More markdown, refactor stuff

src/eva2/cli/Main.java

@@ -6,8 +6,8 @@ import eva2.optimization.OptimizationParameters;
 import eva2.optimization.Processor;
 import eva2.optimization.individuals.IndividualInterface;
 import eva2.optimization.operator.terminators.InterfaceTerminator;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.optimization.statistics.*;
 import eva2.optimization.strategies.InterfaceOptimizer;
 import eva2.problems.InterfaceAdditionalPopulationInformer;

src/eva2/gui/OptimizationEditorPanel.java

@@ -365,6 +365,8 @@ public class OptimizationEditorPanel extends JPanel implements ItemListener {
         boolean found = false;
         for (int i = 0; i < comboBoxModel.getSize(); i++) {
             Item element = (Item)comboBoxModel.getElementAt(i);
+
+            System.out.println(objectName + " - " + element.getId());
             if (objectName.equals(element.getId())) {
                 found = true;
                 objectChooser.getModel().setSelectedItem(element);

src/eva2/optimization/OptimizationParameters.java

@@ -47,6 +47,7 @@ public class OptimizationParameters extends AbstractOptimizationParameters imple
             FileInputStream fileStream = new FileInputStream(yamlFile);
             instance = (OptimizationParameters) new Yaml().load(fileStream);
         } catch (Exception ex) {
+            System.out.println(ex.getStackTrace() + "\n" + ex.getMessage());
             LOGGER.log(Level.INFO, "Could not load OptimizationParameters.yml.", ex);
         }
 

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

@@ -3,8 +3,8 @@ package eva2.optimization.operator.mutation;
 import eva2.optimization.enums.MutateESCrossoverType;
 import eva2.optimization.individuals.AbstractEAIndividual;
 import eva2.optimization.individuals.InterfaceESIndividual;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.problems.InterfaceAdditionalPopulationInformer;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.tools.math.RNG;

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

@@ -1,7 +1,7 @@
 package eva2.optimization.operator.terminators;
 
-import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.util.annotation.Description;
 import eva2.util.annotation.Parameter;

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

@@ -3,9 +3,9 @@ package eva2.optimization.operator.terminators;
 import eva2.optimization.individuals.AbstractEAIndividual;
 import eva2.optimization.individuals.EAIndividualComparator;
 import eva2.optimization.operator.distancemetric.ObjectiveSpaceMetric;
+import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.optimization.population.Population;
-import eva2.optimization.population.PopulationInterface;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.util.annotation.Description;
 

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

@@ -3,8 +3,8 @@ package eva2.optimization.operator.terminators;
 import eva2.gui.BeanInspector;
 import eva2.optimization.operator.paretofrontmetrics.InterfaceParetoFrontMetric;
 import eva2.optimization.operator.paretofrontmetrics.MetricS;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.problems.AbstractMultiObjectiveOptimizationProblem;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.tools.EVAERROR;

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

@@ -1,7 +1,7 @@
 package eva2.optimization.operator.terminators;
 
-import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.problems.InterfaceOptimizationProblem;
 import eva2.util.annotation.Description;
 

src/eva2/optimization/statistics/AbstractStatistics.java

@@ -238,11 +238,11 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
 
     @Override
     public void startOptimizationPerformed(String infoString, int runNumber, InterfaceOptimizationParameters params, List<InterfaceAdditionalPopulationInformer> informerList) {
-        if (printRunIntroVerbosity()) {
-            printToTextListener("# Optimization");
-        }
-
         if (runNumber == 0) {
+            if (printRunIntroVerbosity()) {
+                printToTextListener("# Optimization");
+            }
+
             // store the initial graph selection state, so that modifications during runtime cannot cause inconsistencies
             lastFieldSelection = (StringSelection) statisticsParameter.getFieldSelection().clone();
             lastIsShowFull = statisticsParameter.isOutputAllFieldsAsText();
@@ -513,7 +513,7 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
             }
             if (refineMultiRuns && (sumDataCollection != null)) {
                 if (printFinalVerbosity()) {
-                    printToTextListener(" Averaged performance:\n");
+                    printToTextListener("#### Averaged performance:\n\n");
                 }
                 // the summed-up values of the mean collection is divided by the number of runs
                 for (int i = 0; i < sumDataCollection.size(); i++) {
@@ -588,11 +588,14 @@ public abstract class AbstractStatistics implements InterfaceTextListener, Inter
     }
 
     public String refineToText(ArrayList<Double[]> data, int iterationsToShow) {
-        String hd = getOutputHeaderFieldNamesAsString(lastInformerList);
+        List<String> additionalFields = getOutputHeaderFieldNames(lastInformerList);
         StringBuffer sbuf = new StringBuffer("Iteration");
         sbuf.append(textFieldDelimiter);
-        sbuf.append(hd);
+        sbuf.append(StringTools.concatFields(additionalFields, " | "));
         sbuf.append("\n");
+        String[] tableSeparator = new String[additionalFields.size()+1];
+        Arrays.fill(tableSeparator, "---");
+        sbuf.append(StringTools.concatFields(tableSeparator, " | ") + "\n");
         refineToText(data, iterationsToShow, sbuf, textFieldDelimiter);
         return sbuf.toString();
     }

src/eva2/optimization/strategies/ArtificialBeeColony.java

@@ -2,9 +2,9 @@ package eva2.optimization.strategies;
 
 import eva2.optimization.individuals.AbstractEAIndividual;
 import eva2.optimization.individuals.InterfaceDataTypeDouble;
+import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.optimization.population.Population;
-import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.SolutionSet;
 import eva2.problems.InterfaceAdditionalPopulationInformer;
 import eva2.tools.math.Mathematics;

src/eva2/optimization/strategies/CBNPSO.java

@@ -7,8 +7,8 @@ import eva2.optimization.operator.paramcontrol.CbpsoFitnessThresholdBasedAdaptio
 import eva2.optimization.operator.paramcontrol.LinearParamAdaption;
 import eva2.optimization.operator.paramcontrol.ParamAdaption;
 import eva2.optimization.operator.paramcontrol.SinusoidalParamAdaption;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.optimization.population.SolutionSet;
 import eva2.problems.AbstractProblemDouble;
 import eva2.problems.InterfaceInterestingHistogram;

src/eva2/optimization/strategies/ClusterBasedNichingEA.java

@@ -18,9 +18,9 @@ import eva2.optimization.operator.paramcontrol.ParamAdaption;
 import eva2.optimization.operator.paramcontrol.ParameterControlManager;
 import eva2.optimization.operator.terminators.HistoryConvergenceTerminator;
 import eva2.optimization.operator.terminators.InterfaceTerminator;
+import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.InterfacePopulationChangedEventListener;
 import eva2.optimization.population.Population;
-import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.SolutionSet;
 import eva2.problems.*;
 import eva2.tools.EVAERROR;

src/eva2/optimization/strategies/NichePSO.java

@@ -22,8 +22,8 @@ import eva2.optimization.operator.paramcontrol.ParamAdaption;
 import eva2.optimization.operator.paramcontrol.ParameterControlManager;
 import eva2.optimization.operator.terminators.EvaluationTerminator;
 import eva2.optimization.operator.terminators.InterfaceTerminator;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.optimization.population.SolutionSet;
 import eva2.problems.*;
 import eva2.tools.chart2d.*;

src/eva2/optimization/strategies/ParticleSwarmOptimization.java

@@ -11,9 +11,9 @@ import eva2.optimization.individuals.InterfaceDataTypeDouble;
 import eva2.optimization.operator.distancemetric.PhenotypeMetric;
 import eva2.optimization.operator.paramcontrol.ParamAdaption;
 import eva2.optimization.operator.paramcontrol.ParameterControlManager;
+import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.InterfaceSolutionSet;
 import eva2.optimization.population.Population;
-import eva2.optimization.population.PopulationInterface;
 import eva2.optimization.population.SolutionSet;
 import eva2.problems.Interface2DBorderProblem;
 import eva2.problems.InterfaceAdditionalPopulationInformer;

src/eva2/problems/AbstractMultiModalProblemKnown.java

@@ -6,8 +6,8 @@ import eva2.optimization.individuals.InterfaceDataTypeDouble;
 import eva2.optimization.operator.distancemetric.InterfaceDistanceMetric;
 import eva2.optimization.operator.distancemetric.PhenotypeMetric;
 import eva2.optimization.operator.postprocess.PostProcess;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.tools.EVAERROR;
 import eva2.tools.ToolBox;
 import eva2.tools.math.Mathematics;

src/eva2/problems/AbstractProblemDouble.java

@@ -13,8 +13,8 @@ import eva2.optimization.operator.terminators.FitnessConvergenceTerminator;
 import eva2.optimization.operator.terminators.PopulationMeasureTerminator.ChangeTypeEnum;
 import eva2.optimization.operator.terminators.PopulationMeasureTerminator.DirectionTypeEnum;
 import eva2.optimization.operator.terminators.PopulationMeasureTerminator.StagnationTypeEnum;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.optimization.strategies.InterfaceOptimizer;
 import eva2.tools.Pair;
 import eva2.tools.ToolBox;

src/eva2/problems/PSymbolicRegression.java

@@ -3,8 +3,8 @@ package eva2.problems;
 import eva2.gui.plot.Plot;
 import eva2.optimization.individuals.*;
 import eva2.optimization.individuals.codings.gp.*;
-import eva2.optimization.population.Population;
 import eva2.optimization.population.PopulationInterface;
+import eva2.optimization.population.Population;
 import eva2.optimization.strategies.InterfaceOptimizer;
 import eva2.problems.regression.InterfaceRegressionFunction;
 import eva2.problems.regression.RFKoza_GPI_7_3;