minor system updates

Author: anthonyawuley

ec/algorithms/alps/layers/Layer.java

@@ -45,6 +45,8 @@ public class Layer implements LayerInterface {
 	/** */
 	public int layerCompleteGenerationCount = 0;
 	/** */
+	public int layerCompleteEvaluationCount = 0;
+	/** */
 	public boolean initializerFlag = true;
 
 	public Layer() 

ec/algorithms/alps/replacement/age/Nearest.java

@@ -65,11 +65,7 @@ public Population performAgeLayerMovements(Evolve e, ALPSLayers alpsLayers,
 				}
 				else if(higherPop.size()>0) //once higher layer is filled, do selective replacement based on new individuals that have higher age than in the individual in the  higher layer
 				{
-					@SuppressWarnings("unused")
-					RandomGenerator randGen = new RandomGenerator(); 
-			        MersenneTwisterFast mtf = new MersenneTwisterFast();
-			        mtf.setSeed(alpsLayers.layers.get(alpsLayers.index).getParameters().getSeed()); //set seed
-			        
+					
 			        this.individualID = nearestPopulationIndividualFitness( //select worst individual in population
 									               higherPop,
 									               nextGeneration.get(i).getFitness().getDouble());
@@ -85,9 +81,6 @@ else if(higherPop.size()>0) //once higher layer is filled, do selective replacem
 		for(int id=0;id<deleteList.size();id++)
 			nextGeneration.remove(deleteList.get(id));
 
-		/*System.out.println(deleteList.size()+ " -- Current!! "+nextGeneration.size()+
-				" Next "+alpsLayers.layers.get(alpsLayers.index+1).getEvolution().getCurrentPopulation().size()); //System.exit(0);
-		*/
 		return nextGeneration;
 	}
 

ec/algorithms/alps/replacement/age/Random.java

@@ -65,11 +65,6 @@ public Population performAgeLayerMovements(Evolve e, ALPSLayers alpsLayers,
 				}
 				else if(higherPop.size()>0) //once higher layer is filled, do selective replacement random based on new individuals that have higher age than in the individual in the  higher layer
 				{
-					@SuppressWarnings("unused")
-					RandomGenerator randGen = new RandomGenerator(); 
-			        MersenneTwisterFast mtf = new MersenneTwisterFast();
-			        mtf.setSeed(alpsLayers.layers.get(alpsLayers.index).getParameters().getSeed()); //set seed
-			        
 			        //perform tournament selection on higher layer and choose first individual
 					selectionOperation.performTournamentSelection(e, alpsLayers);
 

ec/algorithms/alps/replacement/sfs/Nearest.java

@@ -69,11 +69,7 @@ public Population performAgeLayerMovements(Evolve e, ALPSLayers alpsLayers,
 				}
 				else if(higherPop.size()>0) //once higher layer is filled, do selective replacement based on new individuals that have higher age than in the individual in the  higher layer
 				{
-					@SuppressWarnings("unused")
-					RandomGenerator randGen = new RandomGenerator(); 
-			        MersenneTwisterFast mtf = new MersenneTwisterFast();
-			        mtf.setSeed(alpsLayers.layers.get(alpsLayers.index).getParameters().getSeed()); //set seed
-			        
+					
 			        this.individualID = nearestPopulationIndividual( //select worst individual in population
 									               higherPop,
 									               nextGeneration.get(i).getAge());

ec/algorithms/alps/replacement/sfs/Random.java

@@ -65,11 +65,6 @@ public Population performAgeLayerMovements(Evolve e, ALPSLayers alpsLayers,
 				}
 				else if(higherPop.size()>0) //once higher layer is filled, do selective replacement randome based on new individuals that have higher age than in the individual in the  higher layer
 				{
-					@SuppressWarnings("unused")
-					RandomGenerator randGen = new RandomGenerator(); 
-			        MersenneTwisterFast mtf = new MersenneTwisterFast();
-			        mtf.setSeed(alpsLayers.layers.get(alpsLayers.index).getParameters().getSeed()); //set seed
-			        
 			        //perform tournament selection on higher layer
 					selectionOperation.performTournamentSelection(e, alpsLayers);
 

ec/algorithms/alps/replacement/sfs/ReverseTournamentNearest.java

@@ -68,15 +68,11 @@ public Population performAgeLayerMovements(Evolve e, ALPSLayers alpsLayers,
 				}
 				else if(higherPop.size()>0) //once higher layer is filled, do selective replacement based on new individuals that have higher age than in the individual in the  higher layer
 				{
-					@SuppressWarnings("unused")
-					RandomGenerator randGen = new RandomGenerator(); 
-			        MersenneTwisterFast mtf = new MersenneTwisterFast();
-			        mtf.setSeed(alpsLayers.layers.get(alpsLayers.index).getParameters().getSeed()); //set seed
-			        
+					
 			        //perform tournament selection on higher layer
 					selectionOperation.performTournamentSelection(e,alpsLayers);
 
-					if(mtf.nextDouble()<= alpsLayers.layers.get(alpsLayers.index).getParameters().getLayerSelectionPressure())
+					if(e.random.nextDouble()<= alpsLayers.layers.get(alpsLayers.index).getParameters().getLayerSelectionPressure())
 					{ // n% worse replacement  : NB: index returned by nearestTournamentIndividual is a value in  getTournamentSelection()
 					   this.individualID = nearestTournamentIndividual(
 									               higherPop,

ec/algorithms/alps/replacement/sfs/ReverseTournamentWorst.java

@@ -70,11 +70,6 @@ public Population performAgeLayerMovements(Evolve e, ALPSLayers alpsLayers,
 				}
 				else if(higherPop.size() > 0) //once higher layer is filled, do selective replacement based on new individuals that have higher age than in the individual in the  higher layer
 				{
-					@SuppressWarnings("unused")
-					RandomGenerator randGen = new RandomGenerator(); 
-			        MersenneTwisterFast mtf = new MersenneTwisterFast();
-			        mtf.setSeed(alpsLayers.layers.get(alpsLayers.index).getParameters().getSeed()); //set seed
-			        
 			        //perform tournament selection on higher layer
 					selectionOperation.performTournamentSelection(e,alpsLayers);
 

ec/algorithms/alps/system/Engine.java

@@ -171,12 +171,17 @@ public void unsetVariables(){
 	public void layeredEvolutionALPS(ArrayList<Layer> layers,int run) {
 		ALPSLayers alps = new ALPSLayers(layers, 0);
 		/* keep running till stopped */
-		/* Engine.completeGenerationalCount<=layers.get(0).getParameters().getEvaluations ()*/
-		while (Engine.completeEvaluationCount <= Engine.evaluations)
+		/* Engine.completeGenerationalCount<=layers.get(0).getParameters().getEvaluations ()
+		 * Engine.completeEvaluationCount <= Engine.evaluations*/
+		while (layers.get(Engine.numberOfLayers-1).layerCompleteEvaluationCount <= Engine.evaluations)
 		{
+			
+			layers.get(Engine.numberOfLayers-1).layerCompleteEvaluationCount = Engine.completeEvaluationCount;
+			
 			sequentialLayerSelection(alps, layers,run);
 
 			Engine.completeGenerationalCount++;
+			
 			// Engine.completeEvaluationCount +=
 			// layers.get(0).getParameters().getPopulationSize(); //all layers
 			// have the same default population size
@@ -186,6 +191,10 @@ public void layeredEvolutionALPS(ArrayList<Layer> layers,int run) {
 
 	/**
 	 * sequentially loop through all layers
+	 * 
+	 * @param alps
+	 * @param layers
+	 * @param run
 	 */
 	public void sequentialLayerSelection(ALPSLayers alps,
 			ArrayList<Layer> layers,int run) {

ec/individuals/Representation.java

@@ -50,6 +50,8 @@ public abstract class Representation{
 	 public void createChromosome(Chromosome ch,Properties p, MersenneTwisterFast rng) 
 	 {}
 
+	 public void createChromosome(Evolve e, Chromosome ch,Properties p) 
+	 {}
 
 	/**
      * 

ec/operator/operations/replacement/SteadyState.java

@@ -349,8 +349,7 @@ public Population nextGenerationALPS(
                 * nextGeneration.addAll(nextGeneration,mtx.performMutationOperation(current.get(generation -1), c1,tournamentIndividuals.get(0)));
                 */
                 mtx.performMutationOperation(
-                		e,
-                		evolvingPopulation,c1.clone(),tournamentIndividuals.get(0),ages);
+                		e,evolvingPopulation,c1.clone(),tournamentIndividuals.get(0),ages);
 
                 this.evaluationCounter += mtx.getOffsprings().size();
                 this.populationCount++;   //increment population