modified for new libraries

MasWag · Jul 30, 2021 · c180f10 · c180f10
1 parent 2930cf4
commit c180f10
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Showing 9 changed files with 67 additions and 41 deletions.
diff --git a/pom.xml b/pom.xml
@@ -303,7 +303,7 @@
         <dependency>
             <groupId>org.uma.jmetal</groupId>
             <artifactId>jmetal-core</artifactId>
-            <version>5.9</version>
+            <version>5.10</version>
         </dependency>
         <dependency>
             <groupId>org.uma.jmetal</groupId>
@@ -315,11 +315,28 @@
             <artifactId>jmetal-problem</artifactId>
             <version>5.10</version>
         </dependency>
+        <dependency>
+            <groupId>org.uma.jmetal</groupId>
+            <artifactId>jmetal-example</artifactId>
+            <version>5.10</version>
+        </dependency>
         <!-- https://mvnrepository.com/artifact/org.projectlombok/lombok -->
         <dependency>
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
             <version>1.18.20</version>
         </dependency>
+
+        <!-- https://mvnrepository.com/artifact/org.jacoco/jacoco-maven-plugin -->
+        <dependency>
+            <groupId>org.jacoco</groupId>
+            <artifactId>jacoco-maven-plugin</artifactId>
+            <version>0.8.7</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.findbugs</groupId>
+            <artifactId>jsr305</artifactId>
+            <version>3.0.0</version>
+        </dependency>
     </dependencies>
 </project>
diff --git a/src/main/java/org/group_mmm/BlackBoxVerifier.java b/src/main/java/org/group_mmm/BlackBoxVerifier.java
@@ -47,7 +47,7 @@ class BlackBoxVerifier {
     private List<MealyMachine<?, String, ?, String>> cexMealy;
     private Alphabet<String> inputAlphabet;
     private LearningAlgorithm.MealyLearner<String, String> learner;
-    private EQOracleChain.MealyEQOracleChain<String, String> eqOracle;
+    private MealyEQOracleChain<String, String> eqOracle;
     private List<String> properties;
     private List<Word<String>> cexInput;
     private List<String> cexProperty;
@@ -95,8 +95,8 @@ class BlackBoxVerifier {
         }
 
         // create an equivalence oracle, that first searches for a counter example using the ltl properties, and next
-        this.eqOracle = new EQOracleChain.MealyEQOracleChain<>(
-                new CExFirstOracle.MealyCExFirstOracle<>(ltlFormulas));
+        this.eqOracle = new MealyEQOracleChain<>(
+                new MealyCExFirstOracle<>(ltlFormulas));
     }
 
     ArrayList<PropertyOracle.MealyPropertyOracle<String, String, String>> getLtlFormulas() {
@@ -113,15 +113,15 @@ public MembershipOracle.MealyMembershipOracle<String, String> getMemOracle() {
     }
 
     void addWpMethodEQOracle(int maxDepth) {
-        addEqOracle(new WpMethodEQOracle.MealyWpMethodEQOracle<>(memOracle, maxDepth));
+        addEqOracle(new MealyWpMethodEQOracle<>(memOracle, maxDepth));
     }
 
     void addBFOracle(double multiplier) {
         addEqOracle(new MealyBFInclusionOracle<>(memOracle, multiplier));
     }
 
     void addRandomWordEQOracle(int minLength, int maxLength, int maxTests, Random random, int batchSize) {
-        addEqOracle(new RandomWordsEQOracle.MealyRandomWordsEQOracle<>(
+        addEqOracle(new MealyRandomWordsEQOracle<>(
                 memOracle, minLength, maxLength, maxTests, random, batchSize));
     }
 
@@ -131,7 +131,7 @@ void addRandomWalkEQOracle(double restartProbability, long maxSteps, Random rand
     }
 
     void addCompleteExplorationEQOracle(int minDepth, int maxDepth, int batchSize) {
-        addEqOracle(new CompleteExplorationEQOracle.MealyCompleteExplorationEQOracle<>(
+        addEqOracle(new MealyCompleteExplorationEQOracle<>(
                 memOracle, minDepth, maxDepth, batchSize));
     }
 

diff --git a/src/main/java/org/group_mmm/EQSearchProblem.java b/src/main/java/org/group_mmm/EQSearchProblem.java
@@ -6,8 +6,8 @@
 import net.automatalib.automata.transducers.MealyMachine;
 import net.automatalib.words.Word;
 import net.automatalib.words.WordBuilder;
-import org.uma.jmetal.problem.impl.AbstractIntegerProblem;
-import org.uma.jmetal.solution.IntegerSolution;
+import org.uma.jmetal.problem.integerproblem.impl.AbstractIntegerProblem;
+import org.uma.jmetal.solution.integersolution.IntegerSolution;
 
 import java.util.Collections;
 import java.util.List;
@@ -37,23 +37,25 @@ public class EQSearchProblem extends AbstractIntegerProblem implements Evaluatio
         setName("EQSearchProblem");
 
         List<Integer> lowerLimit = Collections.nCopies(length, 0);
+        List<Integer> upperLimit = Collections.nCopies(length, Integer.MAX_VALUE);
 
-        setLowerLimit(lowerLimit);
+        setVariableBounds(lowerLimit, upperLimit);
     }
 
     void setSymbolList(List<? extends String> symbolList) {
+        List<Integer> lowerLimit = Collections.nCopies(length, 0);
         List<Integer> upperLimit = Collections.nCopies(length, symbolList.size() - 1);
 
         this.symbolList = symbolList;
-        setUpperLimit(upperLimit);
+        setVariableBounds(lowerLimit, upperLimit);
     }
 
     /** {@inheritDoc} */
     @Override
     public void evaluate(IntegerSolution integerSolution) {
         WordBuilder<String> currentSample = new WordBuilder<>();
         for (int i = 0; i < integerSolution.getNumberOfVariables(); i++) {
-            int value = integerSolution.getVariableValue(i);
+            int value = integerSolution.getVariables().get(i);
             currentSample.append(symbolList.get(value));
         }
         DefaultQuery<String, Word<String>> query = new DefaultQuery<>(currentSample.toWord());

diff --git a/src/main/java/org/group_mmm/GAEQOracle.java b/src/main/java/org/group_mmm/GAEQOracle.java
@@ -7,13 +7,13 @@
 import net.automatalib.words.Word;
 import org.slf4j.LoggerFactory;
 import org.uma.jmetal.algorithm.Algorithm;
-import org.uma.jmetal.operator.CrossoverOperator;
-import org.uma.jmetal.operator.MutationOperator;
-import org.uma.jmetal.operator.SelectionOperator;
-import org.uma.jmetal.operator.impl.selection.BestSolutionSelection;
-import org.uma.jmetal.operator.impl.selection.BinaryTournamentSelection;
-import org.uma.jmetal.solution.IntegerSolution;
-import org.uma.jmetal.util.AlgorithmRunner;
+import org.uma.jmetal.example.AlgorithmRunner;
+import org.uma.jmetal.operator.crossover.CrossoverOperator;
+import org.uma.jmetal.operator.mutation.MutationOperator;
+import org.uma.jmetal.operator.selection.SelectionOperator;
+import org.uma.jmetal.operator.selection.impl.BestSolutionSelection;
+import org.uma.jmetal.operator.selection.impl.BinaryTournamentSelection;
+import org.uma.jmetal.solution.integersolution.IntegerSolution;
 import org.uma.jmetal.util.comparator.ObjectiveComparator;
 import org.uma.jmetal.util.evaluator.impl.SequentialSolutionListEvaluator;
 

diff --git a/src/main/java/org/group_mmm/IntegerRandomMutation.java b/src/main/java/org/group_mmm/IntegerRandomMutation.java
@@ -1,8 +1,8 @@
 package org.group_mmm;
 
 import org.jetbrains.annotations.NotNull;
-import org.uma.jmetal.operator.MutationOperator;
-import org.uma.jmetal.solution.IntegerSolution;
+import org.uma.jmetal.operator.mutation.MutationOperator;
+import org.uma.jmetal.solution.integersolution.IntegerSolution;
 
 import java.util.Objects;
 import java.util.Random;
@@ -50,7 +50,7 @@ public IntegerSolution execute(IntegerSolution solution) {
             if (this.random.nextDouble() < mutationProbability) {
                 int positionToChange = this.random.nextInt(solution.getNumberOfVariables() - 1);
                 Integer newValue = random.nextInt(solution.getUpperBound(i) + 1) + solution.getLowerBound(i);
-                solution.setVariableValue(positionToChange, newValue);
+                solution.getVariables().set(positionToChange, newValue);
             }
         }
         return solution;

diff --git a/src/main/java/org/group_mmm/IntegerUniformCrossover.java b/src/main/java/org/group_mmm/IntegerUniformCrossover.java
@@ -1,7 +1,7 @@
 package org.group_mmm;
 
-import org.uma.jmetal.operator.CrossoverOperator;
-import org.uma.jmetal.solution.IntegerSolution;
+import org.uma.jmetal.operator.crossover.CrossoverOperator;
+import org.uma.jmetal.solution.integersolution.IntegerSolution;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -50,9 +50,9 @@ public List<IntegerSolution> execute(List<IntegerSolution> integerSolutions) {
         offspring.add((IntegerSolution) integerSolutions.get(1).copy());
         for (int i = 0; i < integerSolutions.get(0).getNumberOfVariables(); i++) {
             if (Math.random() < crossoverProbability) {
-                int tmp = offspring.get(0).getVariableValue(i);
-                offspring.get(0).setVariableValue(i, offspring.get(1).getVariableValue(i));
-                offspring.get(1).setVariableValue(i, tmp);
+                int tmp = offspring.get(0).getVariables().get(i);
+                offspring.get(0).getVariables().set(i, offspring.get(1).getVariables().get(i));
+                offspring.get(1).getVariables().set(i, tmp);
             }
         }
         return offspring;

diff --git a/src/main/java/org/group_mmm/SimulinkGenerationalGeneticAlgorithm.java b/src/main/java/org/group_mmm/SimulinkGenerationalGeneticAlgorithm.java
@@ -3,10 +3,10 @@
 import de.learnlib.api.oracle.PropertyOracle;
 import org.slf4j.LoggerFactory;
 import org.uma.jmetal.algorithm.singleobjective.geneticalgorithm.GenerationalGeneticAlgorithm;
-import org.uma.jmetal.operator.CrossoverOperator;
-import org.uma.jmetal.operator.MutationOperator;
-import org.uma.jmetal.operator.SelectionOperator;
-import org.uma.jmetal.solution.IntegerSolution;
+import org.uma.jmetal.operator.crossover.CrossoverOperator;
+import org.uma.jmetal.operator.mutation.MutationOperator;
+import org.uma.jmetal.operator.selection.SelectionOperator;
+import org.uma.jmetal.solution.integersolution.IntegerSolution;
 import org.uma.jmetal.util.evaluator.SolutionListEvaluator;
 
 import java.util.List;

diff --git a/src/main/java/org/group_mmm/SimulinkSULMapper.java b/src/main/java/org/group_mmm/SimulinkSULMapper.java
@@ -5,7 +5,7 @@
 import lombok.extern.slf4j.Slf4j;
 import net.automatalib.words.Alphabet;
 import net.automatalib.words.Word;
-import net.automatalib.words.impl.SimpleAlphabet;
+import net.automatalib.words.impl.GrowingMapAlphabet;
 
 import java.util.*;
 import java.util.stream.Collectors;
@@ -130,10 +130,10 @@ public List<Double> mapConcrete(List<Double> concreteOutput) {
     }
 
     Alphabet<String> constructAbstractAlphabet() {
-        return new SimpleAlphabet<>(this.inputMapper.keySet());
+        return new GrowingMapAlphabet<>(this.inputMapper.keySet());
     }
 
     Alphabet<List<Double>> constructConcreteAlphabet() {
-        return new SimpleAlphabet<>(this.inputMapper.values());
+        return new GrowingMapAlphabet<>(this.inputMapper.values());
     }
 }
diff --git a/src/main/java/org/group_mmm/SimulinkSteadyStateGeneticAlgorithm.java b/src/main/java/org/group_mmm/SimulinkSteadyStateGeneticAlgorithm.java
@@ -3,10 +3,10 @@
 import de.learnlib.api.oracle.PropertyOracle;
 import org.slf4j.LoggerFactory;
 import org.uma.jmetal.algorithm.singleobjective.geneticalgorithm.SteadyStateGeneticAlgorithm;
-import org.uma.jmetal.operator.CrossoverOperator;
-import org.uma.jmetal.operator.MutationOperator;
-import org.uma.jmetal.operator.SelectionOperator;
-import org.uma.jmetal.solution.IntegerSolution;
+import org.uma.jmetal.operator.crossover.CrossoverOperator;
+import org.uma.jmetal.operator.mutation.MutationOperator;
+import org.uma.jmetal.operator.selection.SelectionOperator;
+import org.uma.jmetal.solution.integersolution.IntegerSolution;
 import org.uma.jmetal.util.evaluator.SolutionListEvaluator;
 
 import java.util.List;
@@ -22,13 +22,20 @@ public class SimulinkSteadyStateGeneticAlgorithm extends SteadyStateGeneticAlgor
     private EQSearchProblem problem;
     private PropertyOracle.MealyPropertyOracle<String, String, String> ltlOracle;
 
-    SimulinkSteadyStateGeneticAlgorithm(EQSearchProblem problem, int maxEvaluations, int populationSize, CrossoverOperator<IntegerSolution> crossoverOperator, MutationOperator<IntegerSolution> mutationOperator, SelectionOperator<List<IntegerSolution>, IntegerSolution> selectionOperator, SolutionListEvaluator<IntegerSolution> evaluator, PropertyOracle.MealyPropertyOracle<String, String, String> ltlOracle) {
+    SimulinkSteadyStateGeneticAlgorithm(EQSearchProblem problem, int maxEvaluations, int populationSize,
+                                        CrossoverOperator<IntegerSolution> crossoverOperator,
+                                        MutationOperator<IntegerSolution> mutationOperator,
+                                        SelectionOperator<List<IntegerSolution>, IntegerSolution> selectionOperator,
+                                        SolutionListEvaluator<IntegerSolution> evaluator,
+                                        PropertyOracle.MealyPropertyOracle<String, String, String> ltlOracle) {
         super(problem, maxEvaluations, populationSize, crossoverOperator, mutationOperator, selectionOperator);
         this.problem = problem;
         this.ltlOracle = ltlOracle;
     }
 
-    /** {@inheritDoc} */
+    /**
+     * {@inheritDoc}
+     */
     @Override
     protected boolean isStoppingConditionReached() {
         if (super.isStoppingConditionReached()) {
@@ -40,7 +47,7 @@ protected boolean isStoppingConditionReached() {
 
     /**
      * {@inheritDoc}
-     *
+     * <p>
      * Create initial population only for the initial run
      */
     @Override