Rename init method to initialize and fix a bug for SBMLsimulator interop
This commit is contained in:
parent
ba814ec492
commit
3ac628e85f
@ -2,6 +2,7 @@ package eva2.gui;
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import eva2.EvAInfo;
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import eva2.optimization.modules.*;
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import eva2.problems.InterfaceOptimizationProblem;
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import eva2.util.ClassPreloader;
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import eva2.util.EvAComAdapter;
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import eva2.optimization.OptimizationStateListener;
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@ -775,7 +776,11 @@ public class Main extends JFrame implements OptimizationStateListener {
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ModuleAdapter newModuleAdapter = null;
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//
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try {
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newModuleAdapter = new GOModuleAdapter(selectedModule, OptimizationParameters.getInstance(), withGUI ? null : "EvA2");
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InterfaceOptimizationParameters params = optimizationParameters;
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if (optimizationParameters == null) {
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params = OptimizationParameters.getInstance();
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}
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newModuleAdapter = new GOModuleAdapter(selectedModule, params, withGUI ? null : "EvA2");
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//newModuleAdapter = comAdapter.getModuleAdapter(selectedModule, optimizationParameters, withGUI ? null : "EvA2");
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} catch (Exception e) {
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LOGGER.log(Level.SEVERE, "Error loading module.", e);
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@ -120,7 +120,7 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
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public void initCloneOperators(InterfaceMutation mutOp, double pMut, InterfaceCrossover coOp, double pCross, InterfaceOptimizationProblem problem) {
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mutationProbability = pMut;
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mutationOperator = (InterfaceMutation) mutOp.clone();
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mutationOperator.init(this, problem);
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mutationOperator.initialize(this, problem);
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crossoverProbability = pCross;
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crossoverOperator = (InterfaceCrossover) coOp.clone();
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crossoverOperator.init(this, problem);
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@ -277,7 +277,7 @@ public abstract class AbstractEAIndividual implements IndividualInterface, java.
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*/
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public void init(InterfaceOptimizationProblem opt) {
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initializationOperator.initialize(this, opt);
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -217,7 +217,7 @@ public class ESIndividualBinaryData extends AbstractEAIndividual implements Inte
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this.defaultInit(opt);
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System.out.println("Initial value for ESIndividualBinaryData is no BitSet!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -271,7 +271,7 @@ public class ESIndividualDoubleData extends AbstractEAIndividual implements Inte
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this.defaultInit(opt);
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System.out.println("Initial value for ESIndividualDoubleData is not double[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -240,7 +240,7 @@ public class ESIndividualIntegerData extends AbstractEAIndividual implements Int
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this.defaultInit(opt);
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System.out.println("Initial value for ESIndividualIntegerData is not int[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -260,7 +260,7 @@ public class ESIndividualPermutationData extends AbstractEAIndividual implements
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this.defaultInit(opt);
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System.out.println("Initial value for ESIndividualPermutationData is not int[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -122,7 +122,7 @@ public class GAIndividualBinaryData extends AbstractEAIndividual implements Inte
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this.defaultInit(opt);
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System.out.println("Initial value for GAIndividualBinaryData is no BitSet!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -252,7 +252,7 @@ public class GAIndividualDoubleData extends AbstractEAIndividual implements Inte
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this.defaultInit(opt);
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System.out.println("Initial value for GAIndividualDoubleData is not double[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -286,7 +286,7 @@ public class GAIndividualIntegerData extends AbstractEAIndividual implements Int
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this.defaultInit(opt);
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System.out.println("Initial value for GAIndividualDoubleData is not double[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -595,7 +595,7 @@ public class GEIndividualProgramData extends AbstractEAIndividual implements Int
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this.defaultInit(opt);
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System.out.println("Initial value for GPIndividualDoubleData is no InterfaceProgram[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -240,7 +240,7 @@ public class GIIndividualIntegerData extends AbstractEAIndividual implements Int
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this.defaultInit(opt);
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System.out.println("Initial value for GAIndividualDoubleData is not double[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -241,7 +241,7 @@ public class GPIndividualProgramData extends AbstractEAIndividual implements Int
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this.defaultInit(opt);
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System.out.println("Initial value for GPIndividualDoubleData is no InterfaceProgram[]!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -105,7 +105,7 @@ public class OBGAIndividualPermutationData extends AbstractEAIndividual implemen
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this.defaultInit(opt);
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System.out.println("Initial value for OBGAIndividualBinaryData is no Permutation!");
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}
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this.mutationOperator.init(this, opt);
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this.mutationOperator.initialize(this, opt);
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this.crossoverOperator.init(this, opt);
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}
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@ -23,7 +23,7 @@ public interface InterfaceMutation {
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* @param individual The individual that will be mutated.
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* @param opt The optimization problem.
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*/
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt);
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt);
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/**
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* This method will mutate a given AbstractEAIndividual. If the individual
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@ -41,7 +41,7 @@ public class MutateDefault implements InterfaceMutation, java.io.Serializable {
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -108,10 +108,10 @@ public class MutateEAMixer implements InterfaceMutation, java.io.Serializable {
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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InterfaceMutation[] mutators = this.mutationMixer.getSelectedMutators();
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for (int i = 0; i < mutators.length; i++) {
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mutators[i].init(individual, opt);
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mutators[i].initialize(individual, opt);
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}
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}
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@ -96,7 +96,7 @@ public class MutateESCorrVector implements InterfaceMutation, java.io.Serializab
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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double[] initVelocity = calcInitialVel(initialVelocity, ((InterfaceESIndividual) individual).getDoubleRange());
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individual.putData(vectorKey, initVelocity);
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}
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@ -10,7 +10,7 @@ import eva2.util.annotation.Description;
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/**
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*/
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@Description("The local correlated mutation stores n sigmas for each double attribute and n(n-1) alphas.")
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public class MutateESCorrolated implements InterfaceMutation, java.io.Serializable {
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public class MutateESCorrelated implements InterfaceMutation, java.io.Serializable {
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protected double mutationStepSize = 0.2;
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protected double tau1 = 0.15;
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protected double lowerLimitStepSize = 0.0000005;
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@ -19,12 +19,12 @@ public class MutateESCorrolated implements InterfaceMutation, java.io.Serializab
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private double[] alphas = null;
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protected double tau2 = 0.15;
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public MutateESCorrolated() {
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public MutateESCorrelated() {
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this.sigmas = null;
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this.alphas = null;
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}
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public MutateESCorrolated(MutateESCorrolated mutator) {
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public MutateESCorrelated(MutateESCorrelated mutator) {
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if ((mutator.sigmas != null)) {
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this.sigmas = new double[mutator.sigmas.length];
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System.arraycopy(mutator.sigmas, 0, this.sigmas, 0, this.sigmas.length);
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@ -49,7 +49,7 @@ public class MutateESCorrolated implements InterfaceMutation, java.io.Serializab
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*/
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@Override
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public Object clone() {
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return new MutateESCorrolated(this);
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return new MutateESCorrelated(this);
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}
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/**
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@ -63,8 +63,8 @@ public class MutateESCorrolated implements InterfaceMutation, java.io.Serializab
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if (mutator == this) {
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return true;
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}
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if (mutator instanceof MutateESCorrolated) {
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MutateESCorrolated mut = (MutateESCorrolated) mutator;
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if (mutator instanceof MutateESCorrelated) {
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MutateESCorrelated mut = (MutateESCorrelated) mutator;
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if (this.tau1 != mut.tau1) {
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return false;
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}
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@ -105,7 +105,7 @@ public class MutateESCorrolated implements InterfaceMutation, java.io.Serializab
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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if (individual instanceof InterfaceESIndividual) {
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double[] x = ((InterfaceESIndividual) individual).getDGenotype();
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if (this.sigmas == null) {
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@ -140,7 +140,7 @@ public class MutateESCovarianceMatrixAdaption implements InterfaceMutation, java
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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if (!(individual instanceof InterfaceESIndividual)) {
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return;
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}
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@ -50,13 +50,13 @@ public class MutateESCovarianceMatrixAdaptionPlus extends
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual,
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public void initialize(AbstractEAIndividual individual,
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InterfaceOptimizationProblem opt) {
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if (!(individual instanceof InterfaceESIndividual)) {
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return;
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}
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super.init(individual, opt);
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super.initialize(individual, opt);
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psuccesstarget = 1.0 / (5 + Math.sqrt(lambda) / 2);
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psuccess = psuccesstarget;
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stepd = 1.0 + D / (2.0 * lambda);
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@ -57,7 +57,7 @@ public class MutateESFixedStepSize implements InterfaceMutation, java.io.Seriali
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -91,7 +91,7 @@ public class MutateESGlobal implements InterfaceMutation, java.io.Serializable,
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -102,7 +102,7 @@ public class MutateESLocal implements InterfaceMutation, InterfaceAdditionalPopu
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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if (individual instanceof InterfaceESIndividual) {
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// initialize the Sigmas
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this.sigmas = new double[((InterfaceESIndividual) individual).getDGenotype().length];
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@ -107,7 +107,7 @@ public class MutateESMainVectorAdaption implements InterfaceMutation, java.io.Se
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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if (!(individual instanceof InterfaceESIndividual)) {
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return;
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}
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@ -85,7 +85,7 @@ public class MutateESMutativeStepSizeControl implements InterfaceMutation, java.
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -104,7 +104,7 @@ public class MutateESPathLengthAdaption implements InterfaceMutation, java.io.Se
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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if (!(individual instanceof InterfaceESIndividual)) {
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return;
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}
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@ -58,7 +58,7 @@ public class MutateESPolynomial implements InterfaceMutation, java.io.Serializab
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -519,7 +519,7 @@ public class MutateESRankMuCMA implements InterfaceAdaptOperatorGenerational, In
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}
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@Override
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public void init(AbstractEAIndividual individual,
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public void initialize(AbstractEAIndividual individual,
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InterfaceOptimizationProblem opt) {
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double[][] range = ((InterfaceDataTypeDouble) individual).getDoubleRange();
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int dim = range.length;
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@ -70,7 +70,7 @@ public class MutateGAAdaptive implements InterfaceMutation, java.io.Serializable
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -75,7 +75,7 @@ public class MutateGAGISwapBits implements InterfaceMutation, java.io.Serializab
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -62,7 +62,7 @@ public class MutateGAInvertBits implements InterfaceMutation, java.io.Serializab
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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/**
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@ -57,7 +57,7 @@ public class MutateGANBit implements InterfaceMutation, java.io.Serializable {
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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/**
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@ -65,7 +65,7 @@ public class MutateGAShiftSubstring implements InterfaceMutation, java.io.Serial
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -97,7 +97,7 @@ public class MutateGASwapBitsSegmentwise implements InterfaceMutation, java.io.S
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -53,7 +53,7 @@ public class MutateGAUniform implements InterfaceMutation, Serializable {
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}
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@Override
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public void init(AbstractEAIndividual individual,
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public void initialize(AbstractEAIndividual individual,
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InterfaceOptimizationProblem opt) {
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if (useInvertedLength && (individual instanceof InterfaceGAIndividual)) {
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setBitwiseProb(1. / ((double) ((InterfaceGAIndividual) individual).getGenotypeLength()));
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@ -55,7 +55,7 @@ public class MutateGIInsertDelete implements InterfaceMutation, java.io.Serializ
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -55,7 +55,7 @@ public class MutateGIInvert implements InterfaceMutation, java.io.Serializable {
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -55,7 +55,7 @@ public class MutateGINominal implements InterfaceMutation, java.io.Serializable
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -60,7 +60,7 @@ public class MutateGIOrdinal implements InterfaceMutation, java.io.Serializable
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* @param opt The optimization problem.
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*/
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@Override
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public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
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}
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@ -61,7 +61,7 @@ public class MutateGISubset implements InterfaceMutation, Serializable {
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}
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@Override
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public void init(AbstractEAIndividual individual,
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public void initialize(AbstractEAIndividual individual,
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InterfaceOptimizationProblem opt) {
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// nothing to do
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@ -70,7 +70,7 @@ public class MutateGITranslocate implements InterfaceMutation, java.io.Serializa
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* @param opt The optimization problem.
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*/
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@Override
|
||||
public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
|
||||
}
|
||||
|
||||
|
@ -70,7 +70,7 @@ public class MutateGPAdaptive implements InterfaceMutation, java.io.Serializable
|
||||
* @param opt The optimization problem.
|
||||
*/
|
||||
@Override
|
||||
public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
|
||||
}
|
||||
|
||||
|
@ -45,7 +45,7 @@ public class MutateGPSingleNode implements InterfaceMutation, java.io.Serializab
|
||||
* @param opt The optimization problem.
|
||||
*/
|
||||
@Override
|
||||
public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
|
||||
}
|
||||
|
||||
|
@ -38,7 +38,7 @@ public class MutateOBGAFlip implements InterfaceMutation, java.io.Serializable {
|
||||
}
|
||||
|
||||
@Override
|
||||
public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
//nothing to initialize
|
||||
}
|
||||
|
||||
|
@ -40,7 +40,7 @@ public class MutateOBGAInversion implements java.io.Serializable, InterfaceMutat
|
||||
}
|
||||
|
||||
@Override
|
||||
public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
//nothing to initialize
|
||||
}
|
||||
|
||||
|
@ -39,7 +39,7 @@ public class NoMutation implements InterfaceMutation, java.io.Serializable {
|
||||
* @param opt The optimization problem.
|
||||
*/
|
||||
@Override
|
||||
public void init(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
public void initialize(AbstractEAIndividual individual, InterfaceOptimizationProblem opt) {
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -395,7 +395,7 @@ public class PostProcess {
|
||||
HillClimbing hc = new HillClimbing();
|
||||
// HC depends heavily on the selected mutation operator!
|
||||
hc.setProblem(problem);
|
||||
mute.init(problem.getIndividualTemplate(), problem);
|
||||
mute.initialize(problem.getIndividualTemplate(), problem);
|
||||
hc.setMutationOperator(mute);
|
||||
if (pop.size() != pop.getTargetSize()) {
|
||||
System.err.println(pop.size() + " vs. " + pop.getTargetSize());
|
||||
|
Loading…
x
Reference in New Issue
Block a user