a few cosmetics

src/javaeva/server/go/individuals/GAIndividualIntegerData.java

@@ -196,14 +196,16 @@ public class GAIndividualIntegerData extends AbstractEAIndividual implements Int
      */
     public void SetIntegerDataLamarkian(int[] doubleData) {
         this.SetIntegerData(doubleData);
-        int[] locus = new int[2];
+        if (doubleData != null) {
-        locus[0] = 0;
+	        int[] locus = new int[2];
-        locus[1] = 0;
+	        locus[0] = 0;
-        for (int i = 0; i < doubleData.length; i++) {
+	        locus[1] = 0;
-            locus[0] += locus[1];
+	        for (int i = 0; i < doubleData.length; i++) {
-            locus[1] = this.m_CodingLenghts[i];
+	            locus[0] += locus[1];
-            this.m_IntegerCoding.codeValue(doubleData[i], this.m_Range[i], this.m_Genotype, locus);
+	            locus[1] = this.m_CodingLenghts[i];
-       }
+	            this.m_IntegerCoding.codeValue(doubleData[i], this.m_Range[i], this.m_Genotype, locus);
+	        }
+        }
     }
 
 /************************************************************************************

src/javaeva/server/go/operators/mutation/MutateESGlobal.java

@@ -25,11 +25,12 @@ public class MutateESGlobal implements InterfaceMutation, java.io.Serializable {
     protected SelectedTag m_CrossoverType;
 
     public MutateESGlobal() {
-        Tag[] tag = new Tag[3];
+        initTags();
-        tag[0] = new Tag(0, "None");
+    }
-        tag[1] = new Tag(1, "Intermediate");
+
-        tag[2] = new Tag(2, "Discrete");
+    public MutateESGlobal(double mutationStepSize) {
-        this.m_CrossoverType = new SelectedTag(0, tag);
+        initTags();
+        setMutationStepSize(mutationStepSize);
     }
     
     public MutateESGlobal(MutateESGlobal mutator) {
@@ -39,6 +40,14 @@ public class MutateESGlobal implements InterfaceMutation, java.io.Serializable {
         this.m_CrossoverType        = (SelectedTag)mutator.m_CrossoverType.clone();
     }
 
+    protected void initTags() {
+        Tag[] tag = new Tag[3];
+        tag[0] = new Tag(0, "None");
+        tag[1] = new Tag(1, "Intermediate");
+        tag[2] = new Tag(2, "Discrete");
+        this.m_CrossoverType = new SelectedTag(0, tag);
+    }
+    
     /** This method will enable you to clone a given mutation operator
      * @return The clone
      */

src/javaeva/server/go/problems/FM0Problem.java

@@ -21,8 +21,7 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
     protected InterfaceDistanceMetric   m_Metric = new PhenotypeMetricDoubleData();
     protected double                    m_GlobalOpt = 0;
     protected Population                m_Optima;
-    protected double                    m_XEpsilon = 0.05;
+    protected double                    m_Epsilon = 0.05;
-    protected double                    m_YEpsilon = 0.05;
     protected boolean                   m_UseXCrit = true;
     protected boolean                   m_UseYCrit = true;
     protected double[][]                m_Range;
@@ -64,12 +63,9 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
         this.m_UseTestConstraint = b.m_UseTestConstraint;        
         //FM0Problem
         this.m_GlobalOpt        = b.m_GlobalOpt;
-        this.m_XEpsilon         = b.m_XEpsilon;
+        this.m_Epsilon         = b.m_Epsilon;
-        this.m_YEpsilon         = b.m_YEpsilon;
         this.m_UseXCrit         = b.m_UseXCrit;
         this.m_UseYCrit         = b.m_UseYCrit;
-        this.m_XEpsilon            = b.m_XEpsilon;
-        this.m_YEpsilon          = b.m_YEpsilon;
         this.m_UseXCrit          = b.m_UseXCrit;
         if (b.m_Metric != null)
             this.m_Metric           = (InterfaceDistanceMetric)((InterfaceDistanceMetric)b.m_Metric).clone();
@@ -187,15 +183,21 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
      * @param y
      */
     protected void add2DOptimum(double x, double y) {
-        InterfaceDataTypeDouble tmpIndy;
+        double[] point = new double[2];
-        double[]                point;
-
-        tmpIndy = (InterfaceDataTypeDouble)((AbstractEAIndividual)this.m_Template).clone();
-        point = new double[2];
         point[0] = x;
         point[1] = y;
+        addOptimum(point);
+    }
+    
+    /** This method allows you to add a 2d optima to the list of optima
+     * @param x
+     * @param y
+     */
+    protected void addOptimum(double[] point) {
+        InterfaceDataTypeDouble tmpIndy;
+        tmpIndy = (InterfaceDataTypeDouble)((AbstractEAIndividual)this.m_Template).clone();
         tmpIndy.SetDoubleDataLamarkian(point);
-        ((AbstractEAIndividual)tmpIndy).SetFitness(0, this.doEvaluationUnNormalized(point)[0]);
+        ((AbstractEAIndividual)tmpIndy).SetFitness(this.doEvaluationUnNormalized(point));
         this.m_GlobalOpt = Math.max(this.m_GlobalOpt, ((AbstractEAIndividual)tmpIndy).getFitness(0));
         this.m_Optima.add(tmpIndy);
     }
@@ -244,7 +246,7 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
             for (int j = 0; j < this.m_Optima.size(); j++) {
                 opt = (AbstractEAIndividual) this.m_Optima.get(j);
                 if (!found[j]) {
-                    if (this.m_Metric.distance(posOpt, opt) < this.m_XEpsilon) found[j] = true;
+                    if (this.m_Metric.distance(posOpt, opt) < this.m_Epsilon) found[j] = true;
                 }
             }
         }
@@ -271,7 +273,7 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
             for (int j = 0; j < this.m_Optima.size(); j++) {
                 if (!found[j]) {
                     opt = (AbstractEAIndividual) this.m_Optima.get(j);
-                    if (this.m_Metric.distance(posOpt, opt) < this.m_XEpsilon) {
+                    if (this.m_Metric.distance(posOpt, opt) < this.m_Epsilon) {
                         found[j] = true;
                         result += this.m_GlobalOpt - posOpt.getFitness(0);
                         //System.out.println("Found Optimum " + j + ".: " + (this.m_GlobalOpt - posOpt.getFitness(0)));
@@ -324,4 +326,22 @@ public class FM0Problem extends F1Problem implements Interface2DBorderProblem, I
         range[1] = 5;
         return range;
     }
+
+	/**
+	 * @return the m_Epsilon
+	 */
+	public double getEpsilon() {
+		return m_Epsilon;
+	}
+
+	/**
+	 * @param epsilon the m_Epsilon to set
+	 */
+	public void setEpsilon(double epsilon) {
+		m_Epsilon = epsilon;
+	}
+	
+	public String epsilonTipText() {
+		return "Epsilon criterion indicating whether an optimum was found";
+	}
 }

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

@@ -58,9 +58,10 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
     private int                             m_PopulationSize                = 50;
 
     private boolean                         m_Debug     = true;
-    private int                             m_ShowCycle = 2;
+    private int                             m_ShowCycle = 10;
-    private TopoPlot                        m_Topology;
+    transient private TopoPlot              m_Topology;
     private int                 			haltingWindow         			 = 15;
+    private double							muLambdaRatio					 = 0.5;
 
 
     public ClusterBasedNichingEA() {
@@ -284,6 +285,23 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
         return true;
     }
 
+    private Population optimizeSpecies(Population species) {
+    	m_Optimizer.setPopulation(species);
+    	if (m_Optimizer instanceof EvolutionStrategies) {
+    		EvolutionStrategies es = (EvolutionStrategies)m_Optimizer;
+    		int mu = (int)(muLambdaRatio*species.size());
+    		if (mu < 1) mu = 1;
+    		else if (mu >= species.size()) {
+    			if (m_Debug) System.err.println("warning, muLambdaRatio produced mu >= lambda.. reducing to mu=lambda-1");
+    			mu = species.size() - 1;
+    		}
+    		es.setMyu(mu);
+    		es.setLambda(species.size());
+    	}
+    	this.m_Optimizer.optimize();
+    	return m_Optimizer.getPopulation();
+    }
+    
     public void optimize() {
     	// plot the populations
     	if (this.m_ShowCycle > 0) {
@@ -304,9 +322,7 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
         this.m_Undifferentiated.setPopulationSize(this.m_Undifferentiated.size());
         if (isActive(m_Undifferentiated)) {
             this.capMutationRate(this.m_Undifferentiated, 0); // MK TODO this sets mutation rate to 0! why?
-            this.m_Optimizer.setPopulation(this.m_Undifferentiated);
+            m_Undifferentiated = optimizeSpecies(m_Undifferentiated);
-            this.m_Optimizer.optimize();
-            this.m_Undifferentiated = this.m_Optimizer.getPopulation();
         } else {
             this.m_Undifferentiated.incrGeneration();
         }
@@ -352,13 +368,15 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
                 } else {
                 	// actually optimize D_i
                     this.capMutationRate(curSpecies, 0.05);
-                    this.m_Optimizer.setPopulation(curSpecies);
+                    //this.m_Optimizer.setPopulation(curSpecies);
-                    this.m_Optimizer.optimize();
+                    //this.m_Optimizer.optimize();
-                    this.m_Species.set(i, this.m_Optimizer.getPopulation());
+                    //this.m_Species.set(i, this.m_Optimizer.getPopulation());
+                    this.m_Species.set(i, optimizeSpecies(curSpecies));
                     curSpecies = ((Population)this.m_Species.get(i)); // reset to expected population, just to be sure
                 }
             } else {
                 // a single individual species, this element is inactive
+            	if (m_Debug) System.out.println("inactive species not optimized");
             }
             // This is necessary to keep track to the function calls needed
             this.m_Undifferentiated.SetFunctionCalls(this.m_Undifferentiated.getFunctionCalls() + curSpecies.getFunctionCalls());
@@ -492,9 +510,8 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
         }
         // output the result
         if (this.m_Debug) System.out.println("-Number of species: " + this.m_Species.size());
-        this.m_Population = new Population();
-        m_Population.setUseHistory(true);
         this.m_Population = (Population)this.m_Undifferentiated.clone();
+        m_Population.setUseHistory(true);
         if (this.m_Debug) System.out.println("initing with " + this.m_Undifferentiated.size());
         for (int i = 0; i < this.m_Species.size(); i++) {
             if (this.m_Debug) System.out.println("Adding deme " + i + " with size " + ((Population)this.m_Species.get(i)).size());
@@ -596,7 +613,8 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
      * @return The population of current solutions to a given problem.
      */
     public Population getPopulation() {
-        this.m_Population = (Population)this.m_Undifferentiated.clone();
+        this.m_Population = (Population)m_Undifferentiated.clone();
+//        m_Population.addPopulation(this.m_Undifferentiated);
         for (int i = 0; i < this.m_Species.size(); i++) this.m_Population.addPopulation((Population)this.m_Species.get(i));
         return this.m_Population;
     }
@@ -669,12 +687,16 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
     }
     public void setOptimizer(InterfaceOptimizer b){
         this.m_Optimizer = b;
+    	if (b instanceof EvolutionStrategies) {
+    		EvolutionStrategies es = (EvolutionStrategies)b;
+    		setMuLambdaRatio(es.getMyu()/(double)es.getLambda());
+    	}
     }
     public String optimizerTipText() {
         return "Choose a population based optimizing technique to use.";
     }
 
-    /** The cluster algorithm on which the species differentation is based
+    /** The cluster algorithm on which the species differentiation is based
      * @return The current clustering method
      */
     public InterfaceClustering getDifferentationCA() {
@@ -737,4 +759,23 @@ public class ClusterBasedNichingEA implements InterfacePopulationChangedEventLis
     public String populationSizeTipText() {
         return "Determines the size of the initial population.";
     }
+
+//	/**
+//	 * @return the muLambdaRatio
+//	 */
+//	public double getMuLambdaRatio() {
+//		return muLambdaRatio;
+//	}
+
+	/**
+	 * This is now set if an ES is set as optimizer.
+	 * @param muLambdaRatio the muLambdaRatio to set
+	 */
+	public void setMuLambdaRatio(double muLambdaRatio) {
+		this.muLambdaRatio = muLambdaRatio;
+	}
+	
+//	public String muLambdaRatioTipText() {
+//		return "ratio between mu and lambda for a CBN-ES"; 
+//	}
 }

src/javaeva/server/go/strategies/HillClimbing.java

@@ -83,7 +83,7 @@ public class HillClimbing implements InterfaceOptimizer, java.io.Serializable {
             if (((AbstractEAIndividual)original.get(i)).isDominatingDebConstraints(((AbstractEAIndividual)this.m_Population.get(i)))) {
                 this.m_Population.remove(i);
                 this.m_Population.add(i, original.get(i));
-            }
+            } // else: mutation improved the individual
         }
         this.m_Population.incrGeneration();
 //        for (int i = 0; i < this.m_Population.size(); i++) {

src/javaeva/server/modules/Processor.java

@@ -16,6 +16,7 @@ import javaeva.server.go.PopulationInterface;
 import javaeva.server.go.individuals.AbstractEAIndividual;
 import javaeva.server.go.operators.terminators.EvaluationTerminator;
 import javaeva.server.go.populations.Population;
+import javaeva.server.go.problems.InterfaceMultimodalProblem;
 import javaeva.server.go.strategies.InterfaceOptimizer;
 import javaeva.server.go.tools.RandomNumberGenerator;
 import javaeva.server.stat.Statistics;
@@ -208,7 +209,11 @@ public class Processor extends Thread implements InterfaceProcessor, InterfacePo
 //        		m_Statistics.createNextGenerationPerformed((PopulationInterface)this.m_ModulParameter.getOptimizer().getPopulation());
 //            	m_ListenerModule.updateProgress(getStatusPercent(m_ModulParameter.getOptimizer().getPopulation(), runCounter, m_Statistics.getStatisticsParameter().getMultiRuns()));
 //        	} // end of while (m_doOpt==true)
-
+        	if (m_ModulParameter.getProblem() instanceof InterfaceMultimodalProblem) {
+        		//	TODO improve this?
+        		InterfaceMultimodalProblem mmProb = (InterfaceMultimodalProblem)m_ModulParameter.getProblem();
+        		System.out.println("no optima found: " + mmProb.getNumberOfFoundOptima(m_ModulParameter.getOptimizer().getPopulation()));
+        	}
         	m_Statistics.stopOptPerformed(isOptRunning()); // stop is "normal" if opt wasnt set false by the user
         }
         setOptRunning(false); // normal finish

src/javaeva/tools/ReflectPackage.java

@@ -16,7 +16,7 @@ import java.util.jar.JarInputStream;
 /**
  * Allow for java to list Classes that exist in one package and can be instantiated from
  * the classpath, either directly or through a jar on the classpath.
- * So far, jars which are located <i>whithin</i> another jar will not be searched.
+ * So far, jars which are located <i>within</i> another jar will not be searched.
  * 
  * @author mkron
  *
@@ -44,26 +44,30 @@ public class ReflectPackage {
 		try {
 			// Get a File object for the package
 			File directory = null;
+			String dir = null;
 			try {
 				ClassLoader cld = ClassLoader.getSystemClassLoader();
 				if (cld == null) {
 					throw new ClassNotFoundException("Can't get class loader.");
 				}
-				String dir = path + "/" + pckgname.replace(".","/");
+				dir = path + "/" + pckgname.replace(".","/");
 
-				if (TRACE) System.out.println(path);
+				if (TRACE) System.out.println(".. opening " + path);
 
 				directory = new File(dir);
 
 			} catch (NullPointerException x) {
-				if (TRACE) System.err.println(directory.getPath()+ " not found in " + path);
+				if (TRACE) {
+					System.err.println(directory.getPath()+ " not found in " + path);
+					System.err.println("directory " + (directory.exists() ? "exists" : "doesnt exist"));
+				}
 				return set;
 			}
 			if (directory.exists()) {
 				// Get the list of the files contained in the package
 				getClassesFromDirFltr(set, directory, pckgname, includeSubs, reqSuperCls);
 			} else {
-				if (TRACE) System.err.println(directory.getPath()+ " not found in " + path);
+				if (TRACE) System.err.println(directory.getPath() + " doesnt exist in " + path + ", dir was " + dir);
 			}
 		} catch(ClassNotFoundException e) {
 			System.err.println(e.getMessage());