG.randomInt(0, population.size() - 1);
             }
-            indy = (AbstractEAIndividual) (pop.getEAIndividual(parentIndex)).getClone();
+            indy = (AbstractEAIndividual) (population.getEAIndividual(parentIndex)).getClone();
             esIndy = (InterfaceDataTypeDouble) indy;
         } catch (java.lang.ClassCastException e) {
             throw new RuntimeException("Differential Evolution currently requires InterfaceESIndividual as basic data type!");
@@ -325,9 +326,9 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
         switch (this.DEType) {
             case DE1_Rand_1: {
                 // this is DE1 or DE/rand/1
-                double[] delta = this.fetchDeltaRandom(pop);
+                double[] delta = this.fetchDeltaRandom(population);
                 if (parents != null) {
-                    parents.add(pop.getEAIndividual(parentIndex));
+                    parents.add(population.getEAIndividual(parentIndex));
                 }  // Add wherever oX is used directly
                 for (int i = 0; i < oX.length; i++) {
                     vX[i] = oX[i] + this.getCurrentF() * delta[i];
@@ -336,10 +337,10 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
             }
             case DE_CurrentToRand: {
                 // this is DE/current-to-rand/1
-                double[] rndDelta = this.fetchDeltaRandom(pop);
+                double[] rndDelta = this.fetchDeltaRandom(population);
-                double[] bestDelta = this.fetchDeltaCurrentRandom(pop, esIndy);
+                double[] bestDelta = this.fetchDeltaCurrentRandom(population, esIndy);
                 if (parents != null) {
-                    parents.add(pop.getEAIndividual(parentIndex));
+                    parents.add(population.getEAIndividual(parentIndex));
                 }  // Add wherever oX is used directly
                 for (int i = 0; i < oX.length; i++) {
                     vX[i] = oX[i] + this.getCurrentLambda() * bestDelta[i] + this.getCurrentF() * rndDelta[i];
@@ -348,10 +349,10 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
             }
             case DE2_CurrentToBest: {
                 // this is DE2 or DE/current-to-best/1
-                double[] rndDelta = this.fetchDeltaRandom(pop);
+                double[] rndDelta = this.fetchDeltaRandom(population);
-                double[] bestDelta = this.fetchDeltaBest(pop, esIndy);
+                double[] bestDelta = this.fetchDeltaBest(population, esIndy);
                 if (parents != null) {
-                    parents.add(pop.getEAIndividual(parentIndex));
+                    parents.add(population.getEAIndividual(parentIndex));
                 }  // Add wherever oX is used directly
                 for (int i = 0; i < oX.length; i++) {
                     vX[i] = oX[i] + this.getCurrentLambda() * bestDelta[i] + this.getCurrentF() * rndDelta[i];
@@ -360,12 +361,12 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
             }
             case DE_Best_1: {
                 // DE/best/1
-                AbstractEAIndividual bestIndy = getBestIndy(pop);
+                AbstractEAIndividual bestIndy = getBestIndy(population);
                 oX = getGenotype(bestIndy);
                 if (parents != null) {
                     parents.add(bestIndy);
                 }  // Add best instead of preselected
-                double[] delta1 = this.fetchDeltaRandom(pop);
+                double[] delta1 = this.fetchDeltaRandom(population);
                 for (int i = 0; i < oX.length; i++) {
                     vX[i] = oX[i] + this.getCurrentF() * delta1[i];
                 }
@@ -373,13 +374,13 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
             }
             case DE_Best_2: {
                 // DE/best/2
-                AbstractEAIndividual bestIndy = getBestIndy(pop);
+                AbstractEAIndividual bestIndy = getBestIndy(population);
                 oX = getGenotype(bestIndy);
                 if (parents != null) {
                     parents.add(bestIndy);
                 }  // Add best instead of preselected
-                double[] delta1 = this.fetchDeltaRandom(pop);
+                double[] delta1 = this.fetchDeltaRandom(population);
-                double[] delta2 = this.fetchDeltaRandom(pop);
+                double[] delta2 = this.fetchDeltaRandom(population);
                 for (int i = 0; i < oX.length; i++) {
                     vX[i] = oX[i] + this.getCurrentF() * delta1[i] + this.getCurrentF() * delta2[i];
                 }
@@ -388,7 +389,7 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
             case TrigonometricDE: {
                 // this is trigonometric mutation
                 if (parents != null) {
-                    parents.add(pop.getEAIndividual(parentIndex));
+                    parents.add(population.getEAIndividual(parentIndex));
                 }  // Add wherever oX is used directly
                 if (RNG.flipCoin(this.mt)) {
                     double[] xk, xl;
@@ -396,8 +397,8 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
                     InterfaceDataTypeDouble indy1 = null, indy2 = null;
                     try {
                         // and i got indy!
-                        indy1 = (InterfaceDataTypeDouble) pop.get(RNG.randomInt(0, pop.size() - 1));
+                        indy1 = (InterfaceDataTypeDouble) population.get(RNG.randomInt(0, population.size() - 1));
-                        indy2 = (InterfaceDataTypeDouble) pop.get(RNG.randomInt(0, pop.size() - 1));
+                        indy2 = (InterfaceDataTypeDouble) population.get(RNG.randomInt(0, population.size() - 1));
                         if (parents != null) {
                             parents.add((AbstractEAIndividual) indy1);
                             parents.add((AbstractEAIndividual) indy2);
@@ -416,9 +417,9 @@ public class DifferentialEvolution implements InterfaceOptimizer, java.io.Serial
                     }
                 } else {
                     // this is DE1
-                    double[] delta = this.fetchDeltaRandom(pop);
+                    double[] delta = this.fetchDeltaRandom(population);
                     if (parents != null) {
-                        parents.add(pop.getEAIndividual(parentIndex));
+                        parents.add(population.getEAIndividual(parentIndex));
                     }  // Add wherever oX is used directly
                     for (int i = 0; i < oX.length; i++) {
                         vX[i] = oX[i] + this.getCurrentF() * delta[i];

src/eva2/problems/AbstractDynTransProblem.java

@@ -61,7 +61,6 @@ public abstract class AbstractDynTransProblem extends AbstractSynchronousOptimiz
         double delta = transLength(getCurrentProblemTime());
         if (isExtraPlot()) {
             if (myplot != null) {
-                //	myplot.addGraph(0, 1);
                 myplot.jump();
             } else {
                 double[] tmpD = new double[2];
@@ -71,7 +70,6 @@ public abstract class AbstractDynTransProblem extends AbstractSynchronousOptimiz
                 this.myplot = new Plot("population measures", "x1", "x2", tmpD, tmpD);
             }
             myplot.setConnectedPoint(population.getFunctionCalls(), delta, 0);
-            //myplot.setUnconnectedPoint(population.getFunctionCalls(), population.getPopulationMeasures()[2], 2);
         } else {
             myplot = null;
         }
@@ -142,10 +140,6 @@ public abstract class AbstractDynTransProblem extends AbstractSynchronousOptimiz
         return problemDimension;
     }
 
-    /**
-     * ***************************************************************************
-     * These are for the GUI
-     */
     @Override
     public String getStringRepresentationForProblem(InterfaceOptimizer opt) {
         return "DynTransProblem";

src/eva2/problems/AbstractDynamicOptimizationProblem.java

@@ -52,11 +52,9 @@ public abstract class AbstractDynamicOptimizationProblem extends AbstractOptimiz
      * A constructor.
      */
     public AbstractDynamicOptimizationProblem() {
-        //System.out.println("AbstractDynamicOptimizationProblem()");
         bExtraPlot = false;
         myplot = null;
         idealInd = null;
-//		initialize(0, 1., 0.1);
     }
 
     /**
@@ -103,7 +101,6 @@ public abstract class AbstractDynamicOptimizationProblem extends AbstractOptimiz
      */
     @Override
     public void initializePopulation(Population population) {
-        //initializeProblem();	// this shouldnt be necessary
         this.initPopulationAt(population, getCurrentProblemTime());
     }
 
@@ -225,7 +222,6 @@ public abstract class AbstractDynamicOptimizationProblem extends AbstractOptimiz
      */
     public abstract AbstractEAIndividual getCurrentOptimum();
 
-    /******************** The most important methods ****************************************/
 
     /**
      * This method evaluates a single individual and sets the fitness value at default time stamp 0.
@@ -279,9 +275,6 @@ public abstract class AbstractDynamicOptimizationProblem extends AbstractOptimiz
         evaluateAt(individual, getCurrentProblemTime());
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * Override population evaluation to do some data output.
      *
@@ -289,26 +282,10 @@ public abstract class AbstractDynamicOptimizationProblem extends AbstractOptimiz
      */
     @Override
     public void evaluatePopulationEnd(Population population) {
-        //System.out.println(">> mean distance at " + population.getFunctionCalls() + " / " + getProblemTime() + " is " + population.getMeanDistance());
-        //System.out.println("> current best is " + population.getBestFitness()[0]);
-        //double[] meanMinMax = population.getPopulationMeasures();
-
-        //myplot.setConnectedPoint(population.getFunctionCalls(), population.getPopulationMeasures()[0], 0);
-
         AbstractEAIndividual popBest = (AbstractEAIndividual) (population.getBestIndividual());
         if (idealInd == null) {
             idealInd = (AbstractEAIndividual) popBest.clone();
         }
-
-//		getCurrentOptimum((InterfaceDataTypeDouble)idealInd);
-
-//		double d = new PhenotypeMetric().distance(popBest, idealInd);
-//		double d = distanceBetween(popBest, idealInd);
-
-        //System.out.println("tracking dist is " + d);
-
-        //if (myplot!=null) myplot.setConnectedPoint(population.getFunctionCalls(), d, 0);
-        //myplot.setUnconnectedPoint(population.getFunctionCalls(), population.getPopulationMeasures()[2], 2);
     }
 
     protected void setExtraPlot(boolean doPlot) {

src/eva2/problems/AbstractMultiModalProblemKnown.java

@@ -377,7 +377,7 @@ public abstract class AbstractMultiModalProblemKnown extends AbstractProblemDoub
      */
     @Override
     public void setDefaultAccuracy(double epsilon) {
-        super.SetDefaultAccuracy(epsilon);
+        super.setDefaultAccuracy(epsilon);
     }
 
     @Override

src/eva2/problems/AbstractMultiObjectiveOptimizationProblem.java

@@ -65,16 +65,9 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
             if (border == null) {
                 prob.border = new double[fitness.length][2];
             } else if (fitness.length != prob.border.length) {
-                //System.out.println("AbstractMOOptimizationProblem: Warning fitness.length("+fitness.length+") doesn't fit border.length("+this.border.length+")");
-                //System.out.println("Resetting the border!");
                 prob.border = new double[fitness.length][2];
             }
             for (int j = 0; j < fitness.length; j++) {
-//	                if ((this.border[j][0] > fitness[j]) || (this.border[j][1] < fitness[j])) {
-//	                    System.out.println("border... " + j);
-//	                    System.out.println(this.border[j][0]+" > "+fitness[j]);
-//	                    System.out.println(this.border[j][1]+" < "+fitness[j]);
-//	                }
                 prob.border[j][0] = Math.min(prob.border[j][0], fitness[j]);
                 prob.border[j][1] = Math.max(prob.border[j][1], fitness[j]);
             }
@@ -192,11 +185,9 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
         for (int i = 0; i < pop.size(); i++) {
             tmpFitLen = ((AbstractEAIndividual) pop.get(i)).getFitness().length;
             if (tmpFitLen <= 1) {
-                //System.out.println("There is a single objective individual in the population!");
                 return false;
             }
             if (tmpFitLen != bestFitLen) {
-                //System.out.println("Not all individual have equal length fitness!");
                 return false;
             }
         }
@@ -232,16 +223,9 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
             if (border == null) {
                 this.border = new double[fitness.length][2];
             } else if (fitness.length != this.border.length) {
-                //System.out.println("AbstractMOOptimizationProblem: Warning fitness.length("+fitness.length+") doesn't fit border.length("+this.border.length+")");
-                //System.out.println("Resetting the border!");
                 this.border = new double[fitness.length][2];
             }
             for (int j = 0; j < fitness.length; j++) {
-//                if ((this.border[j][0] > fitness[j]) || (this.border[j][1] < fitness[j])) {
-//                    System.out.println("border... " + j);
-//                    System.out.println(this.border[j][0]+" > "+fitness[j]);
-//                    System.out.println(this.border[j][1]+" < "+fitness[j]);
-//                }
                 this.border[j][0] = Math.min(this.border[j][0], fitness[j]);
                 this.border[j][1] = Math.max(this.border[j][1], fitness[j]);
             }
@@ -330,7 +314,6 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
      */
     public static void drawProblem(Population pFront, Population archive, Plot plot) {
         ArchivingAllDominating tmpArch = new ArchivingAllDominating();
-//  	Population              tmpPop = null;
 
         // i want to plot the pareto front for MOEA and other strategies
         // but i have to differentiate between the case where
@@ -377,7 +360,6 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
         Population tmpPop = null;
 
         if (p.getGeneration() > 2) {
-//            plot = new eva2.gui.plot.Plot("Multiobjective Optimization", "Y1", "Y2");
             // i want to plot the pareto front for MOEA and other strategies
             // but i have to differentiate between the case where
             // there is a true MOEA at work and where the
@@ -519,13 +501,13 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
     @Override
     public Double getDoublePlotValue(Population pop) {
         if (AbstractMultiObjectiveOptimizationProblem.isPopulationMultiObjective(pop)) {
-            return new Double(this.calculateMetric(pop));
+            return this.calculateMetric(pop);
         } else {
             // in this case the local Pareto-Front could be multi-objective
             if (AbstractMultiObjectiveOptimizationProblem.isPopulationMultiObjective(this.paretoFront)) {
-                return new Double(this.calculateMetric(this.paretoFront));
+                return this.calculateMetric(this.paretoFront);
             } else {
-                return new Double(pop.getBestEAIndividual().getFitness(0));
+                return pop.getBestEAIndividual().getFitness(0);
             }
         }
     }
@@ -558,10 +540,6 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
         return ToolBox.appendArrays(result, super.getAdditionalDataValue(pop));
     }
 
-    /*
-     * (non-Javadoc)
-     * @see eva2.problems.AbstractOptimizationProblem#getAdditionalDataInfo(eva2.optimization.PopulationInterface)
-     */
     @Override
     public String[] getAdditionalDataInfo() {
         String[] superInfo = super.getAdditionalDataInfo();
@@ -569,10 +547,6 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
                 "Pareto metric on the collected pareto front"}, superInfo);
     }
 
-    /*
-     * (non-Javadoc)
-     * @see eva2.problems.InterfaceOptimizationProblem#getStringRepresentationForProblem(eva2.optimization.strategies.InterfaceOptimizer)
-     */
     @Override
     public String getStringRepresentationForProblem(InterfaceOptimizer opt) {
         // TODO Auto-generated method stub
@@ -608,32 +582,6 @@ public abstract class AbstractMultiObjectiveOptimizationProblem extends Abstract
         return this.outputDimension;
     }
 
-//    /** This method will calculate the s-Metric if an archive population is present.
-//     * @param population       The population.
-//     * @return s-metric
-//     */
-//    public double tcalculateSMetric(Population population) {
-//        double result = 0;
-//
-//        ((SMetric)this.distanceMetric).setObjectiveSpaceRange(this.border);
-//        result = this.distanceMetric.calculateMetricOn(population);
-//
-//        return result;
-//    }
-//
-//    /** This method will calculate the s-Metric if an archive population is present.
-//     * @param population       The population.
-//     * @return s-metric
-//     */
-//    public double calculateRelativeSMetric(Population population, double[][] ref) {
-//        double result = 0;
-//        SMetricWithReference tmpMetric = new SMetricWithReference();
-//        tmpMetric.setObjectiveSpaceRange(this.border);
-//        tmpMetric.setReferenceFront(ref);
-//        result = tmpMetric.calculateMetricOn(population);
-//        return result;
-//    }
-
     /**
      * This method allows you to set a Multiobjective to
      * Singleobjective converter if you choose to.

src/eva2/problems/AbstractOptimizationProblem.java

@@ -71,7 +71,6 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
     private int parallelthreads = 1;
 
     protected AbstractEAIndividual template = null;
-//    private transient ArrayList<ParamChangeListener> changeListeners = null;
 
     private double defaultAccuracy = 0.001; // default accuracy for identifying optima.
 
@@ -102,8 +101,6 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
     @Override
     public abstract void initializeProblem();
 
-    /******************** The most important methods ****************************************/
-
     /**
      * This method inits a given population
      *
@@ -205,8 +202,6 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
         population.init();
     }
 
-    /******************** Some output methods *******************************************/
-
     /**
      * This method allows you to output a string that describes a found solution
      * in a way that is most suitable for a given problem.
@@ -430,15 +425,12 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
      * @param clusterSigma      minimum cluster distance
      * @param maxEvalsPerIndy   maximum number of evaluations or -1 to take the maximum
      * @return
-     * @see #isPotentialOptimumNMS(AbstractEAIndividual, double, double, int)
      */
     public static Population extractPotentialOptima(AbstractOptimizationProblem prob, Population pop,
                                                     double epsilonPhenoSpace, double epsilonFitConv, double clusterSigma, int maxEvalsPerIndy) {
         Population potOptima = new Population();
         for (int i = 0; i < pop.size(); ++i) {
-            //System.out.println("Refining " + i + " of " + population.size());
             AbstractEAIndividual indy = pop.getEAIndividual(i);
-//    		System.out.println("bef: " + indy.toString());
             boolean isConverged = AbstractOptimizationProblem.isPotentialOptimumNMS(prob, indy, epsilonPhenoSpace, epsilonFitConv, maxEvalsPerIndy);
             if (isConverged) {
                 potOptima.addIndividual(indy);
@@ -514,11 +506,7 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
                 return false; // dont waste any more evaluations on this candidate
             }
         }
-        if (overallDist < epsilon) {
+        return overallDist < epsilon;
-            return true;
-        } else {
-            return false;
-        }
     }
 
     /**
@@ -565,21 +553,8 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
         }
         int evalsPerf = PostProcess.processSingleCandidatesNMCMA(PostProcessMethod.nelderMead, pop, term, initRelPerturb, prob);
         overallDist = metric.distance(indy, pop.getBestEAIndividual());
-        //System.out.println(System.currentTimeMillis() + " in " + evalsPerf + " evals moved by "+ overallDist);
-//    	System.out.println("aft: " + population.getBestEAIndividual().toString() + ", evals performed: " + evalsPerf + ", opt moved by " + overallDist);
-//    	System.out.println("terminated because: " + term.lastTerminationMessage());
         orig.putData(PostProcess.movedDistanceKey, overallDist);
         orig.putData(PostProcess.movedToPositionKey, pop.getBestEAIndividual().getDoublePosition());
-//    	if (overallDist==0) {
-//    		PostProcess.processSingleCandidatesNMCMA(PostProcessMethod.nelderMead, population, term, initPerturb, this);
-//    	}
-
-//    		System.out.println("Checked "+ indy.getStringRepresentation());
-//    		String msg = 								"----discarding ";
-//    		if (overallDist <= epsilonPhenoSpace) msg=	"++++keeping    ";
-//    		System.out.println(msg + BeanInspector.toString(indy.getDoublePosition()));
-//    		System.out.println("which moved to " + BeanInspector.toString(population.getBestEAIndividual().getDoublePosition()));
-//    		System.out.println(" by " + overallDist + " > " + epsilonPhenoSpace);
 
         return (overallDist < epsilonPhenoSpace);
     }
@@ -588,10 +563,6 @@ public abstract class AbstractOptimizationProblem implements InterfaceOptimizati
         return defaultAccuracy;
     }
 
-    public void SetDefaultAccuracy(double defAcc) {
-        defaultAccuracy = defAcc;
-    }
-
     public void setDefaultAccuracy(double defAcc) {
         defaultAccuracy = defAcc;
     }

src/eva2/problems/AbstractParallelOptimizationProblem.java

@@ -8,8 +8,7 @@ public abstract class AbstractParallelOptimizationProblem extends AbstractOptimi
     private boolean parallelize = false;
 
     @Override
-    public void initializeProblem() {
+    public void initializeProblem() { }
-    }
 
     /**
      * This method returns a global info string

src/eva2/problems/AbstractProblemBinary.java

@@ -11,8 +11,6 @@ import java.util.BitSet;
 
 /**
  * An abstract problem based on binary data.
- *
- * @author mkron
  */
 public abstract class AbstractProblemBinary extends AbstractOptimizationProblem {
 
@@ -63,16 +61,6 @@ public abstract class AbstractProblemBinary extends AbstractOptimizationProblem
      */
     public abstract int getProblemDimension();
 
-//	/**
-//	 * Initialize a single individual with index k in the
-//	 * initializePopulation cycle.
-//	 * @param k
-//	 * @param indy
-//	 */
-//    protected void initIndy(int k, AbstractEAIndividual indy) {
-//    	indy.initialize(this);
-//    }
-
     @Override
     public void initializePopulation(Population population) {
         ((InterfaceDataTypeBinary) this.template).setBinaryDataLength(this.getProblemDimension());
@@ -84,9 +72,6 @@ public abstract class AbstractProblemBinary extends AbstractOptimizationProblem
         initTemplate();
     }
 
-    /**********************************************************************************************************************
-     * These are for GUI
-     */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.
@@ -122,5 +107,4 @@ public abstract class AbstractProblemBinary extends AbstractOptimizationProblem
         sb.append(this.getProblemDimension());
         return sb.toString();
     }
-}
+}
-

src/eva2/problems/AbstractProblemDouble.java

@@ -86,7 +86,7 @@ public abstract class AbstractProblemDouble extends AbstractOptimizationProblem
     protected void cloneObjects(AbstractProblemDouble o) {
         this.defaultRange = o.defaultRange;
         this.noise = o.noise;
-        this.SetDefaultAccuracy(o.getDefaultAccuracy());
+        this.setDefaultAccuracy(o.getDefaultAccuracy());
         if (o.template != null) {
             this.template = (AbstractEAIndividual) o.template.clone();
         }

src/eva2/problems/AbstractProblemInteger.java

@@ -77,11 +77,6 @@ public abstract class AbstractProblemInteger extends AbstractOptimizationProblem
      */
     public abstract double[] evaluate(int[] x);
 
-    /**
-     * *******************************************************************************************************************
-     * These are for GUI
-     */
-
     @Override
     public String getName() {
         return "AbstractProblemInteger";

src/eva2/problems/AbstractSynchronousOptimizationProblem.java

@@ -11,10 +11,6 @@ import eva2.optimization.population.Population;
  * so that the problem changes after every evaluation. This of course under the simplification
  * that an evaluation takes no time, or from a different POV, changes within an evaluation
  * can not be taken into account (or just discretely approximated).
- *
- * @author M.Kronfeld
- *         <p/>
- *         Jan 4, 2007
  */
 public abstract class AbstractSynchronousOptimizationProblem extends
         AbstractDynamicOptimizationProblem {
@@ -31,7 +27,6 @@ public abstract class AbstractSynchronousOptimizationProblem extends
      * measures the "distance" which the problem shifts when it changes
      */
     protected double shiftPerChange;
-    //protected double timeIntPerEval			= 1.;	// better assume this to be constant
 
     /**
      *
@@ -51,18 +46,12 @@ public abstract class AbstractSynchronousOptimizationProblem extends
 
     }
 
-    /* (non-Javadoc)
-     * @see eva2.server.oa.go.OptimizationProblems.AbstractDynamicOptimizationProblem#changeProblemAt(double)
-     */
     @Override
     protected void changeProblemAt(double problemTime) {
         incProblemTime(shiftPerChange);
         evalsSinceChange = 0.;
     }
 
-    /* (non-Javadoc)
-     * @see eva2.server.oa.go.OptimizationProblems.AbstractDynamicOptimizationProblem#problemToChangeAt(double)
-     */
     @Override
     protected boolean problemToChangeAt(double problemTime) {
         return (evalsSinceChange >= constantProblemEvals);
@@ -78,9 +67,6 @@ public abstract class AbstractSynchronousOptimizationProblem extends
         constantProblemEvals = constEvals;
     }
 
-    /* (non-Javadoc)
-     * @see eva2.server.oa.go.OptimizationProblems.AbstractDynamicOptimizationProblem#countEvaluation()
-     */
     @Override
     protected void countEvaluation() {
         evalsSinceChange += 1.;
@@ -99,7 +85,6 @@ public abstract class AbstractSynchronousOptimizationProblem extends
     @Override
     public void setFrequency(double frequency) {
         super.setFrequency(frequency);
-        //if (frequency > 1.) System.out.println("warning, frequency should be <= 1 (setFrequency)");
         if (isFrequencyRelative()) {
             // bogus. this must be reset right before population evaluation
             setConstantProblemEvals(9999999);
@@ -109,10 +94,6 @@ public abstract class AbstractSynchronousOptimizationProblem extends
         }
     }
 
-
-    /* (non-Javadoc)
-     * @see eva2.server.oa.go.OptimizationProblems.AbstractDynamicOptimizationProblem#setFrequencyRelative(boolean)
-     */
     @Override
     public void setFrequencyRelative(boolean frequencyRelative) {
         super.setFrequencyRelative(frequencyRelative);
@@ -127,4 +108,4 @@ public abstract class AbstractSynchronousOptimizationProblem extends
             setConstantProblemEvals(population.size() / getFrequency());
         }
     }
-}
+}

src/eva2/problems/BKnapsackProblem.java

@@ -347,7 +347,6 @@ public class BKnapsackProblem extends AbstractProblemBinary implements java.io.S
         result.append(this.punish);
         result.append("\n");
         result.append("Solution representation:\n");
-        //result += this.template.getSolutionRepresentationFor();
         return result.toString();
     }
 

src/eva2/problems/DynJumpProblem.java

@@ -154,11 +154,6 @@ public class DynJumpProblem extends eva2.problems.AbstractDynTransProblem {
         return null;
     }
 
-    /**
-     * ***********************************************************************
-     * These are for the GUI
-     */
-
     @Override
     public String getStringRepresentationForProblem(InterfaceOptimizer opt) {
         return "DynJumpProblem";

src/eva2/problems/ExternalRuntimeProblem.java

@@ -53,7 +53,6 @@ public class ExternalRuntimeProblem extends AbstractOptimizationProblem
                     writer.write(c);
                     writer.flush();
                 }
-//				System.out.println("monitor-thread finished!");
             } catch (IOException ioe) {
                 System.err.println("IOException in MonitorInputStreamThread/ExternalRuntimeProblem: " + ioe.getMessage());
                 ioe.printStackTrace(System.err);
@@ -208,7 +207,6 @@ public class ExternalRuntimeProblem extends AbstractOptimizationProblem
     @Override
     public void evaluate(AbstractEAIndividual individual) {
         double[] x;
-//        double[]        fitness;
 
         x = getXVector(individual);
 
@@ -266,7 +264,6 @@ public class ExternalRuntimeProblem extends AbstractOptimizationProblem
                 line = line.trim();
                 String[] parts = line.split(colSepRegExp);
                 Collections.addAll(results, parts);
-//				results.add(line); 
             }
             br.close();
         } catch (IOException e) {
@@ -463,7 +460,6 @@ public class ExternalRuntimeProblem extends AbstractOptimizationProblem
         this.additionalArg = additionalArg;
     }
 
-    //	@Override
     @Override
     public Object getInitializationRange() {
         if (initializationRange == null) {

src/eva2/problems/F13Problem.java

@@ -69,7 +69,6 @@ public class F13Problem extends AbstractProblemDoubleOffset implements Interface
             result[0] -= xi * Math.sin(Math.sqrt(Math.abs(xi)));
         }
         result[0] += (418.9829 * problemDimension);
-        // res = cn-sum_i(xi*sin(sqrt(abs(xi))))
         return result;
     }
 
@@ -86,19 +85,16 @@ public class F13Problem extends AbstractProblemDoubleOffset implements Interface
         result += "Dimension   : " + this.problemDimension + "\n";
         result += "Noise level : " + this.getNoise() + "\n";
         result += "Solution representation:\n";
-        //result += this.template.getSolutionRepresentationFor();
         return result;
     }
 
     @Override
     public SolutionHistogram getHistogram() {
-//		EVAERROR.errorMsgOnce("Warning: Restore line in getHistogram for evaluation on F13Problem ???");
         if (getProblemDimension() < 15) {
             return new SolutionHistogram(0, 800, 16);
         } else if (getProblemDimension() < 25) {
             return new SolutionHistogram(0, 1600, 16);
         }
-//		else if (getProblemDimension() < 35) return new SolutionHistogram(0, 1600, 16);
         else {
             return new SolutionHistogram(0, 3200, 12);
         }
@@ -117,6 +113,6 @@ public class F13Problem extends AbstractProblemDoubleOffset implements Interface
 
     @Override
     public void setDefaultAccuracy(double v) {
-        super.SetDefaultAccuracy(v);
+        super.setDefaultAccuracy(v);
     }
 }

src/eva2/problems/F15Problem.java

@@ -15,7 +15,7 @@ public class F15Problem extends AbstractProblemDouble implements Serializable, I
 
     public F15Problem() {
         super();
-        super.SetDefaultAccuracy(0.00001);
+        super.setDefaultAccuracy(0.00001);
         setDefaultRange(10);
     }
 

src/eva2/problems/F6Problem.java

@@ -137,7 +137,7 @@ public class F6Problem extends AbstractProblemDoubleOffset
 
     @Override
     public void setDefaultAccuracy(double acc) {
-        super.SetDefaultAccuracy(acc);
+        super.setDefaultAccuracy(acc);
     }
 
     @Override

src/eva2/problems/GPFunctionProblem.java

@@ -12,8 +12,6 @@ import eva2.tools.EVAERROR;
  * function by scaling it logarithmically. This avoids ugly functions in GP. To activate scaling,
  * set the scStart and scLimit parameters to positive values. Function values y with |y|>scStart
  * will be rescaled to values below scLimit.
- *
- * @author mkron
  */
 public class GPFunctionProblem extends AbstractProblemDouble implements InterfaceProgramProblem {
     InterfaceProgram gpProblem = null;
@@ -109,7 +107,7 @@ public class GPFunctionProblem extends AbstractProblemDouble implements Interfac
     /**
      * Scale the allover fitness value.
      *
-     * @param doubleValue
+     * @param v
      * @return
      */
     public double scaleFit(double v) {
@@ -127,12 +125,6 @@ public class GPFunctionProblem extends AbstractProblemDouble implements Interfac
         }
     }
 
-//	public static void main(String[] args) {
-//		for (double x=1.; x<100000000; x*=10.) {
-//			System.out.println("x: " + -x + " sc: " + scaleFit(-x));
-//		}
-//	}
-
     @Override
     public int getProblemDimension() {
         return dim;

src/eva2/problems/MatlabEvalMediator.java

@@ -21,8 +21,6 @@ import java.util.concurrent.Semaphore;
  * Adding sleep time reduces CPU load a lot but reduces efficiency badly at the same time, probably because
  * there's so much going on. For cases where the evaluation function is very time-consuming, adding sleep time
  * might be an option.
- *
- * @author mkron
  */
 public class MatlabEvalMediator {
     volatile Boolean requesting = false;
@@ -71,13 +69,7 @@ public class MatlabEvalMediator {
     double[] requestEval(MatlabProblem mp, Object x) {
         this.mp = mp;
         question = x;
-//		System.err.println("IN REQUESTEVAL, x is " + BeanInspector.toString(x));
         if (question.getClass().isArray()) {
-//			System.err.println("array of type ** " + Array.get(question, 0).getClass().toString());
-//		} else if (question instanceof BitSet){
-//			BitSet b = (BitSet)x;
-//			Integer.decode()
-//			
             if (question == null) {
                 System.err.println("Error: requesting evaluation for null array!");
             }
@@ -86,35 +78,15 @@ public class MatlabEvalMediator {
                 System.err.println("Error, requesting evaluation for invalid data type! " + question.getClass());
             }
         }
-//		logMPAndSysOut("Synch requesting A requestEval " + getState());
         synchronized (requesting) { //MdP
-//			logMPAndSysOut(" in synch requesting A requestEval " + getState());
             if (requesting) {
                 String msg = "Warning: already in requesting state when request arrived!";
                 System.err.println(msg);
                 logMP(msg);
             }
             requesting = true;
-//			logMPAndSysOut("-- Requesting evaluate for " + BeanInspector.toString(x) + ", req state is " + requesting + "\n");
         }
 
-
-//		logMPAndSysOut("Synch requesting A done " + getState());
-        /*int k=0; int mod=25;
-        while (requesting && !quit) {
-			// 	wait for matlab to answer the question
-			if (sleepTime > 0) try { Thread.sleep(sleepTime); } catch(Exception e) {
-				System.err.println("Exception in sleep (MatlabEvalMediator)");
-			};
-			k++;
-			if ((k%mod)==0) {
-//				System.out.println("waiting for matlab to answer...");
-				logMP("waiting for matlab to answer... (" + mod + ") " + getState() + "\n");
-				mod*=2;
-				if (mod <=0) mod=Integer.MAX_VALUE;
-				
-			}
-		}*/
         try {
             requests.acquire();
         } catch (InterruptedException e) {
@@ -123,7 +95,6 @@ public class MatlabEvalMediator {
         }
         logMP("-- Requesting done\n");
         // matlab is finished, answer is here
-        //return null;
         return getAnswer(); // return to JE with answer
     }
 

src/eva2/problems/MatlabProblem.java

@@ -53,15 +53,10 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
         this.handler = o.handler;
         this.runnable = o.runnable;
         this.allowSingleRunnable = o.allowSingleRunnable;
-//		this.jmInterface = new String(o.jmInterface);
         this.problemDimension = o.problemDimension;
-//		this.res = new ResultArr();
-//		if (o.res != null) if (o.res.get() != null) res.set(o.res.get());
         this.range = o.range;
         this.dataType = o.dataType;
         this.initialRange = o.initialRange;
-//		this.mtCmd = o.mtCmd;
-//		currArray = null;
     }
 
     @Override
@@ -69,15 +64,6 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
         return new MatlabProblem(this);
     }
 
-    /**
-     * Constructor of a real valued problem.
-     * @param dim
-     * @param range
-     */
-//	public MatlabProblem(int dim, double[][] range) {
-//		initialize(dim, ProblemDataTypeEnum.typeDouble, range, null, defTestOut);
-//	}
-
     /**
      * Constructor of a binary problem with given bit length.
      *
@@ -87,16 +73,6 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
         init(dim, MatlabProblemDataTypeEnum.typeBinary, null, null, defTestOut);
     }
 
-    /**
-     * Constructor of a real valued problem with initialization range.
-     * @param dim
-     * @param range
-     * @param initRange
-     */
-//	public MatlabProblem(int dim, double[][] range, double[][] initRange) {
-//		initialize(dim, ProblemDataTypeEnum.typeDouble, range, initRange, defTestOut);
-//	}
-
     /**
      * Constructor of real or integer valued problem, the range will be converted
      * to integer in the latter case.
@@ -187,7 +163,6 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
      */
     private void init(int dim, MatlabProblemDataTypeEnum datType, double[][] globalRange, double[][] initRange, String outFile) {
         this.problemDimension = dim;
-//		if ((rng != null) && (dim != rng.length)) throw new ArrayIndexOutOfBoundsException("Mismatching dimension and range!");
         if (globalRange != null) { // these may be Matlab objects, so I do it by foot, just to be sure not to clone them within Matlab instead of here
             this.range = new double[globalRange.length][globalRange[0].length];
             for (int i = 0; i < this.range.length; i++) {
@@ -344,7 +319,6 @@ public class MatlabProblem extends AbstractOptimizationProblem implements Interf
      * @param outputFilePrefix
      * @param specParams
      * @param specValues
-     * @see OptimizerFactory.getOptRunnable
      */
     public void optimize(final int optType, String outputFilePrefix, Object[] specParams, Object[] specValues) {
         if (allowSingleRunnable && (runnable != null) && (!runnable.isFinished())) {

src/eva2/problems/PSymbolicRegression.java

@@ -150,7 +150,10 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
     /**
      * This method inits a given population
      *
-     * @param population The populations that is to be inited
+     * @param pop The populations that is to be inited
+     * @param prob
+     * @param useInnerConsts
+     * @param numConsts
      */
     public static void initPopulation(Population pop, InterfaceProgramProblem prob, boolean useInnerConsts, int numConsts) {
         AbstractEAIndividual template;
@@ -240,8 +243,8 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
 
         for (int j = 0; j < this.numberOfCheckPoints; j++) {
             setCheckPoint(x, j);
-            tmpValue = ((Double) program.evaluate(this)).doubleValue();
+            tmpValue = (Double) program.evaluate(this);
-            fitness += Math.pow((this.targetFunction.evaluateFunction(this.x) - ((Double) program.evaluate(this)).doubleValue()), 2);
+            fitness += Math.pow((this.targetFunction.evaluateFunction(this.x) - (Double) program.evaluate(this)), 2);
         }
 
         fitness /= (double) this.numberOfCheckPoints;
@@ -262,7 +265,7 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
                 program = ((InterfaceDataTypeProgram) this.overallBestIndividuum).getProgramData()[0];
                 for (int i = 0; i < this.numberOfCheckPoints; i++) {
                     setCheckPoint(x, i);
-                    tmpValue = ((Double) program.evaluate(this)).doubleValue();
+                    tmpValue = (Double) program.evaluate(this);
                     this.plot.setConnectedPoint(this.x[0], tmpValue, 0);
                     tmpValue = this.targetFunction.evaluateFunction(this.x);
                     this.plot.setConnectedPoint(this.x[0], tmpValue, 1);
@@ -309,9 +312,6 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
     @Override
     public Object getSensorValue(String sensor) {
         return PSymbolicRegression.getSensorValue(sensor, x, constants);
-//        for (int i = 0; i < this.x.length; i++) if (sensor.equalsIgnoreCase("X"+i)) return new Double(this.x[i]);
-//        for (int i = 0; i < this.c.length; i++) if (sensor.equalsIgnoreCase("C"+i)) return new Double(this.c[i]);
-//        return new Double(0);
     }
 
     /**
@@ -333,22 +333,19 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
                     return vars;
                 }
                 int index = Integer.parseInt(sensor.substring(1));
-                return new Double(vars[index]);
+                return vars[index];
             } catch (Exception e) {
                 System.err.println("Warning, unable to access " + sensor);
                 return vars;
             }
         } else if (sensor.charAt(0) == 'C') {
             int index = Integer.parseInt(sensor.substring(1));
-            return new Double(consts[index]);
+            return consts[index];
         } else if (sensor.charAt(0) == 'N') {
             return (double) vars.length;
         } else {
-            return new Double(0);
+            return (double) 0;
         }
-//        for (int i = 0; i < this.x.length; i++) if (sensor.equalsIgnoreCase("X"+i)) return new Double(this.x[i]);
-//        for (int i = 0; i < this.c.length; i++) if (sensor.equalsIgnoreCase("C"+i)) return new Double(this.c[i]);
-//        return new Double(0);
     }
 
     /**
@@ -362,9 +359,6 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
         // no actuators in this problem
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.
@@ -702,10 +696,4 @@ public class PSymbolicRegression extends AbstractOptimizationProblem implements
         System.out.println("Evaluated individual: " + indy);
         return indy.getFitness();
     }
-
-//	public static void main(String[] args) {
-//		String bestStudentSol = "-(abs(abs(-(-(X0, -(-(X0, X0), X0)), sin(abs(-(-(X0, X0), X0)))))), -(-(sin(-(abs(X0), -(-(-(X0, X0), X0), abs(abs(X0))))), -(-(abs(abs(abs(X0))), -(-(-(X0, X0), X0), abs(-(X0,X0)))), sin(-(abs(X0), sin(sin(X0)))))), X0))";
-////    	String bestStudentSol = "-(abs(-(sqrt(-(-(abs(1.0), X0), X0)), -(sqrt(-(sqrt(1.0), sqrt(pi))), X0))),-(-(sin(sqrt(-(-(sqrt(1.0), X0), pi))), abs(X0)), -(sqrt(pi), -(sqrt(sqrt(-(abs(1.0), X0))),X0))))";
-//		evalNodeString(bestStudentSol);
-//	}
 }

src/eva2/problems/TF1Problem.java

@@ -257,9 +257,6 @@ public class TF1Problem extends AbstractMultiObjectiveOptimizationProblem implem
         }
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.
@@ -344,24 +341,6 @@ public class TF1Problem extends AbstractMultiObjectiveOptimizationProblem implem
         return "Length of the x vector at is to be optimized.";
     }
 
-//    /** This method allows you to set the number of objective variables
-//     * @param a The number of objective variables
-//     */
-//    public void setOutputDimension(int a) {
-//        this.outputDimension = a;
-//        this.border = new double[this.outputDimension][2];
-//        for (int i = 0; i < this.border.length; i++) {
-//            this.border[i][0] = 0;
-//            this.border[i][1] = 5;
-//        }
-//    }
-//    public int getOutputDimension() {
-//        return this.outputDimension;
-//    }
-//    public String outputDimensionTipText() {
-//        return "Number of objective variables.";
-//    }
-
     /**
      * This method allows you to choose the EA individual
      *
@@ -397,19 +376,6 @@ public class TF1Problem extends AbstractMultiObjectiveOptimizationProblem implem
         return "Choose a Multiobjective to Singleobjective converter.";
     }
 
-//    /** This method allows you to toggel the application of constraints on the problem
-//     * @param b     state.
-//     */
-//    public void setApplyConstraints(boolean b) {
-//        this.applyConstraints = b;
-//    }
-//    public boolean getApplyConstraints() {
-//        return this.applyConstraints;
-//    }
-//    public String applyConstraintsTipText() {
-//        return "Toggle application of constraint (works only for T1).";
-//    }
-
     /**
      * Since you can apply single objective optimization algorithms on
      * multi-objective problems, the problem needs a way to log the pareto-

src/eva2/problems/regression/InterfaceRegressionFunction.java

@@ -1,11 +1,6 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 27.06.2003
- * Time: 15:51:48
- * To change this template use Options | File Templates.
  */
 public interface InterfaceRegressionFunction {
 

src/eva2/problems/regression/RFKoza_GPI_10_1.java

@@ -1,11 +1,6 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 27.06.2003
- * Time: 15:55:28
- * To change this template use Options | File Templates.
  */
 public class RFKoza_GPI_10_1 implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +32,6 @@ public class RFKoza_GPI_10_1 implements InterfaceRegressionFunction, java.io.Ser
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/problems/regression/RFKoza_GPI_10_2.java

@@ -1,11 +1,6 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 27.06.2003
- * Time: 15:58:06
- * To change this template use Options | File Templates.
  */
 public class RFKoza_GPI_10_2 implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +32,6 @@ public class RFKoza_GPI_10_2 implements InterfaceRegressionFunction, java.io.Ser
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/problems/regression/RFKoza_GPI_7_3.java

@@ -1,11 +1,6 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 09.10.2003
- * Time: 11:36:54
- * To change this template use Options | File Templates.
  */
 public class RFKoza_GPI_7_3 implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +32,6 @@ public class RFKoza_GPI_7_3 implements InterfaceRegressionFunction, java.io.Seri
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/problems/regression/RFKoza_GPI_7_3_extended.java

@@ -1,11 +1,6 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 09.10.2003
- * Time: 11:38:20
- * To change this template use Options | File Templates.
  */
 public class RFKoza_GPI_7_3_extended implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +32,6 @@ public class RFKoza_GPI_7_3_extended implements InterfaceRegressionFunction, jav
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/problems/regression/RFRaidl_F1.java

@@ -1,11 +1,6 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 30.09.2003
- * Time: 14:02:41
- * To change this template use Options | File Templates.
  */
 public class RFRaidl_F1 implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +32,6 @@ public class RFRaidl_F1 implements InterfaceRegressionFunction, java.io.Serializ
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/problems/regression/RFRaidl_F2.java

@@ -1,11 +1,7 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
+ *
- * User: streiche
- * Date: 30.09.2003
- * Time: 14:02:50
- * To change this template use Options | File Templates.
  */
 public class RFRaidl_F2 implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +33,6 @@ public class RFRaidl_F2 implements InterfaceRegressionFunction, java.io.Serializ
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/problems/regression/RFRaidl_F3.java

@@ -1,11 +1,7 @@
 package eva2.problems.regression;
 
 /**
- * Created by IntelliJ IDEA.
+ *
- * User: streiche
- * Date: 30.09.2003
- * Time: 14:02:59
- * To change this template use Options | File Templates.
  */
 public class RFRaidl_F3 implements InterfaceRegressionFunction, java.io.Serializable {
 
@@ -37,9 +33,6 @@ public class RFRaidl_F3 implements InterfaceRegressionFunction, java.io.Serializ
         return result;
     }
 
-/**********************************************************************************************************************
- * These are for GUI
- */
     /**
      * This method allows the CommonJavaObjectEditorPanel to read the
      * name to the current object.

src/eva2/tools/Serializer.java

@@ -48,10 +48,6 @@ public class Serializer {
             objectStream.writeObject(objToStore);
             objectStream.flush();
             objectStream.close();
-            String output;
-            Gson gson = new Gson();
-            output = gson.toJson(objToStore);
-            System.out.println(output);
         } catch (java.io.NotSerializableException ex) {
             LOGGER.log(Level.SEVERE, "Object is not serializable!", ex);
         }

src/eva2/tools/chart2d/Chart2DDPointContentSelectable.java

@@ -68,10 +68,6 @@ public class Chart2DDPointContentSelectable implements InterfaceDPointWithConten
         this.size = d;
     }
 
-    /*********************************************************************************************
-     *  The InterfaceSelectablePointIcon
-     */
-
     /**
      * This method allows to add a selection listner to the PointIcon
      * it should need more than one listener to this abstruse event

src/eva2/tools/chart2d/Chart2DDPointIconCircle.java

@@ -2,7 +2,6 @@ package eva2.tools.chart2d;
 
 import java.awt.*;
 
-
 /**
  *
  */

src/eva2/tools/chart2d/Chart2DDPointIconContent.java

@@ -1,6 +1,5 @@
 package eva2.tools.chart2d;
 
-
 import eva2.gui.plot.InterfaceDPointWithContent;
 import eva2.optimization.individuals.AbstractEAIndividual;
 import eva2.problems.InterfaceOptimizationProblem;
@@ -10,13 +9,6 @@ import java.awt.*;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 
-/**
- * Created by IntelliJ IDEA.
- * User: streiche
- * Date: 13.04.2004
- * Time: 13:31:48
- * To change this template use File | Settings | File Templates.
- */
 public class Chart2DDPointIconContent implements InterfaceDPointWithContent, DPointIcon {
 
     AbstractEAIndividual individual;

src/eva2/tools/chart2d/Chart2DDPointIconCross.java

@@ -1,9 +1,7 @@
 package eva2.tools.chart2d;
 
-
 import java.awt.*;
 
-
 /**
  *
  */

src/eva2/tools/chart2d/Chart2DDPointIconPoint.java

@@ -5,11 +5,7 @@ import java.awt.*;
 
 
 /**
- * Created by IntelliJ IDEA.
+ *
- * User: streiche
- * Date: 17.08.2005
- * Time: 16:52:34
- * To change this template use File | Settings | File Templates.
  */
 public class Chart2DDPointIconPoint implements DPointIcon {
 

src/eva2/tools/chart2d/DArea.java

@@ -36,8 +36,7 @@ public class DArea extends JComponent implements DParent, Printable {
      */
     private static final long serialVersionUID = 1461387400381365146L;
 
-    private boolean auto_focus = false, auto_grid = false,
+    private boolean autoFocus = false, autoGrid = false, gridToFront = false;
-            grid_to_front = false;
 
     /**
      * the container in which all DElements of the area are contained except the
@@ -55,7 +54,7 @@ public class DArea extends JComponent implements DParent, Printable {
     /**
      * maximal number of grid lines
      */
-    private int max_grid = 10;
+    private int maxGrid = 10;
 
     /**
      * the measures of the area it calculates the coordinates
@@ -64,12 +63,12 @@ public class DArea extends JComponent implements DParent, Printable {
 
     /**
      * min_rectangle is set, when all elements are removed the intersection of
-     * visible_rect and max_rectangle is the currently visible rectangle
+     * visibleRect and max_rectangle is the currently visible rectangle
      */
-    protected DRectangle min_rect = DEFAULT_MIN_RECT,
+    protected DRectangle minRect = DEFAULT_MIN_RECT,
-            visible_rect = DEFAULT_MIN_RECT;
+            visibleRect = DEFAULT_MIN_RECT;
 
-    protected Double min_x, min_y, max_x, max_y;
+    protected Double minX, minY, maxX, maxY;
 
     /**
      * initializes the DArea with the initial capacity of 10 components
@@ -82,12 +81,12 @@ public class DArea extends JComponent implements DParent, Printable {
      * initializes the DArea with the specialized initial capacity of components
      * (@see java.util.Vector)
      *
-     * @param the initial capacity
+     * @param initialCapacity the initial capacity
      */
-    public DArea(int initial_capacity) {
+    public DArea(int initialCapacity) {
         container = new DContainer();
         container.setDParent(this);
-        grid = new DGrid(visible_rect, 1, 1);
+        grid = new DGrid(visibleRect, 1, 1);
         grid.setVisible(false);
         grid.setDParent(this);
         measures = new DMeasures(this);
@@ -162,17 +161,17 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return DRectangle the size and position of the visible area
      */
     public DRectangle getDRectangle() {
-        DRectangle rect = (DRectangle) visible_rect.clone();
+        DRectangle rect = (DRectangle) visibleRect.clone();
-        if (min_x != null) {
+        if (minX != null) {
             rect.setX(Math.max(rect.getX(), getMinX()));
         }
-        if (min_y != null) {
+        if (minY != null) {
             rect.setY(Math.max(rect.getY(), getMinY()));
         }
-        if (max_x != null) {
+        if (maxX != null) {
             rect.setWidth(Math.min(rect.getWidth(), getMaxX() - getMinX()));
         }
-        if (max_y != null) {
+        if (maxY != null) {
             rect.setHeight(Math.min(rect.getHeight(), getMaxY() - getMinY()));
         }
         return rect;
@@ -185,10 +184,7 @@ public class DArea extends JComponent implements DParent, Printable {
      * @deprecated see getMaxX, getMaxY, getMinX, getMinY
      */
     public DRectangle getMaxRectangle() {
-        return new DRectangle(min_x.doubleValue(), min_y.doubleValue(), max_x
+        return new DRectangle(minX, minY, maxX - minX, maxY - minY);
-                .doubleValue()
-                - min_x.doubleValue(), max_y.doubleValue()
-                - min_y.doubleValue());
     }
 
     /**
@@ -197,8 +193,8 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return the maxmal x-value
      */
     public double getMaxX() {
-        if (max_x != null) {
+        if (maxX != null) {
-            return max_x.doubleValue();
+            return maxX;
         }
         return 0;
     }
@@ -209,46 +205,12 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return the maximal y-value
      */
     public double getMaxY() {
-        if (max_y != null) {
+        if (maxY != null) {
-            return max_y.doubleValue();
+            return maxY;
         }
         return 0;
     }
 
-    // /**
-    // * method sets the maximal rectangle whioch can be viewed with the
-    // * DArea. This method can be used if the area is used with scale functions
-    // * which are not invertible on all reals
-    // *
-    // * @param x the minmal x value
-    // * @param y the minmal y value
-    // * @param width of the maximal rectangle
-    // * @param height of the maximal rectangle
-    // */
-    // public void setMaxRectangle( double x, double y, double width, double
-    // height ){
-    // setMaxRectangle( new DRectangle( x, y, width, height ) );
-    // }
-
-    // /**
-    // * method sets the maximal rectangle whioch can be viewed with the
-    // * DArea. This method can be used if the area is used with scale functions
-    // * which are not invertible on all reals
-    // *
-    // * @param the rect maximal rectangle of the DArea
-    // * @deprecated see setMinX, setMinY, setMaxX, setMaxY
-    // */
-    // public void setMaxRectangle( DRectangle rect ){
-    // if( !rect.contains( min_rect ) ) throw
-    // new
-    // IllegalArgumentException("Maximal rectangle does not contain minmal rectangle");
-    //
-    // setMinX( rect.x );
-    // setMinY( rect.y );
-    // setMaxX( rect.x + rect.width );
-    // setMaxY( rect.y + rect.height );
-    // }
-
     /**
      * method returns the minimal rectangle which is set as the visible when all
      * elements are removed and the area is on auto focus
@@ -256,7 +218,7 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return the minmal rectangle
      */
     public DRectangle getMinRectangle() {
-        return (DRectangle) min_rect.clone();
+        return (DRectangle) minRect.clone();
     }
 
     /**
@@ -265,8 +227,8 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return the minmal x-value
      */
     public double getMinX() {
-        if (min_x != null) {
+        if (minX != null) {
-            return min_x.doubleValue();
+            return minX;
         }
         return 0;
     }
@@ -277,8 +239,8 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return the minmal y-value
      */
     public double getMinY() {
-        if (min_y != null) {
+        if (minY != null) {
-            return min_y.doubleValue();
+            return minY;
         }
         return 0;
     }
@@ -289,25 +251,25 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return DRectangle the size and position of the visible area
      */
     public SlimRect getSlimRectangle() {
-        SlimRect srect = new SlimRect(visible_rect.getX(), visible_rect.getY(),
+        SlimRect srect = new SlimRect(visibleRect.getX(), visibleRect.getY(),
-                visible_rect.getWidth(), visible_rect.getHeight());
+                visibleRect.getWidth(), visibleRect.getHeight());
-        if (min_x != null) {
+        if (minX != null) {
             srect.x = Math.max(srect.x, getMinX());
         }
-        if (min_y != null) {
+        if (minY != null) {
             srect.y = Math.max(srect.y, getMinY());
         }
-        if (max_x != null) {
+        if (maxX != null) {
             srect.width = Math.min(srect.width, getMaxX() - getMinX());
         }
-        if (max_y != null) {
+        if (maxY != null) {
             srect.height = Math.min(srect.height, getMaxY() - getMinY());
         }
         return srect;
     }
 
     public DFunction getYScale() {
-        return measures.y_scale;
+        return measures.yScale;
     }
 
     /**
@@ -316,7 +278,7 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return true if the grid is on, else false
      */
     public boolean hasAutoGrid() {
-        return auto_grid;
+        return autoGrid;
     }
 
     /**
@@ -335,7 +297,7 @@ public class DArea extends JComponent implements DParent, Printable {
      * @return <code>true</code> or <code>false</code>
      */
     public boolean isOnAutoFocus() {
-        return auto_focus;
+        return autoFocus;
     }
 
     /**
@@ -355,23 +317,23 @@ public class DArea extends JComponent implements DParent, Printable {
      */
     @Override
     public void paint(Graphics g) {
-        if (auto_focus) {
+        if (autoFocus) {
             container.restore();
-            visible_rect = (DRectangle) container.getRectangle().clone();
+            visibleRect = (DRectangle) container.getRectangle().clone();
-            // grid.updateDistByRect(visible_rect);
+            // grid.updateDistByRect(visibleRect);
         }
-        if (visible_rect.isEmpty()) {
+        if (visibleRect.isEmpty()) {
-            visible_rect = (DRectangle) min_rect.clone();
+            visibleRect = (DRectangle) minRect.clone();
-            // grid.updateDistByRect(visible_rect);
+            // grid.updateDistByRect(visibleRect);
         }
         super.paint(g);
 
         measures.setGraphics(g);
-        if (grid.isVisible() && !grid_to_front) {
+        if (grid.isVisible() && !gridToFront) {
             paintGrid(measures);
         }
         container.paint(measures);
-        if (grid.isVisible() && grid_to_front) {
+        if (grid.isVisible() && gridToFront) {
             paintGrid(measures);
         }
     }
@@ -379,11 +341,11 @@ public class DArea extends JComponent implements DParent, Printable {
     /**
      * method paints the grid how the method paints the grid depends on whether
      * the area is wrapped in a <code>ScaledBorder</code> or not and on the
-     * auto_grid option
+     * autoGrid option
      */
     private void paintGrid(DMeasures m) {
         grid.rectangle = getDRectangle();
-        if (auto_grid) {
+        if (autoGrid) {
             Border b = getBorder();
             if (b instanceof ScaledBorder) {
                 ScaledBorder sb = (ScaledBorder) b;
@@ -392,16 +354,16 @@ public class DArea extends JComponent implements DParent, Printable {
             } else {
                 grid.setDistances(ScaledBorder.aBitBigger(grid.rectangle
                         .getWidth()
-                        / max_grid), ScaledBorder.aBitBigger(grid.rectangle
+                        / maxGrid), ScaledBorder.aBitBigger(grid.rectangle
                         .getHeight()
-                        / max_grid));
+                        / maxGrid));
             }
         }
         grid.paint(m);
     }
 
     /**
-     * paints the grid when auto_grid is selected and the area is surrounded by
+     * paints the grid when autoGrid is selected and the area is surrounded by
      * an instance of ScaledBorder
      *
      * @param sb the ScaledBorder around the area
@@ -412,9 +374,9 @@ public class DArea extends JComponent implements DParent, Printable {
         FontMetrics fm = m.getGraphics().getFontMetrics();
         grid.setDistances(sb.getSrcdX(fm, d), sb.getSrcdY(fm, d));
 
-        if (m.x_scale == null && m.y_scale == null) {
+        if (m.xScale == null && m.yScale == null) {
             grid.paint(m);
-        } else {// selber malen
+        } else {
             Graphics g = m.g;
             g.setColor(grid.getColor());
 
@@ -438,16 +400,16 @@ public class DArea extends JComponent implements DParent, Printable {
             double pos;
 
             for (; (pos = x * grid.getHorDist()) < src_rect.x + src_rect.width; x++) {
-                if (m.x_scale != null) {
+                if (m.xScale != null) {
-                    pos = m.x_scale.getImageOf(pos);
+                    pos = m.xScale.getImageOf(pos);
                 }
                 Point p1 = m.getPoint(pos, miny), p2 = m.getPoint(pos, maxy);
                 g.drawLine(p1.x, p1.y, p2.x, p2.y);
             }
 
             for (; (pos = y * grid.getVerDist()) < src_rect.y + src_rect.height; y++) {
-                if (m.y_scale != null) {
+                if (m.yScale != null) {
-                    pos = m.y_scale.getImageOf(pos);
+                    pos = m.yScale.getImageOf(pos);
                 }
                 Point p1 = m.getPoint(minx, pos), p2 = m.getPoint(maxx, pos);
                 g.drawLine(p1.x, p1.y, p2.x, p2.y);
@@ -475,12 +437,12 @@ public class DArea extends JComponent implements DParent, Printable {
         if (!(sb instanceof ScaledBorder)) {
             sb = null;
         } else {
-            ((ScaledBorder) sb).show_outer_border = false;
+            ((ScaledBorder) sb).showOuterBorder = false;
         }
         PagePrinter printer = new PagePrinter(this, g, pf);
         int ret = printer.print();
         if (sb != null) {
-            ((ScaledBorder) sb).show_outer_border = true;
+            ((ScaledBorder) sb).showOuterBorder = true;
         }
         return ret;
     }
@@ -489,35 +451,35 @@ public class DArea extends JComponent implements DParent, Printable {
      * method resets the maximal x-value
      */
     public void releaseMaxX() {
-        max_x = null;
+        maxX = null;
     }
 
     /**
      * method resets the maximal y-value
      */
     public void releaseMaxY() {
-        max_y = null;
+        maxY = null;
     }
 
     /**
      * method resets the minimal x-value
      */
     public void releaseMinX() {
-        min_x = null;
+        minX = null;
     }
 
     /**
      * method resets the minimal y-value
      */
     public void releaseMinY() {
-        min_y = null;
+        minY = null;
     }
 
     /**
      * removes all elements from the area
      */
     public void removeAllDElements() {
-        visible_rect = (DRectangle) min_rect.clone();
+        visibleRect = (DRectangle) minRect.clone();
         container.removeAllDElements();
     }
 
@@ -542,13 +504,11 @@ public class DArea extends JComponent implements DParent, Printable {
             throw new IllegalArgumentException(
                     "Cannot repaint a null DRectangle");
         }
-        if (r.isAll() || auto_focus) {
+        if (r.isAll() || autoFocus) {
             repaint();
         } else {
             Point p1 = measures.getPoint(r.getX(), r.getY()), p2 = measures
                     .getPoint(r.getX() + r.getWidth(), r.getY() + r.getHeight());
-            // Point p1 = measures.getPoint( r.x, r.y ),
-            // p2 = measures.getPoint( r.x + r.width, r.y + r.height);
             if (p1 == null || p2 == null) {
                 repaint();
             } else {
@@ -570,8 +530,8 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param b on or off
      */
     public void setAutoFocus(boolean b) {
-        boolean old = auto_focus;
+        boolean old = autoFocus;
-        auto_focus = b;
+        autoFocus = b;
         if (old != b) {
             repaint();
         }
@@ -588,10 +548,10 @@ public class DArea extends JComponent implements DParent, Printable {
             grid.rectangle = getDRectangle();
             grid.setVisible(true);
         }
-        if (b == auto_grid) {
+        if (b == autoGrid) {
             return;
         }
-        auto_grid = b;
+        autoGrid = b;
         repaint();
     }
 
@@ -603,16 +563,16 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param ver_dist the vertical distance
      */
     public void setGrid(double hor_dist, double ver_dist) {
-        grid = new DGrid(visible_rect, hor_dist, ver_dist);
+        grid = new DGrid(visibleRect, hor_dist, ver_dist);
         grid.setDParent(this);
-        auto_grid = false;
+        autoGrid = false;
         repaint();
     }
 
     /**
      * sets the color of the grid
      *
-     * @param java .awt.Color
+     * @param color The new grid color
      */
     public void setGridColor(Color color) {
         grid.setColor(color);
@@ -625,8 +585,8 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param aFlag grid t front or not
      */
     public void setGridToFront(boolean aFlag) {
-        boolean old = grid_to_front;
+        boolean old = gridToFront;
-        grid_to_front = aFlag;
+        gridToFront = aFlag;
         if (old != aFlag && grid.isVisible()) {
             repaint();
         }
@@ -652,8 +612,8 @@ public class DArea extends JComponent implements DParent, Printable {
         if (no < 1) {
             return;
         }
-        int old = max_grid;
+        int old = maxGrid;
-        max_grid = no;
+        maxGrid = no;
         if (old != no) {
             repaint();
         }
@@ -666,11 +626,11 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param max the maximal x-value
      */
     public void setMaxX(double max) {
-        if (max < min_rect.getX() + min_rect.getWidth()) {
+        if (max < minRect.getX() + minRect.getWidth()) {
             throw new IllegalArgumentException(
                     "Maximal x-value axes intersects minmal rectangle.");
         }
-        max_x = new Double(max);
+        maxX = max;
     }
 
     /**
@@ -681,11 +641,11 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param may the maximal y-value
      */
     public void setMaxY(double may) {
-        if (may < min_rect.getY() + min_rect.getHeight()) {
+        if (may < minRect.getY() + minRect.getHeight()) {
             throw new IllegalArgumentException(
                     "Maximal y-value axes intersects minmal rectangle.");
         }
-        max_y = new Double(may);
+        maxY = may;
     }
 
     /**
@@ -707,9 +667,9 @@ public class DArea extends JComponent implements DParent, Printable {
      */
     public void setMinRectangle(DRectangle rect) {
         if (rect.isEmpty()) {
-            min_rect = DEFAULT_MIN_RECT;
+            minRect = DEFAULT_MIN_RECT;
         } else {
-            min_rect = (DRectangle) rect.clone();
+            minRect = (DRectangle) rect.clone();
         }
     }
 
@@ -720,11 +680,11 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param mix the minimal x-value
      */
     public void setMinX(double mix) {
-        if (mix > min_rect.getX()) {
+        if (mix > minRect.getX()) {
             throw new IllegalArgumentException(
                     "Mimimal y-value axes intersects minmal rectangle.");
         }
-        min_x = new Double(mix);
+        minX = mix;
     }
 
     /**
@@ -734,11 +694,11 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param miy the minimal y-value
      */
     public void setMinY(double miy) {
-        if (miy > min_rect.getY()) {
+        if (miy > minRect.getY()) {
             throw new IllegalArgumentException(
                     "Mimimal y-value axes intersects minmal rectangle.");
         }
-        min_y = new Double(miy);
+        minY = miy;
     }
 
     /**
@@ -767,10 +727,10 @@ public class DArea extends JComponent implements DParent, Printable {
                             + "as the visible rectangle of an DArea");
         }
 
-        if (!rect.equals(visible_rect) && rect.getWidth() > 0
+        if (!rect.equals(visibleRect) && rect.getWidth() > 0
                 && rect.getHeight() > 0) {
-            auto_focus = false;
+            autoFocus = false;
-            visible_rect = (DRectangle) rect.clone();
+            visibleRect = (DRectangle) rect.clone();
             repaint();
         }
     }
@@ -783,10 +743,10 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param x_s the scale function for the x-axis
      */
     public void setXScale(DFunction x_s) {
-        if (x_s == null && measures.x_scale == null) {
+        if (x_s == null && measures.xScale == null) {
             return;
         }
-        measures.x_scale = x_s;
+        measures.xScale = x_s;
         repaint();
     }
 
@@ -798,14 +758,10 @@ public class DArea extends JComponent implements DParent, Printable {
      * @param y_s the scale function for the y-axis
      */
     public void setYScale(DFunction y_s) {
-        if (y_s == null && measures.y_scale == null) {
+        if (y_s == null && measures.yScale == null) {
             return;
         }
-        measures.y_scale = y_s;
+        measures.yScale = y_s;
         repaint();
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DArray.java

@@ -1,14 +1,5 @@
 package eva2.tools.chart2d;
 
-/**
- * Title:
- * Description:
- * Copyright:    Copyright (c) 2001
- * Company:
- * @author
- * @version 1.0
- */
-
 /**
  * This class stores an array of double values.
  * It can be used as data stack for an DPointSet object.
@@ -16,8 +7,8 @@ package eva2.tools.chart2d;
  * been modified.
  */
 public class DArray implements DIntDoubleMap {
-    private int initial_capacity, size;
+    private int initialCapacity, size;
-    private double capacity_multiplier = 2, max, min, minPositive = -1;
+    private double capacityMultiplier = 2, max, min, minPositive = -1;
     private double[] value;
 
     /**
@@ -32,30 +23,28 @@ public class DArray implements DIntDoubleMap {
      * Constructor for an DArray object with default value for the capacity
      * multiplier (2).
      *
-     * @param initial_capacity the initial capacity of the array
+     * @param initialCapacity the initial capacity of the array
      */
-    public DArray(int initial_capacity) {
+    public DArray(int initialCapacity) {
-        this(initial_capacity, 2);
+        this(initialCapacity, 2);
     }
 
     /**
      * Constructor for an DArray object
      *
-     * @param initial_capacity    the initial capacity of the array
+     * @param initialCapacity    the initial capacity of the array
-     * @param capacity_multiplier the capacity multiplier when the array overflows
+     * @param capacityMultiplier the capacity multiplier when the array overflows
      */
-    public DArray(int initial_capacity, double capacity_multiplier) {
+    public DArray(int initialCapacity, double capacityMultiplier) {
-        if (initial_capacity < 1) {
+        if (initialCapacity < 1) {
-            throw
+            throw new IllegalArgumentException("The initial capacity has to be at least 1");
-                    new IllegalArgumentException("The initial capacity has to be at least 1");
         }
-        if (capacity_multiplier <= 1) {
+        if (capacityMultiplier <= 1) {
-            throw
+            throw new IllegalArgumentException("The capacity multiplier has to be bigger than 1");
-                    new IllegalArgumentException("The capacity multiplier has to be bigger than 1");
         }
-        this.initial_capacity = initial_capacity;
+        this.initialCapacity = initialCapacity;
-        value = new double[initial_capacity];
+        value = new double[initialCapacity];
-        this.capacity_multiplier = capacity_multiplier;
+        this.capacityMultiplier = capacityMultiplier;
     }
 
     /**
@@ -67,25 +56,24 @@ public class DArray implements DIntDoubleMap {
     @Override
     public boolean setImage(int source, double image) {
         if (source < 0 || source >= size) {
-            throw
+            throw new ArrayIndexOutOfBoundsException(source);
-                    new ArrayIndexOutOfBoundsException(source);
         }
-        boolean min_max_changed = false, restore = false;
+        boolean minMaxChanged = false, restore = false;
         if (image < min) {
             min = image;
-            min_max_changed = true;
+            minMaxChanged = true;
         } else if (image > max) {
             max = image;
-            min_max_changed = true;
+            minMaxChanged = true;
         }
         if (value[source] == min || value[source] == max || (value[source] == minPositive)) {
             restore = true;
         }
         value[source] = image;
         if (restore) {
-            min_max_changed = restore() || min_max_changed;
+            minMaxChanged = restore() || minMaxChanged;
         }
-        return min_max_changed;
+        return minMaxChanged;
     }
 
     /**
@@ -94,15 +82,10 @@ public class DArray implements DIntDoubleMap {
      * @param source the source value
      * @return the image value
      */
-//  public double getImage(int source){
-//    if(source<0 || source>=size) throw
-//      new ArrayIndexOutOfBoundsException(source);
-//    return value[source];
-//  }
     @Override
     public double getImage(int source) {
         if (source < 0) {
-            new ArrayIndexOutOfBoundsException(source);
+            throw new ArrayIndexOutOfBoundsException(source);
         }
         if (source >= size && size > 1) {
             return value[size - 1];
@@ -121,37 +104,37 @@ public class DArray implements DIntDoubleMap {
     @Override
     public boolean addImage(double image) {
         if (size >= value.length) {
-            int new_length = (int) (value.length * capacity_multiplier);
+            int newLength = (int) (value.length * capacityMultiplier);
-            if (!(new_length > value.length)) {
+            if (!(newLength > value.length)) {
-                new_length++;
+                newLength++;
             }
-            double[] new_val = new double[new_length];
+            double[] new_val = new double[newLength];
             System.arraycopy(value, 0, new_val, 0, value.length);
             value = new_val;
         }
-        boolean min_max_changed = false;
+        boolean minMaxChanged = false;
         if (size == 0) {
             min = image;
             max = image;
-            min_max_changed = true;
+            minMaxChanged = true;
             if (image > 0) {
                 minPositive = image;
             }
         } else {
             if ((image > 0) && ((image < minPositive) || (minPositive < 0))) {
                 minPositive = image;
-                min_max_changed = true;
+                minMaxChanged = true;
             }
             if (image > max) {
                 max = image;
-                min_max_changed = true;
+                minMaxChanged = true;
             } else if (image < min) {
                 min = image;
-                min_max_changed = true;
+                minMaxChanged = true;
             }
         }
         value[size++] = image;
-        return min_max_changed;
+        return minMaxChanged;
     }
 
     /**
@@ -200,7 +183,7 @@ public class DArray implements DIntDoubleMap {
     @Override
     public void reset() {
         size = 0;
-        value = new double[initial_capacity];
+        value = new double[initialCapacity];
     }
 
     /**
@@ -211,8 +194,7 @@ public class DArray implements DIntDoubleMap {
     @Override
     public double getMinImageValue() {
         if (size == 0) {
-            throw
+            throw new IllegalArgumentException("DArray is empty. No minimal value exists");
-                    new IllegalArgumentException("DArray is empty. No minimal value exists");
         }
         return min;
     }
@@ -225,8 +207,7 @@ public class DArray implements DIntDoubleMap {
     @Override
     public double getMinPositiveImageValue() {
         if (size == 0) {
-            throw
+            throw new IllegalArgumentException("DArray is empty. No minimal value exists");
-                    new IllegalArgumentException("DArray is empty. No minimal value exists");
         }
         return (minPositive < 0) ? max : minPositive;
     }
@@ -239,8 +220,7 @@ public class DArray implements DIntDoubleMap {
     @Override
     public double getMaxImageValue() {
         if (size == 0) {
-            throw
+            throw new IllegalArgumentException("DArray is empty. No maximal value exists");
-                    new IllegalArgumentException("DArray is empty. No maximal value exists");
         }
         return max;
     }

src/eva2/tools/chart2d/DBorder.java

@@ -1,14 +1,3 @@
-/**
- *  Filename: $RCSfile: DBorder.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
 package eva2.tools.chart2d;
 
 import java.awt.*;

src/eva2/tools/chart2d/DComponent.java

@@ -1,27 +1,7 @@
-/**
- *  Filename: $RCSfile: DComponent.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import java.awt.*;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 /**
  * <code>DComponent</code> is the mother of all objects which can be displayed
  * by a <code>DArea</code> object, even when it would be also enough to
@@ -133,7 +113,6 @@ public abstract class DComponent implements DElement {
      */
     @Override
     public void repaint() {
-        //System.out.println("DComponent.repaint()");
         if (parent != null) {
             parent.repaint(getRectangle());
         }
@@ -179,8 +158,4 @@ public abstract class DComponent implements DElement {
         return visible;
     }
 
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DContainer.java

@@ -1,28 +1,8 @@
-/**
- *  Filename: $RCSfile: DContainer.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import java.awt.*;
 import java.util.Vector;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 public class DContainer extends DComponent implements DParent {
     /**
      * the elements of the container and their keys ( Strings )
@@ -78,14 +58,12 @@ public class DContainer extends DComponent implements DParent {
         if (e instanceof DParent) {
             DParent he = (DParent) e, me = this;
             if (he == me) {
-                throw new
+                throw new IllegalArgumentException("Adding DParent to itself");
-                        IllegalArgumentException("Adding DParent to itself");
             }
             me = getDParent();
             while (me != null) {
                 if (he == me) {
-                    throw new
+                    throw new IllegalArgumentException("Adding DContainer's parent to itself");
-                            IllegalArgumentException("Adding DContainer's parent to itself");
                 }
                 if (me instanceof DElement) {
                     me = ((DElement) me).getDParent();
@@ -164,8 +142,6 @@ public class DContainer extends DComponent implements DParent {
         return (index < keys.size()) ? elements.get(index) : null;
     }
 
-// implementing DComponent:
-
     /**
      * method calls all currently visible DElements of the container to paint
      * themselves by the given DMeasures object
@@ -247,8 +223,4 @@ public class DContainer extends DComponent implements DParent {
         }
         return !old.equals(rectangle);
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DElement.java

@@ -1,27 +1,7 @@
-/**
- *  Filename: $RCSfile: DElement.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import java.awt.*;
 
-/*==========================================================================*
- * INTERFACE DECLARATION
- *==========================================================================*/
-
 /**
  * some useful methods for objects which should be paintable in a scaled area
  */
@@ -49,8 +29,4 @@ public interface DElement {
     void setDBorder(DBorder b);
 
     DBorder getDBorder();
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DFunction.java

@@ -50,8 +50,8 @@ public abstract class DFunction extends DComponent {
         Point last = null, next;
         for (int i = 0; i < int_w; i++) {
             double x_val = src_rect.x + i / (double) int_w * src_rect.width;
-            if (m.x_scale != null) {
+            if (m.xScale != null) {
-                x_val = m.x_scale.getImageOf(x_val);
+                x_val = m.xScale.getImageOf(x_val);
             }
             if (isDefinedAt(x_val)) {
                 next = m.getPoint(x_val, getImageOf(x_val));

src/eva2/tools/chart2d/DGrid.java

@@ -1,29 +1,9 @@
-/**
- *  Filename: $RCSfile: DGrid.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import eva2.tools.math.Mathematics;
 
 import java.awt.*;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 /**
  * this class paints a grid with certain line distances on a DParent
  */
@@ -31,7 +11,7 @@ public class DGrid extends DComponent {
     /**
      * the distances between the lines
      */
-    private double hor_dist, ver_dist;
+    private double horDist, verDist;
 
     private Color DEFAULT_COLOR = Color.lightGray;
 
@@ -39,15 +19,15 @@ public class DGrid extends DComponent {
      * constructor with the size and position of the grid and the line distances
      *
      * @param rectangle the rectangle around the grid
-     * @param hor_dist  the horizontal distance between the lines in D-coordinates,
+     * @param horDist   the horizontal distance between the lines in D-coordinates,
      *                  not in pixel coordinates!
-     * @param ver_dist  vertical distance between the lines in D-coordinates,
+     * @param verDist   vertical distance between the lines in D-coordinates,
      *                  not in pixel coordinates!
      */
-    public DGrid(DRectangle rectangle, double hor_dist, double ver_dist) {
+    public DGrid(DRectangle rectangle, double horDist, double verDist) {
         this.rectangle = rectangle;
-        this.hor_dist = hor_dist;
+        this.horDist = horDist;
-        this.ver_dist = ver_dist;
+        this.verDist = verDist;
         color = DEFAULT_COLOR;
     }
 
@@ -55,32 +35,31 @@ public class DGrid extends DComponent {
      * constructor with the size and position of the grid and the line distances
      *
      * @param rectangle the rectangle around the grid
-     * @param hor_dist  the horizontal distance between the lines in D-coordinates,
+     * @param horDist   the horizontal distance between the lines in D-coordinates,
      *                  not in pixel coordinates!
-     * @param ver_dist  the vertical distance between the lines in D-coordinates,
+     * @param verDist   the vertical distance between the lines in D-coordinates,
      *                  not in pixel coordinates!
      * @param color     the color of the grid
      *                  ( can also be set by setColor( java.awt.Color ) )
      */
-    public DGrid(DRectangle rectangle, double hor_dist, double ver_dist, Color color) {
+    public DGrid(DRectangle rectangle, double horDist, double verDist, Color color) {
         this.rectangle = rectangle;
-        this.hor_dist = hor_dist;
+        this.horDist = horDist;
-        this.ver_dist = ver_dist;
+        this.verDist = verDist;
         this.color = color;
     }
 
     public void setDistances(double hor, double ver) {
-        hor_dist = hor;
+        horDist = hor;
-        ver_dist = ver;
+        verDist = ver;
-//	  System.out.println("set new Grid distances " + this.toString());
     }
 
     public double getHorDist() {
-        return hor_dist;
+        return horDist;
     }
 
     public double getVerDist() {
-        return ver_dist;
+        return verDist;
     }
 
     /**
@@ -98,18 +77,12 @@ public class DGrid extends DComponent {
         DPoint p1, p2;
         DLine l;
 
-        minX = Mathematics.firstMultipleAbove(rectangle.getX(), hor_dist);
+        minX = Mathematics.firstMultipleAbove(rectangle.getX(), horDist);
-        minY = Mathematics.firstMultipleAbove(rectangle.getY(), ver_dist);
+        minY = Mathematics.firstMultipleAbove(rectangle.getY(), verDist);
-//    minX = (int)( rectangle.x / hor_dist );
-//    if( minX * hor_dist <= rectangle.x ) minX++;
-//    minX *= hor_dist;
-//    minY = (int)( rectangle.y / ver_dist );
-//    if( minY * ver_dist <= rectangle.y ) minY++;
-//    minY *= ver_dist;
 
         p1 = new DPoint(0, rectangle.getY());
         p2 = new DPoint(0, rectangle.getY() + rectangle.getHeight());
-        for (pos = minX; pos <= rectangle.getX() + rectangle.getWidth(); pos += hor_dist) {
+        for (pos = minX; pos <= rectangle.getX() + rectangle.getWidth(); pos += horDist) {
             p1.x = p2.x = pos;
             l = new DLine(p1, p2, color);
             l.paint(m);
@@ -122,22 +95,17 @@ public class DGrid extends DComponent {
             p1.y = p2.y = pos;
             l = new DLine(p1, p2, color);
             l.paint(m);
-            if (pos + ver_dist <= pos) {
+            if (pos + verDist <= pos) {
                 System.err.println("Overflow error in DGrid!");
                 pos *= 1.01;
             } else {
-                pos += ver_dist;
+                pos += verDist;
             }
-//      System.out.println("pos is " + pos + ", loop until " + rectangle.y + rectangle.height);
         }
     }
 
     @Override
     public String toString() {
-        return "chart2d.DGrid[ hor: " + hor_dist + ", ver: " + ver_dist + " ]";
+        return "chart2d.DGrid[ hor: " + horDist + ", ver: " + verDist + " ]";
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DIntDoubleMap.java

@@ -1,14 +1,5 @@
 package eva2.tools.chart2d;
 
-/**
- * Title:
- * Description:
- * Copyright:    Copyright (c) 2001
- * Company:
- * @author
- * @version 1.0
- */
-
 /**
  * This interface is used by DPointSet to store values as images of integer
  * values which can be displayed in a DArea. All modifications of the values can

src/eva2/tools/chart2d/DLine.java

@@ -1,27 +1,7 @@
-/**
- *  Filename: $RCSfile: DLine.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import java.awt.*;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 public class DLine extends DComponent {
     DPoint start, end;
 
@@ -78,8 +58,4 @@ public class DLine extends DComponent {
     public String toString() {
         return "DLine[(" + start.x + "," + start.y + ") --> (" + end.x + "," + end.y + ", color: " + color + "]";
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DMeasures.java

@@ -14,13 +14,12 @@ public class DMeasures implements Serializable {
      *
      */
     private static final long serialVersionUID = 243092480517044848L;
-    private boolean under_construction = false;
     // when in use for a DArea:
     Graphics g;
     // when in use for a ScaledBorder:
     ScaledBorder sb;
     // for both:
-    DFunction x_scale, y_scale;
+    DFunction xScale, yScale;
     Component comp;
     Insets insets;
 
@@ -55,11 +54,11 @@ public class DMeasures implements Serializable {
             return null;
         }
         try {
-            if (x_scale != null) {
+            if (xScale != null) {
-                x = x_scale.getSourceOf(x);
+                x = xScale.getSourceOf(x);
             }
-            if (y_scale != null) {
+            if (yScale != null) {
-                y = y_scale.getSourceOf(y);
+                y = yScale.getSourceOf(y);
             }
         } catch (IllegalArgumentException e) {
             return null;
@@ -93,11 +92,11 @@ public class DMeasures implements Serializable {
         dx = rect.x + rect.width * x / (double) dim.width;
         dy = rect.y + rect.height * (1 - y / (double) dim.height);
         try {
-            if (x_scale != null) {
+            if (xScale != null) {
-                dx = x_scale.getImageOf(dx);
+                dx = xScale.getImageOf(dx);
             }
-            if (y_scale != null) {
+            if (yScale != null) {
-                dy = y_scale.getImageOf(dy);
+                dy = yScale.getImageOf(dy);
             }
         } catch (IllegalArgumentException nde) {
             return null;
@@ -105,16 +104,6 @@ public class DMeasures implements Serializable {
         return new DPoint(dx, dy);
     }
 
-//  /**
-//   * returns the visible rectangle in D-coordinates of the shown component
-//   *
-//   * @return the visible rectangle
-//   */
-//  public DRectangle getDRectangle(){
-//    if( under_construction ) System.out.println("DMeasures.getDRectangle");
-//    if( sb != null ) return getImageOf( sb.src_rect );
-//    return ((DArea)comp).getDRectangle();
-//  }
 
     /**
      * Returns the visible rectangle in D-coordinates of the shown component as slim structure.
@@ -122,9 +111,8 @@ public class DMeasures implements Serializable {
      * @return the visible rectangle
      */
     public SlimRect getSlimRectangle() {
-//	    if( under_construction ) System.out.println("DMeasures.getDRectangle");
         if (sb != null) {
-            return getImageOf(sb.src_rect.x, sb.src_rect.y, sb.src_rect.width, sb.src_rect.height);
+            return getImageOf(sb.srcRect.x, sb.srcRect.y, sb.srcRect.width, sb.srcRect.height);
         }
         return ((DArea) comp).getSlimRectangle();
     }
@@ -138,9 +126,6 @@ public class DMeasures implements Serializable {
      * @return the Graphics object ( or null if no object was set )
      */
     public Graphics getGraphics() {
-        if (under_construction) {
-            System.out.println("DMeasures.getGraphics");
-        }
         if (g != null) {
             Dimension d = comp.getSize();
             Insets insets = getInsets();
@@ -156,9 +141,6 @@ public class DMeasures implements Serializable {
      * used by DArea to set a new Graphics object
      */
     void setGraphics(Graphics g) {
-        if (under_construction) {
-            System.out.println("DMeasures.setGraphics");
-        }
         this.g = g;
     }
 
@@ -170,8 +152,8 @@ public class DMeasures implements Serializable {
     void update(Component c, Insets insets) {
         this.comp = c;
         this.insets = insets;
-        x_scale = sb.x_scale;
+        xScale = sb.xScale;
-        y_scale = sb.y_scale;
+        yScale = sb.yScale;
     }
 
     private Dimension getInner() {
@@ -182,60 +164,28 @@ public class DMeasures implements Serializable {
         return d;
     }
 
-//  /**
-//   * method returns the image rectangle of the given rectangle
-//   * they differ if there are scale functions selected which are not the identity
-//   * if the given rectangle does not belong to the defintion area of the scale
-//   * functions, the method returns <code>null</code>
-//   *
-//   * @param rect the source rectangle
-//   * @return the source of it
-//   */
-//  DRectangle getImageOf( DRectangle rect ){
-//    if( under_construction ) System.out.println("DMeasures.getImageOf: "+rect);
-//    if( x_scale == null && y_scale == null ) return rect;
-//    if( rect.isEmpty() ) return (DRectangle)rect.clone();
-//    DPoint p1 = new DPoint( rect.x, rect.y ),
-//           p2 = new DPoint( rect.x + rect.width, rect.y + rect.height );
-//    try{
-//      if( x_scale != null ){
-//        p1.x = x_scale.getImageOf( p1.x );
-//        p2.x = x_scale.getImageOf( p2.x );
-//      }
-//      if( y_scale != null ){
-//        p1.y = y_scale.getImageOf( p1.y );
-//        p2.y = y_scale.getImageOf( p2.y );
-//      }
-//    }
-//    catch( IllegalArgumentException nde ){ return null; }
-//    return new DRectangle( p1.x, p1.y, p2.x - p1.x, p2.y - p1.y );
-//  }
-
     /**
      * method returns the image rectangle of the given rectangle
      * they differ if there are scale functions selected which are not the identity
      * if the given rectangle does not belong to the definition area of the scale
      * functions, the method returns <code>null</code>
      *
-     * @param rect the source rectangle
      * @return the source of it
      */
     SlimRect getImageOf(double xpos, double ypos, double width, double height) {
-//    if( under_construction ) System.out.println("DMeasures.getImageOf: "+rect);
+        if (xScale == null && yScale == null) {
-
-        if (x_scale == null && y_scale == null) {
             return new SlimRect(xpos, ypos, width, height);
         }
         double x1 = xpos, y1 = ypos, x2 = xpos + width, y2 = ypos + height;
 
         try {
-            if (x_scale != null) {
+            if (xScale != null) {
-                x1 = x_scale.getImageOf(x1);
+                x1 = xScale.getImageOf(x1);
-                x2 = x_scale.getImageOf(x2);
+                x2 = xScale.getImageOf(x2);
             }
-            if (y_scale != null) {
+            if (yScale != null) {
-                y1 = y_scale.getImageOf(y1);
+                y1 = yScale.getImageOf(y1);
-                y2 = y_scale.getImageOf(y2);
+                y2 = yScale.getImageOf(y2);
             }
         } catch (IllegalArgumentException nde) {
             return null;
@@ -247,47 +197,6 @@ public class DMeasures implements Serializable {
         return getImageOf(srect.x, srect.y, srect.width, srect.height);
     }
 
-//  /**
-//   * method returns the source rectangle of the given rectangle
-//   * they differ if there are scale functions selected which are not the identity
-//   * if the given rectangle does not belong to the image area of the scale
-//   * functions, the method returns <code>null</code>
-//   *
-//   * @param rect the image rectangle
-//   * @return the source of it
-//   */
-//  DRectangle getSourceOf( DRectangle rect ){
-//    if( under_construction ) System.out.println("DMeasures.getSourceOf: "+rect);
-//    if( !getDRectangle().contains( rect ) ) {
-////    	System.out.println("case not contains");
-//    	return null;
-//    	//throw new IllegalArgumentException("The rectangle lies not in the currently painted rectangle");
-//    }
-//      
-//    if( x_scale == null && y_scale == null ) {
-////    	System.out.println("Case scale null");
-//    	return rect;
-//    }
-//    if( rect.isEmpty() ) {
-////    	System.out.println("Case isEmpty");
-//    	return (DRectangle)rect.clone();
-//    }
-//    DPoint p1 = new DPoint( rect.x, rect.y ),
-//           p2 = new DPoint( rect.x + rect.width, rect.y + rect.height );
-//    try{
-//      if( x_scale != null ){
-//        p1.x = x_scale.getSourceOf( p1.x );
-//        p2.x = x_scale.getSourceOf( p2.x );
-//      }
-//      if( y_scale != null ){
-//        p1.y = y_scale.getSourceOf( p1.y );
-//        p2.y = y_scale.getSourceOf( p2.y );
-//      }
-//    }
-//    catch( IllegalArgumentException nde ){ return null; }
-//    return new DRectangle( p1.x, p1.y, p2.x - p1.x, p2.y - p1.y );
-//  }
-
     /**
      * method returns the source rectangle of the given rectangle
      * they differ if there are scale functions selected which are not the identity
@@ -300,27 +209,23 @@ public class DMeasures implements Serializable {
      * @return the source of it
      */
     SlimRect getSourceOf(double x, double y, double width, double height) {
-//	    if( under_construction ) System.out.println("DMeasures.getSourceOf: "+rect);
         if (!getSlimRectangle().contains(x, y, width, height)) {
-//	    	System.out.println("case not contains");
             return null;
-            //throw new IllegalArgumentException("The rectangle lies not in the currently painted rectangle");
         }
 
-        if (x_scale == null && y_scale == null) {
+        if (xScale == null && yScale == null) {
-//	    	System.out.println("Case scale null");
             return new SlimRect(x, y, width, height);
         }
 
         double x1 = x, y1 = y, x2 = x + width, y2 = y + height;
         try {
-            if (x_scale != null) {
+            if (xScale != null) {
-                x1 = x_scale.getSourceOf(x1);
+                x1 = xScale.getSourceOf(x1);
-                x2 = x_scale.getSourceOf(x2);
+                x2 = xScale.getSourceOf(x2);
             }
-            if (y_scale != null) {
+            if (yScale != null) {
-                y1 = y_scale.getSourceOf(y1);
+                y1 = yScale.getSourceOf(y1);
-                y2 = y_scale.getSourceOf(y2);
+                y2 = yScale.getSourceOf(y2);
             }
         } catch (IllegalArgumentException nde) {
             return null;
@@ -329,15 +234,6 @@ public class DMeasures implements Serializable {
         }
         return new SlimRect(x1, y1, x2 - x1, y2 - y1);
     }
-//  SlimRect getSourceOf( double xpos, double ypos, double width, double height){
-//    if( !getSlimRectangle().contains( xpos, ypos, width, height ) ) {
-//    	System.err.println("The rectangle lies not in the currently painted rectangle");
-//    	return null;
-//    	//throw new IllegalArgumentException("The rectangle lies not in the currently painted rectangle");
-//    }
-//     // MK: this now strangely does the same as getImageOf
-//    return getImageOf(xpos, ypos, width, height);
-//  }
 
     SlimRect getSourceOf(SlimRect srect) {
         return getSourceOf(srect.x, srect.y, srect.width, srect.height);
@@ -349,8 +245,4 @@ public class DMeasures implements Serializable {
         }
         return ((DArea) comp).getInsets();
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DParent.java

@@ -1,22 +1,5 @@
-/**
- *  Filename: $RCSfile: DParent.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:41 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-
-/*==========================================================================*
- * INTERFACE DECLARATION
- *==========================================================================*/
-
 public interface DParent {
     void addDElement(DElement e);
 
@@ -31,8 +14,4 @@ public interface DParent {
     void addDBorder(DBorder b);
 
     void restoreBorder();
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DPoint.java

@@ -1,27 +1,7 @@
-/**
- *  Filename: $RCSfile: DPoint.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:42 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import java.awt.*;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 public class DPoint extends DComponent {
     public double x, y;
     public String label;
@@ -104,8 +84,4 @@ public class DPoint extends DComponent {
         text += "x: " + x + ", y: " + y + ", color: " + color + "]";
         return text;
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/DPointIcon.java

@@ -1,15 +1,5 @@
 package eva2.tools.chart2d;
 
-/**
- *  Filename: $RCSfile: DPointIcon.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 import java.awt.*;
 
 /**

src/eva2/tools/chart2d/DPointSet.java

@@ -1,15 +1,5 @@
-/**
- * Filename: $RCSfile: DPointSet.java,v $ Purpose: Language: Java Compiler: JDK 1.3 Authors: Fabian
- * Hennecke Version: $Revision: 1.1.1.1 $ $Date: 2003/07/03 14:59:42 $ $Author: ulmerh $ Copyright
- * (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
 package eva2.tools.chart2d;
 
-/*
- * ==========================================================================* IMPORTS
- *==========================================================================
- */
-
 import eva2.tools.math.Mathematics;
 
 import java.awt.*;
@@ -19,11 +9,6 @@ public class DPointSet extends DComponent {
 
     protected DPointIcon icon = null;
 
-    /*
-     * -------------------------------------------------------------------------* private member
-     * variables
-   *-------------------------------------------------------------------------
-     */
     protected DIntDoubleMap x, y;
     protected boolean connected;
     protected Stroke stroke = new BasicStroke();
@@ -48,8 +33,7 @@ public class DPointSet extends DComponent {
 
     public DPointSet(DIntDoubleMap x_values, DIntDoubleMap y_values) {
         if (x_values.getSize() != y_values.getSize()) {
-            throw new IllegalArgumentException(
+            throw new IllegalArgumentException("The number of x-values has to be the same than the number of y-values");
-                    "The number of x-values has to be the same than the number of y-values");
         }
         x = x_values;
         y = y_values;
@@ -57,10 +41,6 @@ public class DPointSet extends DComponent {
         setDBorder(new DBorder(1, 1, 1, 1));
     }
 
-    /*
-     * -------------------------------------------------------------------------* public methods
-   *-------------------------------------------------------------------------
-     */
     @Override
     public void paint(DMeasures m) {
         Graphics2D g = (Graphics2D) m.getGraphics();
@@ -298,16 +278,6 @@ public class DPointSet extends DComponent {
         }
     }
 
-//  public int 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/tools/chart2d/DRectangle.java

@@ -1,29 +1,9 @@
-/**
- *  Filename: $RCSfile: DRectangle.java,v $
- *  Purpose:
- *  Language: Java
- *  Compiler: JDK 1.3
- *  Authors:  Fabian Hennecke
- *  Version:  $Revision: 1.1.1.1 $
- *            $Date: 2003/07/03 14:59:42 $
- *            $Author: ulmerh $
- *  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
- */
-
 package eva2.tools.chart2d;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 import eva2.tools.EVAERROR;
 
 import java.awt.*;
 
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 public class DRectangle extends DComponent {
     private double x, y;
     private double width, height;
@@ -356,8 +336,4 @@ public class DRectangle extends DComponent {
     public boolean isEmpty() {
         return status == EMPTY;
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

src/eva2/tools/chart2d/ScaledBorder.java

@@ -33,23 +33,23 @@ public class ScaledBorder implements Border {
     /**
      * distance between the x-values in digits
      */
-    int x_value2value = 2;
+    int xValue2value = 2;
 
     /**
      * distance between y-label and y-values in digit width
      */
-    int y_label2values = 1;
+    int yLabel2values = 1;
 
     /**
      * distance between y-values and y-axis markers in parts of the digit width
      */
-    int y_values2marker = 2;
+    int yValues2marker = 2;
 
     /**
      * distance between values and arrows in pixels
      */
-    int x_values2arrow = 10,
+    int xValues2arrow = 10,
-            y_values2arrow = 10;
+            yValues2arrow = 10;
 
     /**
      * distance between arrows and outer border
@@ -59,19 +59,19 @@ public class ScaledBorder implements Border {
     /**
      * distance between labels and the border in pixels
      */
-    public int x_label2border = 6,
+    public int xLabel2border = 6,
-            y_label2border = 6;
+            yLabel2border = 6;
 
     /**
      * the size of the source rectangle
      * that means before the values are mdified by scale functions
      */
-    SlimRect src_rect = null;
+    SlimRect srcRect = null;
 
     /**
      * the minimal increment of the scales
      */
-    public double minimal_increment;
+    public double minimalIncrement;
 
     /**
      * the  displayed labels
@@ -86,26 +86,26 @@ public class ScaledBorder implements Border {
     /**
      * the border which is shown around the scaled border
      */
-    Border outer_border;
+    Border outerBorder;
 
     /**
      * flag if the outer border should be displayed
      */
-    boolean show_outer_border = true;
+    boolean showOuterBorder = true;
 
     /**
      * scale functions if, for example, an logarithmic function is needed instead
      * of a linear.
      */
-    public DFunction x_scale, y_scale;
+    public DFunction xScale, yScale;
 
     /**
      * formatters of the x- and y-axis numbers
      *
      * @see java.text.NumberFormat
      */
-    private NumberFormat format_x = new DecimalFormat(),
+    private NumberFormat formatX = new DecimalFormat(),
-            format_y = new DecimalFormat();
+            formatY = new DecimalFormat();
 
     /**
      * Possible patterns for the number formats used by a border.
@@ -118,13 +118,13 @@ public class ScaledBorder implements Border {
     private int nextYPattern = 1;
     private int nextXPattern = 1;
 
-    private double src_dX = -1, src_dY = -1;
+    private double srcDX = -1, srcDY = -1;
 
-    private boolean do_refresh,
+    private boolean doRefresh,
-            auto_scale_x = true,
+            autoScaleX = true,
-            auto_scale_y = true;
+            autoScaleY = true;
 
-    private Insets old_insets;
+    private Insets oldInsets;
 
     private DMeasures m;
 
@@ -148,7 +148,7 @@ public class ScaledBorder implements Border {
      * surrounded by the specified <code>Border<code/>
      */
     public ScaledBorder(Border outer) {
-        outer_border = outer;
+        outerBorder = outer;
         m = new DMeasures(this);
     }
 
@@ -157,7 +157,7 @@ public class ScaledBorder implements Border {
      * x-values by itself
      */
     public void setAutoScaleX() {
-        auto_scale_x = true;
+        autoScaleX = true;
     }
 
     /**
@@ -165,7 +165,7 @@ public class ScaledBorder implements Border {
      * y-values by itself
      */
     public void setAutoScaleY() {
-        auto_scale_y = true;
+        autoScaleY = true;
     }
 
     /**
@@ -176,8 +176,8 @@ public class ScaledBorder implements Border {
      *      and the source values
      */
     public void setSrcdX(double dX) {
-        auto_scale_x = false;
+        autoScaleX = false;
-        src_dX = dX;
+        srcDX = dX;
     }
 
     /**
@@ -188,8 +188,8 @@ public class ScaledBorder implements Border {
      *      and the source values
      */
     public void setSrcdY(double dY) {
-        auto_scale_y = false;
+        autoScaleY = false;
-        src_dY = dY;
+        srcDY = dY;
     }
 
     /**
@@ -217,61 +217,61 @@ public class ScaledBorder implements Border {
         if (background == null) {
             background = c.getBackground();
         }
-        Color old_color = g.getColor();
+        Color oldColor = g.getColor();
         g.setColor(background);
         g.fillRect(x, y, width, height);
-        g.setColor(old_color);
+        g.setColor(oldColor);
 
-        Insets outer_insets = new Insets(0, 0, 0, 0);// insets of the outer border
+        Insets outerInsets = new Insets(0, 0, 0, 0);// insets of the outer border
-        if (show_outer_border) {
+        if (showOuterBorder) {
-            outer_border.paintBorder(c, g, x, y, width, height);
+            outerBorder.paintBorder(c, g, x, y, width, height);
-            outer_insets = outer_border.getBorderInsets(c);
+            outerInsets = outerBorder.getBorderInsets(c);
         }
 
-        do_refresh = true;
+        doRefresh = true;
-        Insets inner_insets = getBorderInsets(c);
+        Insets innerInsets = getBorderInsets(c);
 
         Dimension d = c.getSize(),
-                cd = new Dimension(d.width - inner_insets.left - inner_insets.right,
+                cd = new Dimension(d.width - innerInsets.left - innerInsets.right,
-                        d.height - inner_insets.top - inner_insets.bottom);
+                        d.height - innerInsets.top - innerInsets.bottom);
 
         FontMetrics fm = g.getFontMetrics();
         int fontAsc = fm.getAscent();
-        do_refresh = false;
+        doRefresh = false;
 
-        m.update(c, inner_insets);
+        m.update(c, innerInsets);
 
         // axes
         g.setColor(foreground);
-        g.drawLine(inner_insets.left, inner_insets.top,
+        g.drawLine(innerInsets.left, innerInsets.top,
-                inner_insets.left, inner_insets.top + cd.height);
+                innerInsets.left, innerInsets.top + cd.height);
-        g.drawLine(inner_insets.left, inner_insets.top + cd.height,
+        g.drawLine(innerInsets.left, innerInsets.top + cd.height,
-                inner_insets.left + cd.width, inner_insets.top + cd.height);
+                innerInsets.left + cd.width, innerInsets.top + cd.height);
 
         if (showArrows) {
-            g.drawLine(inner_insets.left, inner_insets.top,
+            g.drawLine(innerInsets.left, innerInsets.top,
-                    inner_insets.left, inner_insets.top - y_values2arrow);
+                    innerInsets.left, innerInsets.top - yValues2arrow);
-            g.drawLine(inner_insets.left - markerLength, inner_insets.top - y_values2arrow,
+            g.drawLine(innerInsets.left - markerLength, innerInsets.top - yValues2arrow,
-                    inner_insets.left, inner_insets.top - y_values2arrow - arrowLength);
+                    innerInsets.left, innerInsets.top - yValues2arrow - arrowLength);
-            g.drawLine(inner_insets.left + markerLength, inner_insets.top - y_values2arrow,
+            g.drawLine(innerInsets.left + markerLength, innerInsets.top - yValues2arrow,
-                    inner_insets.left, inner_insets.top - y_values2arrow - arrowLength);
+                    innerInsets.left, innerInsets.top - yValues2arrow - arrowLength);
-            g.drawLine(inner_insets.left - markerLength, inner_insets.top - y_values2arrow,
+            g.drawLine(innerInsets.left - markerLength, innerInsets.top - yValues2arrow,
-                    inner_insets.left + markerLength, inner_insets.top - y_values2arrow);
+                    innerInsets.left + markerLength, innerInsets.top - yValues2arrow);
 
-            g.drawLine(inner_insets.left + cd.width, inner_insets.top + cd.height,
+            g.drawLine(innerInsets.left + cd.width, innerInsets.top + cd.height,
-                    inner_insets.left + cd.width + x_values2arrow, inner_insets.top + cd.height);
+                    innerInsets.left + cd.width + xValues2arrow, innerInsets.top + cd.height);
-            g.drawLine(inner_insets.left + cd.width + x_values2arrow,
+            g.drawLine(innerInsets.left + cd.width + xValues2arrow,
-                    inner_insets.top + cd.height - markerLength,
+                    innerInsets.top + cd.height - markerLength,
-                    inner_insets.left + cd.width + x_values2arrow + arrowLength,
+                    innerInsets.left + cd.width + xValues2arrow + arrowLength,
-                    inner_insets.top + cd.height);
+                    innerInsets.top + cd.height);
-            g.drawLine(inner_insets.left + cd.width + x_values2arrow,
+            g.drawLine(innerInsets.left + cd.width + xValues2arrow,
-                    inner_insets.top + cd.height + markerLength,
+                    innerInsets.top + cd.height + markerLength,
-                    inner_insets.left + cd.width + x_values2arrow + arrowLength,
+                    innerInsets.left + cd.width + xValues2arrow + arrowLength,
-                    inner_insets.top + cd.height);
+                    innerInsets.top + cd.height);
-            g.drawLine(inner_insets.left + cd.width + x_values2arrow,
+            g.drawLine(innerInsets.left + cd.width + xValues2arrow,
-                    inner_insets.top + cd.height - markerLength,
+                    innerInsets.top + cd.height - markerLength,
-                    inner_insets.left + cd.width + x_values2arrow,
+                    innerInsets.left + cd.width + xValues2arrow,
-                    inner_insets.top + cd.height + markerLength);
+                    innerInsets.top + cd.height + markerLength);
         }
 
         if (yLabel != null) {
@@ -279,31 +279,31 @@ public class ScaledBorder implements Border {
             AffineTransform T = new AffineTransform(0, 1, 1, 0, 0, 0);
             Font old = g.getFont(), f = old.deriveFont(T);
             g.setFont(f);
-            g.drawString(yLabel, y_label2border + fm.getAscent(), inner_insets.top + (cd.height + yld.height) / 2);
+            g.drawString(yLabel, yLabel2border + fm.getAscent(), innerInsets.top + (cd.height + yld.height) / 2);
             g.setFont(old);
         }
 
         if (xLabel != null) {
             g.drawString(
-                    xLabel, inner_insets.left + (cd.width - fm.stringWidth(xLabel)) / 2,
+                    xLabel, innerInsets.left + (cd.width - fm.stringWidth(xLabel)) / 2,
-                    d.height - outer_insets.bottom - x_label2border - fm.getDescent());
+                    d.height - outerInsets.bottom - xLabel2border - fm.getDescent());
         }
 
-        if (src_rect.x == 0 && src_rect.y == 0) {
+        if (srcRect.x == 0 && srcRect.y == 0) {
-            int v2m = fm.stringWidth("0") / y_values2marker;
+            int v2m = fm.stringWidth("0") / yValues2marker;
-            g.drawString("0", inner_insets.left - fm.stringWidth("0") - v2m - markerLength,
+            g.drawString("0", innerInsets.left - fm.stringWidth("0") - v2m - markerLength,
-                    inner_insets.top + cd.height + fontAsc);
+                    innerInsets.top + cd.height + fontAsc);
-            g.drawLine(inner_insets.left, inner_insets.top + cd.height + fm.getAscent(),
+            g.drawLine(innerInsets.left, innerInsets.top + cd.height + fm.getAscent(),
-                    inner_insets.left, inner_insets.top + cd.height);
+                    innerInsets.left, innerInsets.top + cd.height);
-            g.drawLine(inner_insets.left, inner_insets.top + cd.height,
+            g.drawLine(innerInsets.left, innerInsets.top + cd.height,
-                    inner_insets.left - fm.stringWidth("0") - v2m - markerLength,
+                    innerInsets.left - fm.stringWidth("0") - v2m - markerLength,
-                    inner_insets.top + cd.height);
+                    innerInsets.top + cd.height);
         }
 
-        drawYValues(g, inner_insets);
+        drawYValues(g, innerInsets);
-        drawXValues(g, inner_insets, cd);
+        drawXValues(g, innerInsets, cd);
 
-        g.setColor(old_color);
+        g.setColor(oldColor);
     }
 
     /**
@@ -314,24 +314,24 @@ public class ScaledBorder implements Border {
      */
     private void drawYValues(Graphics g, Insets insets) {
         FontMetrics fm = g.getFontMetrics();
-        int fontAsc = fm.getAscent(), v2m = fm.stringWidth("0") / y_values2marker;
+        int fontAsc = fm.getAscent(), v2m = fm.stringWidth("0") / yValues2marker;
 
-        double startVal = Mathematics.firstMultipleAbove(src_rect.y, src_dY);
+        double startVal = Mathematics.firstMultipleAbove(srcRect.y, srcDY);
 
-        double v, scaledV, minx = src_rect.x;
+        double v, scaledV, minx = srcRect.x;
-        if (x_scale != null) {
+        if (xScale != null) {
-            minx = x_scale.getImageOf(minx);
+            minx = xScale.getImageOf(minx);
         }
         v = startVal;
-        while (v <= src_rect.y + src_rect.height) {
+        while (v <= srcRect.y + srcRect.height) {
-            if (y_scale != null) {
+            if (yScale != null) {
-                scaledV = y_scale.getImageOf(v);
+                scaledV = yScale.getImageOf(v);
             } else {
                 scaledV = v;
             }
-            String text = format_y.format(scaledV);
+            String text = formatY.format(scaledV);
             try {
-                scaledV = format_y.parse(text).doubleValue();
+                scaledV = formatY.parse(text).doubleValue();
             } catch (java.text.ParseException ex) {
             }
             Point p = m.getPoint(minx, scaledV);
@@ -341,11 +341,10 @@ public class ScaledBorder implements Border {
                         p.y + fontAsc / 2);
                 g.drawLine(insets.left - markerLength, p.y, insets.left, p.y);
             }
-            if (v + src_dY <= v) {
+            if (v + srcDY <= v) {
-//			  System.err.println("Overflow error B in ScaledBorder! v,src_dY:" + v + ", " + src_dY);
                 v *= 1.01;
             }
-            v += src_dY;
+            v += srcDY;
         }
     }
 
@@ -354,82 +353,82 @@ public class ScaledBorder implements Border {
     }
 
     public double getSrcdY(int fontMetricsHeight, int componentHeight) {
-        if ((!do_refresh && src_dY != -1) || !auto_scale_y) {
+        if ((!doRefresh && srcDY != -1) || !autoScaleY) {
-            return src_dY;
+            return srcDY;
         }
         int max = componentHeight / fontMetricsHeight;
-        if (Double.isInfinite(src_rect.height) || Double.isInfinite(src_rect.width)) {
+        if (Double.isInfinite(srcRect.height) || Double.isInfinite(srcRect.width)) {
             System.err.println("Error, infinite value in ScaledBorder:getSrcdY !!");
         }
-        double minsrc_dY = 2 * src_rect.height / (double) max; // die 2 einfach mal so eingesetzt   <--------------------------
+        double minsrc_dY = 2 * srcRect.height / (double) max; // die 2 einfach mal so eingesetzt   <--------------------------
-        src_dY = aBitBigger(minsrc_dY);
+        srcDY = aBitBigger(minsrc_dY);
-        if (src_dY < minimal_increment) {
+        if (srcDY < minimalIncrement) {
-            src_dY = minimal_increment;
+            srcDY = minimalIncrement;
         }
-        return src_dY;
+        return srcDY;
     }
 
     private void drawXValues(Graphics g, Insets insets, Dimension cd) {
         FontMetrics fm = g.getFontMetrics();
-        double mx = cd.width / src_rect.width;
+        double mx = cd.width / srcRect.width;
         int n, labelX,
-                xnull = insets.left + (int) (-src_rect.x * mx);
+                xnull = insets.left + (int) (-srcRect.x * mx);
 
-        n = (int) (src_rect.x / src_dX);
+        n = (int) (srcRect.x / srcDX);
-        if (n * src_dX < src_rect.x || (src_rect.x == 0 && src_rect.y == 0)) {
+        if (n * srcDX < srcRect.x || (srcRect.x == 0 && srcRect.y == 0)) {
             n++;
         }
 
         int fontAsc = fm.getAscent(), xLineY = insets.top + cd.height;
-        labelX = xnull + (int) (n * src_dX * mx);
+        labelX = xnull + (int) (n * srcDX * mx);
-        while (n * src_dX <= src_rect.x + src_rect.width) {
+        while (n * srcDX <= srcRect.x + srcRect.width) {
-            double v = n * src_dX;
+            double v = n * srcDX;
-            if (x_scale != null) {
+            if (xScale != null) {
-                v = x_scale.getImageOf(v);
+                v = xScale.getImageOf(v);
             }
-            String text = format_x.format(v);
+            String text = formatX.format(v);
             try {
-                v = format_x.parse(text).doubleValue();
+                v = formatX.parse(text).doubleValue();
             } catch (java.text.ParseException ex) {
             }
             int strW = fm.stringWidth(text);
             g.drawString(text, labelX - strW / 2, xLineY + fontAsc);
             g.drawLine(labelX, xLineY, labelX, xLineY + markerLength);
             n++;
-            labelX = xnull + (int) (n * src_dX * mx);
+            labelX = xnull + (int) (n * srcDX * mx);
         }
     }
 
     public double getSrcdX(FontMetrics fm, Dimension cd) {
-        if ((!do_refresh && src_dX != -1) || !auto_scale_x) {
+        if ((!doRefresh && srcDX != -1) || !autoScaleX) {
-            return src_dX;
+            return srcDX;
         }
         int digit_width = fm.stringWidth("0"),
-                max = cd.width / (digit_width * (x_value2value + 1));
+                max = cd.width / (digit_width * (xValue2value + 1));
-        src_dX = src_rect.width / (double) max;
+        srcDX = srcRect.width / (double) max;
         int n, labelX, olsrc_dX;
 
         boolean ok = false;
         while (!ok) {
-            src_dX = aBitBigger(src_dX);
+            srcDX = aBitBigger(srcDX);
 
-            n = (int) (src_rect.x / src_dX);
+            n = (int) (srcRect.x / srcDX);
-            if (n * src_dX < src_rect.x) {
+            if (n * srcDX < srcRect.x) {
                 n++;
             }
 
             olsrc_dX = 0;
 
             boolean suits = true, first = true;
-            while (suits && n * src_dX <= src_rect.x + src_rect.width) {
+            while (suits && n * srcDX <= srcRect.x + srcRect.width) {
-                double v = n * src_dX;
+                double v = n * srcDX;
-                if (x_scale != null) {
+                if (xScale != null) {
-                    v = x_scale.getImageOf(v);
+                    v = xScale.getImageOf(v);
                 }
-                String text = format_x.format(v);
+                String text = formatX.format(v);
                 int strW = fm.stringWidth(text);
-                labelX = (int) (((n * src_dX - src_rect.x) / src_rect.width) * cd.width) - strW / 2;
+                labelX = (int) (((n * srcDX - srcRect.x) / srcRect.width) * cd.width) - strW / 2;
-                if (!first && labelX <= olsrc_dX + digit_width * x_value2value) {
+                if (!first && labelX <= olsrc_dX + digit_width * xValue2value) {
                     suits = false;
                 } else {
                     olsrc_dX = labelX + strW;
@@ -439,10 +438,10 @@ public class ScaledBorder implements Border {
             }
             ok = suits;
         }
-        if (src_dX < minimal_increment) {
+        if (srcDX < minimalIncrement) {
-            src_dX = minimal_increment;
+            srcDX = minimalIncrement;
         }
-        return src_dX;
+        return srcDX;
     }
 
     /**
@@ -484,7 +483,7 @@ public class ScaledBorder implements Border {
 
     @Override
     public boolean isBorderOpaque() {
-        return outer_border.isBorderOpaque();
+        return outerBorder.isBorderOpaque();
     }
 
     /**
@@ -545,13 +544,12 @@ public class ScaledBorder implements Border {
      *
      * @param bXorY
      * @param pattern
-     * @see #java.text.DecimalFormat.applyPattern
      */
     public void applyPattern(boolean bXorY, String pattern) {
         if (bXorY) {
-            ((java.text.DecimalFormat) format_x).applyPattern(pattern);
+            ((java.text.DecimalFormat) formatX).applyPattern(pattern);
         } else {
-            ((java.text.DecimalFormat) format_y).applyPattern(pattern);
+            ((java.text.DecimalFormat) formatY).applyPattern(pattern);
         }
     }
 
@@ -562,15 +560,15 @@ public class ScaledBorder implements Border {
      */
     @Override
     public Insets getBorderInsets(Component c) {
-        if (!do_refresh && old_insets != null) {
+        if (!doRefresh && oldInsets != null) {
-            return old_insets;
+            return oldInsets;
         }
 
         Graphics g = c.getGraphics();
 
         Insets insets = new Insets(0, 0, 0, 0);
-        if (show_outer_border) {
+        if (showOuterBorder) {
-            insets = outer_border.getBorderInsets(c);
+            insets = outerBorder.getBorderInsets(c);
         }
 
         if (g == null) {
@@ -584,76 +582,76 @@ public class ScaledBorder implements Border {
         if (c instanceof DArea) {
             DArea area = (DArea) c;
             DMeasures m = area.getDMeasures();
-            src_rect = m.getSourceOf(area.getSlimRectangle());
+            srcRect = m.getSourceOf(area.getSlimRectangle());
-            x_scale = area.getDMeasures().x_scale;
+            xScale = area.getDMeasures().xScale;
-            y_scale = area.getDMeasures().y_scale;
+            yScale = area.getDMeasures().yScale;
         }
 
         // left:
         if (yLabel != null) {
             insets.left += fm.getAscent() + fm.getDescent();
         }
-        insets.left += y_label2values * digit_width;
+        insets.left += yLabel2values * digit_width;
         getSrcdY(fm, c.getSize());
         double start, n, inc;
         int maxWidth = 0;
-        start = src_dY * (int) (src_rect.y / src_dY);
+        start = srcDY * (int) (srcRect.y / srcDY);
         n = start;
-        if (n < src_rect.y) {
+        if (n < srcRect.y) {
-            n += src_dY;
+            n += srcDY;
         }
 
-        if (((src_rect.y + src_rect.height) - start) / src_dY > 20) {
+        if (((srcRect.y + srcRect.height) - start) / srcDY > 20) {
-            inc = ((src_rect.y + src_rect.height) - start) / 20.;
+            inc = ((srcRect.y + srcRect.height) - start) / 20.;
         } else {
-            inc = src_dY;
+            inc = srcDY;
         }
         if ((n + inc) == n) {
             System.err.println("Warning, too small increase step size!");
         }
-        for (; n <= src_rect.y + src_rect.height; n += inc) {
+        for (; n <= srcRect.y + srcRect.height; n += inc) {
             // TODO here might be a bug for mean values
             double v = n;
-            if (y_scale != null) {
+            if (yScale != null) {
-                v = y_scale.getImageOf(v);
+                v = yScale.getImageOf(v);
             }
-            int w = fm.stringWidth(format_y.format(v));
+            int w = fm.stringWidth(formatY.format(v));
             if (w > maxWidth) {
                 maxWidth = w;
             }
-            // avoid nearly endless loop for large src_rect.y value and small src_dY
+            // avoid nearly endless loop for large srcRect.y value and small srcDY
         }
 
-        insets.left += 1 + y_label2border + maxWidth + digit_width / y_values2marker + markerLength;
+        insets.left += 1 + yLabel2border + maxWidth + digit_width / yValues2marker + markerLength;
 
         // bottom:
-        insets.bottom += 1 + fontHeight + x_label2border;
+        insets.bottom += 1 + fontHeight + xLabel2border;
         if (xLabel != null) {
             insets.bottom += fontHeight;
         }
 
         // top:
         if (showArrows) {
-            insets.top += y_values2arrow + arrowLength;
+            insets.top += yValues2arrow + arrowLength;
         }
         insets.top += axis2border;
 
         // right:
         if (showArrows) {
-            insets.right += x_values2arrow + arrowLength;
+            insets.right += xValues2arrow + arrowLength;
         }
         insets.right += axis2border;
         getSrcdX(fm, c.getSize());
-        int k = (int) (src_rect.x + src_rect.width / src_dX);
+        int k = (int) (srcRect.x + srcRect.width / srcDX);
         if (k < 0) {
             k++;
         }
-        int w = fm.stringWidth(format_x.format(k * src_dX));
+        int w = fm.stringWidth(formatX.format(k * srcDX));
         if (w / 2 > insets.right) {
             insets.right = w / 2;
         }
 
-        old_insets = insets;
+        oldInsets = insets;
         return insets;
     }
 }

src/eva2/tools/chart2d/SlimRect.java

@@ -3,8 +3,6 @@ package eva2.tools.chart2d;
 /**
  * Encapsulates a slim rectangle structure with x, y, width and height and
  * nothing else. Makes some painting calculations quite a bit faster.
- *
- * @author mkron
  */
 public class SlimRect {
     double x, y, width, height;

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

@@ -13,10 +13,6 @@ package eva2.tools.math.Jama;
 
 public class CholeskyDecomposition implements java.io.Serializable {
 
-/* ------------------------
-   Class variables
- * ------------------------ */
-
     /**
      * Array for internal storage of decomposition.
      *
@@ -38,10 +34,6 @@ public class CholeskyDecomposition implements java.io.Serializable {
      */
     private boolean isspd;
 
-/* ------------------------
-   Constructor
- * ------------------------ */
-
     /**
      * Cholesky algorithm for symmetric and positive definite matrix.
      *

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

@@ -64,10 +64,6 @@ public class EigenvalueDecomposition implements java.io.Serializable {
      */
     private double[] ort;
 
-/* ------------------------
-   Private Methods
- * ------------------------ */
-
     // Symmetric Householder reduction to tridiagonal form.
 
     private void tred2() {
@@ -855,21 +851,16 @@ public class EigenvalueDecomposition implements java.io.Serializable {
         }
     }
 
-
-/* ------------------------
-   Constructor
- * ------------------------ */
-
     /**
      * Check for symmetry, then construct the eigenvalue decomposition
      *
-     * @param A Square matrix
+     * @param arg A Square matrix
      * @return Structure to access D and V.
      */
 
-    public EigenvalueDecomposition(Matrix Arg) {
+    public EigenvalueDecomposition(Matrix matrix) {
-        double[][] A = Arg.getArray();
+        double[][] A = matrix.getArray();
-        n = Arg.getColumnDimension();
+        n = matrix.getColumnDimension();
         V = new double[n][n];
         d = new double[n];
         e = new double[n];
@@ -910,10 +901,6 @@ public class EigenvalueDecomposition implements java.io.Serializable {
         }
     }
 
-/* ------------------------
-   Public Methods
- * ------------------------ */
-
     /**
      * Return the eigenvector matrix
      *

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

@@ -40,10 +40,6 @@ public class LUDecomposition implements java.io.Serializable {
      */
     private int[] piv;
 
-/* ------------------------
-   Constructor
- * ------------------------ */
-
     /**
      * LU Decomposition
      *
@@ -52,11 +48,6 @@ public class LUDecomposition implements java.io.Serializable {
      */
 
     public LUDecomposition(Matrix A) {
-
-        // Use a "left-looking", dot-product, Crout/Doolittle algorithm.
-//      System.out.println("A=");
-//      A.print(A.getRowDimension(),A.getColumnDimension());
-
         LU = A.getArrayCopy();
         m = A.getRowDimension();
         n = A.getColumnDimension();
@@ -124,69 +115,6 @@ public class LUDecomposition implements java.io.Serializable {
         }
     }
 
-/* ------------------------
-   Temporary, experimental code.
-   ------------------------ *\
-
-   \** LU Decomposition, computed by Gaussian elimination.
-   <P>
-   This constructor computes L and U with the "daxpy"-based elimination
-   algorithm used in LINPACK and MATLAB.  In Java, we suspect the dot-product,
-   Crout algorithm will be faster.  We have temporarily included this
-   constructor until timing experiments confirm this suspicion.
-   <P>
-   @param  A             Rectangular matrix
-   @param  linpackflag   Use Gaussian elimination.  Actual value ignored.
-   @return               Structure to access L, U and piv.
-   *\
-
-   public LUDecomposition (Matrix A, int linpackflag) {
-      // Initialize.
-      LU = A.getArrayCopy();
-      m = A.getRowDimension();
-      n = A.getColumnDimension();
-      piv = new int[m];
-      for (int i = 0; i < m; i++) {
-         piv[i] = i;
-      }
-      pivsign = 1;
-      // Main loop.
-      for (int k = 0; k < n; k++) {
-         // Find pivot.
-         int p = k;
-         for (int i = k+1; i < m; i++) {
-            if (Math.abs(LU[i][k]) > Math.abs(LU[p][k])) {
-               p = i;
-            }
-         }
-         // Exchange if necessary.
-         if (p != k) {
-            for (int j = 0; j < n; j++) {
-               double t = LU[p][j]; LU[p][j] = LU[k][j]; LU[k][j] = t;
-            }
-            int t = piv[p]; piv[p] = piv[k]; piv[k] = t;
-            pivsign = -pivsign;
-         }
-         // Compute multipliers and eliminate k-th column.
-         if (LU[k][k] != 0.0) {
-            for (int i = k+1; i < m; i++) {
-               LU[i][k] /= LU[k][k];
-               for (int j = k+1; j < n; j++) {
-                  LU[i][j] -= LU[i][k]*LU[k][j];
-               }
-            }
-         }
-      }
-   }
-
-\* ------------------------
-   End of temporary code.
- * ------------------------ */
-
-/* ------------------------
-   Public Methods
- * ------------------------ */
-
     /**
      * Is the matrix nonsingular?
      *
@@ -195,7 +123,6 @@ public class LUDecomposition implements java.io.Serializable {
 
     public boolean isNonsingular() {
         for (int j = 0; j < n; j++) {
-            //System.out.println("LU[j][j]"+LU[j][j]);
             if (LU[j][j] == 0) {
                 return false;
             }
@@ -253,7 +180,6 @@ public class LUDecomposition implements java.io.Serializable {
      *
      * @return piv
      */
-
     public int[] getPivot() {
         int[] p = new int[m];
         System.arraycopy(piv, 0, p, 0, m);
@@ -265,7 +191,6 @@ public class LUDecomposition implements java.io.Serializable {
      *
      * @return (double) piv
      */
-
     public double[] getDoublePivot() {
         double[] vals = new double[m];
         for (int i = 0; i < m; i++) {
@@ -280,7 +205,6 @@ public class LUDecomposition implements java.io.Serializable {
      * @return det(A)
      * @throws IllegalArgumentException Matrix must be square
      */
-
     public double det() {
         if (m != n) {
             throw new IllegalArgumentException("Matrix must be square.");
@@ -300,14 +224,11 @@ public class LUDecomposition implements java.io.Serializable {
      * @throws IllegalArgumentException Matrix row dimensions must agree.
      * @throws RuntimeException         Matrix is singular.
      */
-
     public Matrix solve(Matrix B) {
         if (B.getRowDimension() != m) {
             throw new IllegalArgumentException("Matrix row dimensions must agree.");
         }
         if (!this.isNonsingular()) {
-            //System.out.println("B=");
-            //B.print(B.getRowDimension(),B.getColumnDimension());
             throw new RuntimeException("Matrix is singular.");
         }
 

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

@@ -17,7 +17,6 @@ import java.util.Arrays;
 import java.util.Locale;
 import java.util.Vector;
 
-
 /**
  * Jama = Java Matrix class.
  * <p/>

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

@@ -15,13 +15,8 @@ import eva2.tools.math.Jama.util.Maths;
  * of simultaneous linear equations.  This will fail if isFullRank()
  * returns false.
  */
-
 public class QRDecomposition implements java.io.Serializable {
 
-/* ------------------------
-   Class variables
- * ------------------------ */
-
     /**
      * Array for internal storage of decomposition.
      *
@@ -44,17 +39,12 @@ public class QRDecomposition implements java.io.Serializable {
      */
     private double[] Rdiag;
 
-/* ------------------------
-   Constructor
- * ------------------------ */
-
     /**
      * QR Decomposition, computed by Householder reflections.
      *
      * @param A Rectangular matrix
      * @return Structure to access R and the Householder vectors and compute Q.
      */
-
     public QRDecomposition(Matrix A) {
         // Initialize.
         QR = A.getArrayCopy();
@@ -96,16 +86,11 @@ public class QRDecomposition implements java.io.Serializable {
         }
     }
 
-/* ------------------------
-   Public Methods
- * ------------------------ */
-
     /**
      * Is the matrix full rank?
      *
      * @return true if R, and hence A, has full rank.
      */
-
     public boolean isFullRank() {
         for (int j = 0; j < n; j++) {
             if (Rdiag[j] == 0) {
@@ -120,7 +105,6 @@ public class QRDecomposition implements java.io.Serializable {
      *
      * @return Lower trapezoidal matrix whose columns define the reflections
      */
-
     public Matrix getH() {
         Matrix X = new Matrix(m, n);
         double[][] H = X.getArray();
@@ -141,7 +125,6 @@ public class QRDecomposition implements java.io.Serializable {
      *
      * @return R
      */
-
     public Matrix getR() {
         Matrix X = new Matrix(n, n);
         double[][] R = X.getArray();
@@ -164,7 +147,6 @@ public class QRDecomposition implements java.io.Serializable {
      *
      * @return Q
      */
-
     public Matrix getQ() {
         Matrix X = new Matrix(m, n);
         double[][] Q = X.getArray();
@@ -197,7 +179,6 @@ public class QRDecomposition implements java.io.Serializable {
      * @throws IllegalArgumentException Matrix row dimensions must agree.
      * @throws RuntimeException         Matrix is rank deficient.
      */
-
     public Matrix solve(Matrix B) {
         if (B.getRowDimension() != m) {
             throw new IllegalArgumentException("Matrix row dimensions must agree.");

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

@@ -20,10 +20,6 @@ import eva2.tools.math.Jama.util.Maths;
 
 public class SingularValueDecomposition implements java.io.Serializable {
 
-/* ------------------------
-   Class variables
- * ------------------------ */
-
     /**
      * Arrays for internal storage of U and V.
      *
@@ -47,24 +43,20 @@ public class SingularValueDecomposition implements java.io.Serializable {
      */
     private int m, n;
 
-/* ------------------------
-   Constructor
- * ------------------------ */
-
     /**
      * Construct the singular value decomposition
      *
-     * @param A Rectangular matrix
+     * @param arg A Rectangular matrix
      * @return Structure to access U, S and V.
      */
 
-    public SingularValueDecomposition(Matrix Arg) {
+    public SingularValueDecomposition(Matrix matrix) {
 
         // Derived from LINPACK code.
         // Initialize.
-        double[][] A = Arg.getArrayCopy();
+        double[][] A = matrix.getArrayCopy();
-        m = Arg.getRowDimension();
+        m = matrix.getRowDimension();
-        n = Arg.getColumnDimension();
+        n = matrix.getColumnDimension();
         int nu = Math.min(m, n);
         s = new double[Math.min(m + 1, n)];
         U = new double[m][nu];
@@ -476,10 +468,6 @@ public class SingularValueDecomposition implements java.io.Serializable {
         }
     }
 
-/* ------------------------
-   Public Methods
- * ------------------------ */
-
     /**
      * Return the left singular vectors
      *

src/eva2/tools/math/Mathematics.java

@@ -112,7 +112,6 @@ public class Mathematics {
      *
      * @param x    a vector
      * @param y    another vector
-     * @param root what kind of distance funktion
      * @return the distance of x and y
      * @throws Exception if x and y have different dimensions an exception is thrown.
      */
@@ -139,8 +138,6 @@ public class Mathematics {
      */
     public static double[] expandVector(double[] x, int len, double v) {
         if (len <= x.length) {// not really an error, just perform identity
-            // System.err.println("Error, invalid length in expandVector, expecting l>"
-            // + x.length);
             return x;
         } else {
             double[] expanded = new double[len];

src/eva2/tools/math/StatisticUtils.java

@@ -399,43 +399,6 @@ public class StatisticUtils {
         return corrCoefficient;
     }
 
-    /**
-     * Main method for testing this class.
-     */
-    public static void main(String[] ops) {
-        double[][] vs = {{356.873, -498.563, 130.923, -223.684, 494.296, 380.739, 481.353, 344.571, 501.105, -166.109},
-                {199.116, -423.448, 487.898, 344.579, 140.709, 89.007, -259.310, 512.000, 152.069, -440.778},
-                {439.128, 112.370, -422.820, -43.119, -297.609, -438.940, 488.914, -512.000, -407.847, 386.611},
-                {395.772, 191.634, -511.999, -93.078, -282.853, -444.621, 491.291, -512.000, -407.620, 386.493}};
-
-        vs[1] = Mathematics.rotate(vs[0], AbstractProblemDouble.initializeDefaultRotationMatrix(10, 10));
-
-        for (int i = 0; i < vs.length; i++) {
-            for (int j = 0; j < vs.length; j++) {
-                System.out.print("\t" + correlation(vs[i], vs[j]));
-            }
-            System.out.println();
-        }
-//		vs[1]=Mathematics.rotate(vs[0], AbstractProblemDouble.initializeDefaultRotationMatrix(30, 10));
-//		vs[2]=Mathematics.rotate(vs[0], AbstractProblemDouble.initializeDefaultRotationMatrix(50, 10));
-//		vs[3]=Mathematics.rotate(vs[0], AbstractProblemDouble.initializeDefaultRotationMatrix(70, 10));
-
-        vs = new double[][]{{0.1, 0.9},
-                {0.8, 0.2},
-//							{0.8,0.2},
-                {0.0, 1.0}};
-        System.out.println("---");
-
-//		for (int i=0; i<vs.length; i++) {
-//			Mathematics.svAdd(512, vs[i], vs[i]);
-//			Mathematics.normVect(vs[i], vs[i]);
-//			System.out.println(BeanInspector.toString(vs[i]));
-//		}
-
-//		System.out.println("entropy cols: " + entropyOverColumns(vs));
-//		System.out.println("entropy rows: " + entropyOverRows(vs));
-    }
-
     /**
      * Computes the entropy of the given array.
      *
@@ -500,9 +463,6 @@ public class StatisticUtils {
      * @return
      */
     public static Matrix rlh(int samples, int dim, double lb, double ub, boolean edges) {
-        //    		System.out.println( "Latin Hypercube sampling" );
-        //    		++rlhsamplings;
-
         // perform Latin-Hypercube-Sampling to obtain a stratified sample of
         // function values over the optimization domain
 
@@ -593,9 +553,7 @@ public class StatisticUtils {
      * Returns a list of point matrices which form a latin hypercube sampling of the given space.
      *
      * @param samples
-     * @param dim
+     * @param range
-     * @param lb
-     * @param ub
      * @param edges
      * @return
      */

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

@@ -1,37 +1,11 @@
-///////////////////////////////////////////////////////////////////////////////
-//  Filename: $RCSfile: AbstractDataModifier.java,v $
-//  Purpose:  Some interpolation stuff.
-//  Language: Java
-//  Compiler: JDK 1.4
-//  Authors:  Joerg K. Wegner
-//  Version:  $Revision: 1.1 $
-//            $Date: 2003/07/22 19:24:58 $
-//            $Author: wegnerj $
-//
-//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-//
-///////////////////////////////////////////////////////////////////////////////
-
 package eva2.tools.math.interpolation;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
-/*==========================================================================*
-* CLASS DECLARATION
-*==========================================================================*/
-
 /**
  * The minimal set of functions which should implemented in a data modifier for
  * <code>AbstractDataSet</code>.
  */
 public abstract class AbstractDataModifier {
 
-	/*-------------------------------------------------------------------------*
-     * abstract methods
-	 *-------------------------------------------------------------------------*/
-
     /**
      * Modifies the X data.
      */
@@ -46,8 +20,4 @@ public abstract class AbstractDataModifier {
      * Modifies the data.
      */
     public abstract void modify(double[] setX, double[] setY);
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

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

@@ -1,35 +1,6 @@
-///////////////////////////////////////////////////////////////////////////////
-//  Filename: $RCSfile: AbstractDataSet.java,v $
-//  Purpose:  Some interpolation stuff.
-//  Language: Java
-//  Compiler: JDK 1.4
-//  Authors:  Joerg K. Wegner
-//  Version:  $Revision: 1.1 $
-//            $Date: 2003/07/22 19:25:04 $
-//            $Author: wegnerj $
-//
-//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-//
-///////////////////////////////////////////////////////////////////////////////
-
 package eva2.tools.math.interpolation;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
-/*==========================================================================*
-* CLASS DECLARATION
-*==========================================================================*/
-
 public abstract class AbstractDataSet {
-    /*-------------------------------------------------------------------------*
-     * public member variables
-	 *-------------------------------------------------------------------------*/
-
-	/*--------------------------------------------------------------o-----------*
-     * protected member variables
-	 *-------------------------------------------------------------------------*/
     /**
      * double array of X data.
      *
@@ -43,10 +14,6 @@ public abstract class AbstractDataSet {
      */
     protected double[] yDoubleData = {1, 1};
 
-	/*-------------------------------------------------------------------------*
-	 * abstract methods
-	 *-------------------------------------------------------------------------*/
-
     /**
      * Returns the length of the data set
      *
@@ -115,6 +82,3 @@ public abstract class AbstractDataSet {
         modifier.modify(xDoubleData, yDoubleData);
     }
 }
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

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

@@ -1,17 +1,3 @@
-///////////////////////////////////////////////////////////////////////////////
-//  Filename: $RCSfile: BasicDataSet.java,v $
-//  Purpose:  Some interpolation stuff.
-//  Language: Java
-//  Compiler: JDK 1.4
-//  Authors:  Joerg K. Wegner
-//  Version:  $Revision: 1.1 $
-//            $Date: 2003/07/22 19:25:11 $
-//            $Author: wegnerj $
-//
-//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-//
-///////////////////////////////////////////////////////////////////////////////
-
 package eva2.tools.math.interpolation;
 
 /**

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

@@ -1,28 +1,4 @@
-///////////////////////////////////////////////////////////////////////////////
-//  Filename: $RCSfile: InterpolationException.java,v $
-//  Purpose:  Some interpolation stuff.
-//  Language: Java
-//  Compiler: JDK 1.4
-//  Authors:  Joerg K. Wegner
-//  Version:  $Revision: 1.1 $
-//            $Date: 2003/07/22 19:25:17 $
-//            $Author: wegnerj $
-//
-//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-//
-///////////////////////////////////////////////////////////////////////////////
-
 package eva2.tools.math.interpolation;
-
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
-
-/*==========================================================================*
- * CLASS DECLARATION
- *==========================================================================*/
-
 /**
  * Exception for interpolation error.
  */
@@ -35,8 +11,4 @@ public class InterpolationException extends Exception {
     public InterpolationException(String s) {
         super(s);
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/

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

@@ -15,12 +15,6 @@
 
 package eva2.tools.math.interpolation;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
-//import cern.jet.stat.*;
-
 /**
  * Defines the routines for the spline interpolation of data.
  */

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

@@ -1,405 +0,0 @@
-package eva2.tools.math.interpolation;
-
-/**
- * Defines the routines for the interpolation of data.
- */
-public class PolyInterpolation {
-    AbstractDataSet abstractDataSet = null;
-    boolean sloppy = true;
-    double[] polynomialCoefficients = null;
-
-    /**
-     * Initializes this class.
-     */
-    public PolyInterpolation() throws InterpolationException {
-        this.abstractDataSet = null;
-        sloppy = true;
-        polynomialCoefficients = null;
-    }
-
-    /**
-     * Initializes this class and calculates the coefficients of the polynom.
-     *
-     * @param abstractDataSet the <code>AbstractDataSet</code>
-     */
-    public PolyInterpolation(AbstractDataSet abstractDataSet)
-            throws InterpolationException {
-        this.abstractDataSet = abstractDataSet;
-        sloppy = true;
-        this.polynomialCoefficients = calculatePolynomialCoefficients();
-    }
-
-    /**
-     * Initializes this class and calculates the coefficients of the polynom.
-     *
-     * @param abstractDataSet the <code>AbstractDataSet</code>
-     * @param sloppy          if <code>true</code> Neville's algorithm which is used in the
-     *                        <code>polynomialInterpolation</code>-routines does only print a
-     *                        warning message on the screen and does not throw an
-     *                        <code>Exception</code> if two x values are identical.
-     */
-    public PolyInterpolation(AbstractDataSet abstractDataSet, boolean sloppy)
-            throws InterpolationException {
-        this.abstractDataSet = abstractDataSet;
-        this.sloppy = sloppy;
-        this.polynomialCoefficients = calculatePolynomialCoefficients();
-    }
-
-    /**
-     * Sets the new <code>AbstractDataSet</code> and calculates the coefficients
-     * of the polynom.
-     *
-     * @param abstractDataSet the <code>AbstractDataSet</code>
-     */
-    public void setAbstractDataSet(AbstractDataSet abstractDataSet)
-            throws InterpolationException {
-        this.abstractDataSet = abstractDataSet;
-        this.polynomialCoefficients = calculatePolynomialCoefficients();
-    }
-
-    /**
-     * Uses the polynom with the calculated coefficients to calculate the
-     * <code>y</code> value. This algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 5, pages 173-176.</a><br>
-     * The Neville's algorithm which is used in the <code>polynomialInterpolation</code>-
-     * routines returns also the error of this interpolated point.
-     *
-     * @param x the x value
-     * @return the interpolated y value
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #getYandDerivatives(double, int)
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     */
-
-    public double getY(double x) {
-        int n = polynomialCoefficients.length - 1;
-        double y = polynomialCoefficients[n];
-        for (int j = n - 1; j >= 0; j--) {
-            y = y * x + polynomialCoefficients[j];
-        }
-
-        return y;
-    }
-
-    /**
-     * Uses the polynom with the calculated coefficients to calculate the
-     * <code>y</code> value and the derivatives at the point <code>x</code>,
-     * <code>y</code>. This algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 5, pages 173-176.</a><br>
-     * The Neville's algorithm which is used in the <code>polynomialInterpolation</code>-
-     * routines returns also the error of this interpolated point.
-     *
-     * @param x                the x value
-     * @param ndDerivateNumber the number of the calculated derivatives
-     * @return the interpolated y value at ...[0], the 1st derivativ value at
-     *         ...[1], the 2nd derivativ at ...[2] and so on ...
-     * @see #getY(double)
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     */
-    public double[] getYandDerivatives(double x, int ndDerivateNumber)
-            throws InterpolationException {
-        if (ndDerivateNumber < 0) {
-            throw new InterpolationException("Negative derivative numbers make no sense.");
-        } else if (ndDerivateNumber == 0) {
-            double[] pd = new double[1];
-            pd[0] = getY(x);
-            return pd;
-        }
-
-        int nnd, j, i;
-        int nc = polynomialCoefficients.length - 1;
-        double[] pd = new double[ndDerivateNumber + 1];
-        double cnst = 1.0;
-
-        pd[0] = polynomialCoefficients[nc];
-        for (j = 1; j <= ndDerivateNumber; j++) {
-            pd[j] = 0.0;
-        }
-        for (i = nc - 1; i >= 0; i--) {
-            nnd = (ndDerivateNumber < (nc - i) ? ndDerivateNumber : nc - i);
-            for (j = nnd; j >= 1; j--) {
-                pd[j] = pd[j] * x + pd[j - 1];
-            }
-            pd[0] = pd[0] * x + polynomialCoefficients[i];
-        }
-        for (i = 2; i <= ndDerivateNumber; i++) {
-            cnst *= i;
-            pd[i] *= cnst;
-        }
-
-        return pd;
-    }
-
-    /**
-     * Neville's interpolation algorithm. This algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 3, pages 108-122.</a><br>
-     *
-     * @param x the x value
-     * @return the interpolated y value and the interpolation error
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #getY(double)
-     * @see #getYandDerivatives(double, int)
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     */
-    public PolynomialInterpolationResult polynomialInterpolation(double x)
-            throws InterpolationException {
-        if (abstractDataSet == null) {
-            throw new InterpolationException(
-                    "No data." + " The AbstractDataSet was not defined.");
-        }
-        return polynomialInterpolation(
-                abstractDataSet.getXData(),
-                abstractDataSet.getYData(),
-                x);
-    }
-
-    /**
-     * Neville's interpolation algorithm. This algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 3, pages 108-122.</a><br>
-     *
-     * @param abstractDataSet the <code>AbstractDataSet</code>
-     * @param x               the x value
-     * @return the interpolated y value and the interpolation error
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #getY(double)
-     * @see #getYandDerivatives(double, int)
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     */
-    public PolynomialInterpolationResult polynomialInterpolation(
-            AbstractDataSet abstractDataSet,
-            double x)
-            throws InterpolationException {
-        if (abstractDataSet == null) {
-            throw new InterpolationException(
-                    "No data." + " The AbstractDataSet was not defined.");
-        }
-        return polynomialInterpolation(
-                abstractDataSet.getXData(),
-                abstractDataSet.getYData(),
-                x);
-    }
-
-    /**
-     * Neville's interpolation algorithm. This algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 3, pages 108-122.</a><br>
-     *
-     * @param xa the array of x values
-     * @param ya the array of y values
-     * @param x  the x value
-     * @return the interpolated y value and the interpolation error
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #getY(double)
-     * @see #getYandDerivatives(double, int)
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     */
-    public PolynomialInterpolationResult polynomialInterpolation(
-            double[] xa,
-            double[] ya,
-            double x)
-            throws InterpolationException {
-        if (xa == null || ya == null) {
-            throw new InterpolationException("No data.");
-        }
-        int i, m, ns = 1;
-        double den, dif, dift, ho, hp, w;
-        double[] c = new double[xa.length + 1];
-        double[] d = new double[xa.length + 1];
-        PolynomialInterpolationResult result =
-                new PolynomialInterpolationResult();
-
-        dif = Math.abs(x - xa[0]);
-        for (i = 1; i <= xa.length; i++) {
-            if ((dift = Math.abs(x - xa[i - 1])) < dif) {
-                ns = i;
-                dif = dift;
-            }
-            c[i] = ya[i - 1];
-            d[i] = ya[i - 1];
-        }
-        result.y = ya[ns - 1];
-        ns--;
-        for (m = 1; m < xa.length; m++) {
-            for (i = 1; i <= xa.length - m; i++) {
-                ho = xa[i - 1] - x;
-                hp = xa[i + m - 1] - x;
-                w = c[i + 1] - d[i];
-                if ((den = ho - hp) == 0.0) {
-                    if (sloppy) {
-                        System.out.println("Two identical x values. The values must be distinct.");
-                        den = 1.0;
-                    } else {
-                        throw new InterpolationException("Two identical x values.");
-                    }
-                }
-                den = w / den;
-                d[i] = hp * den;
-                c[i] = ho * den;
-            }
-            result.y
-                    += (result.yError =
-                    (2 * ns < (xa.length - m) ? c[ns + 1] : d[ns--]));
-        }
-        return result;
-    }
-
-    /**
-     * Calculates the coefficients of a polynom of the grade <code>N-1</code>. This
-     * interpolation algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 3, pages 108-122.</a><br>
-     *
-     * @return the array with the polynomial coefficients y = ...[0] +
-     *         ...[1]*x<SUP>2</SUP> + ...[2]*x<SUP>3</SUP> + ...
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #getY(double)
-     * @see #getYandDerivatives(double, int)
-     */
-    public double[] calculatePolynomialCoefficients()
-            throws InterpolationException {
-        if (abstractDataSet == null) {
-            throw new InterpolationException(
-                    "No data." + " The AbstractDataSet was not defined.");
-        }
-        return calculatePolynomialCoefficients(
-                abstractDataSet.getXData(),
-                abstractDataSet.getYData());
-    }
-
-    /**
-     * Calculates the coefficients of a polynom of the grade <code>N-1</code>. This
-     * interpolation algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 3, pages 108-122.</a><br>
-     *
-     * @param abstractDataSet the <code>AbstractDataSet</code>
-     * @return the array with the polynomial coefficients y = ...[0] +
-     *         ...[1]*x<SUP>2</SUP> + ...[2]*x<SUP>3</SUP> + ...
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(double[], double[])
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #getY(double)
-     * @see #getYandDerivatives(double, int)
-     */
-    public double[] calculatePolynomialCoefficients(AbstractDataSet abstractDataSet)
-            throws InterpolationException {
-        if (abstractDataSet == null) {
-            throw new InterpolationException(
-                    "No data." + " The AbstractDataSet was not defined.");
-        }
-        return calculatePolynomialCoefficients(
-                abstractDataSet.getXData(),
-                abstractDataSet.getYData());
-    }
-
-    /**
-     * Calculates the coefficients of a polynom of the grade <code>N-1</code>. This
-     * interpolation algorithm was taken from:<br>
-     * <a href="http://www.ulib.org/webRoot/Books/Numerical_Recipes/" target="_top">
-     * William H. Press, Saul A. Teukolosky, William T. Vetterling, Brian P. Flannery,
-     * "Numerical Recipes in C - The Art of Scientific Computing", Second Edition,
-     * Cambridge University Press,
-     * ISBN 0-521-43108-5,
-     * chapter 3, pages 108-122.</a><br>
-     *
-     * @param x the array of x values
-     * @param y the array of y values
-     * @return the array with the polynomial coefficients y = ...[0] +
-     *         ...[1]*x<SUP>2</SUP> + ...[2]*x<SUP>3</SUP> + ...
-     * @see #calculatePolynomialCoefficients()
-     * @see #calculatePolynomialCoefficients(AbstractDataSet)
-     * @see #polynomialInterpolation(double)
-     * @see #polynomialInterpolation(AbstractDataSet, double)
-     * @see #polynomialInterpolation(double[], double[], double)
-     * @see #getY(double)
-     * @see #getYandDerivatives(double, int)
-     */
-    public double[] calculatePolynomialCoefficients(double x[], double y[]) {
-        int k, j, i, n = x.length - 1;
-        double phi, ff, b;
-        double[] s = new double[n + 1];
-        double[] cof = new double[n + 1];
-
-        for (i = 0; i <= n; i++) {
-            s[i] = cof[i] = 0.0;
-        }
-        s[n] = -x[0];
-
-        for (i = 1; i <= n; i++) {
-            for (j = n - i; j <= n - 1; j++) {
-                s[j] -= x[i] * s[j + 1];
-            }
-            s[n] -= x[i];
-        }
-
-        for (j = 0; j < n; j++) {
-            phi = n + 1;
-            for (k = n; k >= 1; k--) {
-                phi = k * s[k] + x[j] * phi;
-            }
-            ff = y[j] / phi;
-            b = 1.0;
-            for (k = n; k >= 0; k--) {
-                cof[k] += b * ff;
-                b = s[k] + x[j] * b;
-            }
-        }
-        return cof;
-    }
-}

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

@@ -1,23 +1,5 @@
-///////////////////////////////////////////////////////////////////////////////
-//  Filename: $RCSfile: SplineInterpolation.java,v $
-//  Purpose:  Some interpolation stuff.
-//  Language: Java
-//  Compiler: JDK 1.4
-//  Authors:  Joerg K. Wegner
-//  Version:  $Revision: 1.1 $
-//            $Date: 2003/07/22 19:25:42 $
-//            $Author: wegnerj $
-//
-//  Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-//
-///////////////////////////////////////////////////////////////////////////////
-
 package eva2.tools.math.interpolation;
 
-/*==========================================================================*
- * IMPORTS
- *==========================================================================*/
-
 /**
  * Defines the routines for the spline interpolation of data.
  */
@@ -28,16 +10,10 @@ public class SplineInterpolation {
     double[] yArray = null;
     boolean ascendingData = true;
 
-	/*------------------------------------------------------------------------*
-     * constructor
-	 *------------------------------------------------------------------------*/
-
     /**
      * Initializes this class.
      */
     public SplineInterpolation() throws InterpolationException {
-        this.abstractDataSet = null;
-        this.secondDerivative = null;
     }
 
     /**
@@ -62,7 +38,6 @@ public class SplineInterpolation {
         double[] x = abstractDataSet.getXData();
         double[] y = abstractDataSet.getYData();
         boolean ascending = false;
-        boolean descending = false;
         int n = x.length;
 
         xArray = new double[n];
@@ -76,17 +51,11 @@ public class SplineInterpolation {
                 //if(descending)throw new InterpolationException("The x values must be"+
                 //          " in continous ascending/descending order.");
                 ascending = true;
-            } else {
-                //if(ascending)throw new InterpolationException("The x values must be"+
-                //          " in continous ascending/descending order.");
-                descending = true;
             }
         }
         ascendingData = ascending;
 
         if (ascendingData) {
-            xArray = null;
-            yArray = null;
             xArray = abstractDataSet.getXData();
             yArray = abstractDataSet.getYData();
         }
@@ -212,7 +181,7 @@ public class SplineInterpolation {
             }
         }
         h = xa[khi] - xa[klo];
-        //System.out.println(""+x+" between "+xa[khi]+" "+xa[klo]);
+
         if (h == 0.0) {
             throw new InterpolationException("Two identical x values. The values must be distinct.");
         }
@@ -262,7 +231,6 @@ public class SplineInterpolation {
             }
         }
         h = xa[khi] - xa[klo];
-        //System.out.println(""+x+" between "+xa[khi]+" "+xa[klo]);
         if (h == 0.0) {
             throw new InterpolationException("Two identical x values. The values must be distinct.");
         }
@@ -274,8 +242,4 @@ public class SplineInterpolation {
                         + ((3 * (b * b) - 1) * h * y2a[khi]) / 6.0;
         return dydx;
     }
-}
+}
-
-/****************************************************************************
- * END OF FILE
- ****************************************************************************/