avijitbasak · avijitbasak · Sep 23, 2021 · Sep 23, 2021 · Sep 23, 2021
diff --git a/commons-math-examples/examples-genetics/examples-genetics-math-functions/pom.xml b/commons-math-examples/examples-genetics/examples-genetics-math-functions/pom.xml
@@ -1,21 +1,15 @@
-<!--
-   Licensed to the Apache Software Foundation (ASF) under one or more
-   contributor license agreements.  See the NOTICE file distributed with
-   this work for additional information regarding copyright ownership.
-   The ASF licenses this file to You under the Apache License, Version 2.0
-   (the "License"); you may not use this file except in compliance with
-   the License.  You may obtain a copy of the License at
-
-       http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-   See the License for the specific language governing permissions and
-   limitations under the License.
--->
-
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor 
+	license agreements. See the NOTICE file distributed with this work for additional 
+	information regarding copyright ownership. The ASF licenses this file to 
+	You under the Apache License, Version 2.0 (the "License"); you may not use 
+	this file except in compliance with the License. You may obtain a copy of 
+	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
+	by applicable law or agreed to in writing, software distributed under the 
+	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+	OF ANY KIND, either express or implied. See the License for the specific 
+	language governing permissions and limitations under the License. -->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
@@ -25,20 +19,20 @@
 	</parent>
 	<artifactId>examples-genetics-math-functions</artifactId>
 
-	<dependencies>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math4-genetics</artifactId>
-			<version>4.0-SNAPSHOT</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math3</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.jfree</groupId>
-			<artifactId>jfreechart</artifactId>
-			<version>1.5.3</version>
-		</dependency>
-	</dependencies>
+	<properties>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
+
+		<!-- OSGi -->
+		<commons.osgi.symbolicName>org.apache.commons.math4.examples.genetics.mathfunctions</commons.osgi.symbolicName>
+		<commons.osgi.export>org.apache.commons.math4.examples.genetics.mathfunctions</commons.osgi.export>
+		<!-- Java 9+ -->
+		<commons.automatic.module.name>org.apache.commons.math4.examples.genetics.mathfunctions</commons.automatic.module.name>
+		<!-- Workaround to avoid duplicating config files. -->
+		<math.parent.dir>${basedir}/../../..</math.parent.dir>
+
+		<uberjar.name>examples-genetics-mathfunctions</uberjar.name>
+		<project.mainClass>org.apache.commons.math4.examples.genetics.mathfunctions.Dimension2FunctionOptimizer</project.mainClass>
+	</properties>
+
 </project>
diff --git a/...ns/src/main/java/org/apache/commons/math4/examples/genetics/mathfunctions/Coordinate.java b/...ns/src/main/java/org/apache/commons/math4/examples/genetics/mathfunctions/Coordinate.java
@@ -1,24 +1,61 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.apache.commons.math4.examples.genetics.mathfunctions;
 
+/**
+ * This class represents the coordinate of the problem domain i.e. the phenotype of chromosome.
+ */
 public class Coordinate {
 
-    private double x;
+    /** coordinate of first dimension. **/
+    private final double x;
 
-    private double y;
+    /** coordinate of second dimension. **/
+    private final double y;
 
+    /**
+     * constructor.
+     * @param x coordinate of first dimension
+     * @param y coordinate of second dimension
+     */
     public Coordinate(double x, double y) {
         this.x = x;
         this.y = y;
     }
 
+    /**
+     * returns the coordinate of first dimension.
+     * @return coordinate of first dimension
+     */
     public double getX() {
         return x;
     }
 
+    /**
+     * returns the coordinate of second dimension.
+     * @return coordinate of second dimension
+     */
     public double getY() {
         return y;
     }
 
+    /**
+     * Returns a string representation of coordinate.
+     */
     @Override
     public String toString() {
         return "Coordinate [x=" + x + ", y=" + y + "]";

diff --git a/...main/java/org/apache/commons/math4/examples/genetics/mathfunctions/Dimension2Decoder.java b/...main/java/org/apache/commons/math4/examples/genetics/mathfunctions/Dimension2Decoder.java
@@ -1,25 +1,49 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.apache.commons.math4.examples.genetics.mathfunctions;
 
 import java.util.List;
 
-import org.apache.commons.math4.genetics.AbstractListChromosome;
-import org.apache.commons.math4.genetics.BinaryChromosome;
+import org.apache.commons.math4.genetics.chromosome.AbstractListChromosome;
+import org.apache.commons.math4.genetics.chromosome.BinaryChromosome;
 import org.apache.commons.math4.genetics.decoder.AbstractListChromosomeDecoder;
 
+/**
+ * Decoder to convert chromosome's binary genotype to phenotype
+ * {@link Coordinate}.
+ */
 public class Dimension2Decoder extends AbstractListChromosomeDecoder<Integer, Coordinate> {
 
+    /**
+     * decode the binary representation of chromosome to {@link Coordinate}.
+     * @param chromosome The {@link AbstractListChromosome}
+     */
     @Override
     protected Coordinate decode(AbstractListChromosome<Integer, Coordinate> chromosome) {
-        BinaryChromosome<Coordinate> binaryChromosome = (BinaryChromosome<Coordinate>) chromosome;
-        List<Integer> alleles = binaryChromosome.getRepresentation();
+        final BinaryChromosome<Coordinate> binaryChromosome = (BinaryChromosome<Coordinate>) chromosome;
+        final List<Integer> alleles = binaryChromosome.getRepresentation();
 
-        StringBuilder allelesStr = new StringBuilder();
+        final StringBuilder allelesStr = new StringBuilder();
         for (Integer allele : alleles) {
             allelesStr.append(Integer.toBinaryString(allele));
         }
 
-        double x = Integer.parseInt(allelesStr.substring(0, 12), 2) / 100.0;
-        double y = Integer.parseInt(allelesStr.substring(12, 24), 2) / 100.0;
+        final double x = Integer.parseInt(allelesStr.substring(0, 12), 2) / 100.0;
+        final double y = Integer.parseInt(allelesStr.substring(12, 24), 2) / 100.0;
 
         return new Coordinate(x, y);
     }

diff --git a/...a/org/apache/commons/math4/examples/genetics/mathfunctions/Dimension2FitnessFunction.java b/...a/org/apache/commons/math4/examples/genetics/mathfunctions/Dimension2FitnessFunction.java
@@ -17,16 +17,24 @@
 
 package org.apache.commons.math4.examples.genetics.mathfunctions;
 
-import org.apache.commons.math4.genetics.FitnessFunction;
+import org.apache.commons.math4.genetics.fitness.FitnessFunction;
 
+/**
+ * This class represents the mathematical fitness function for optimizing a 2
+ * dimension mathematical function.
+ */
 public class Dimension2FitnessFunction implements FitnessFunction<Coordinate> {
 
+    /**
+     * Computes the fitness value based on the decoded chromosome.
+     * @param coordinate The {@link Coordinate}
+     * @return the fitness value
+     */
     @Override
     public double compute(Coordinate coordinate) {
-        double computedValue = Math.pow((Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2)), .25) * (Math
-                .pow(Math.sin(50 * Math.pow((Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2)), .1)), 2)
-                + 1);
-        return -computedValue;
+        return -Math.pow(Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2), .25) *
+                (Math.pow(Math.sin(50 * Math.pow(Math.pow(coordinate.getX(), 2) + Math.pow(coordinate.getY(), 2), .1)),
+                        2) + 1);
     }
 
 }
diff --git a/...org/apache/commons/math4/examples/genetics/mathfunctions/Dimension2FunctionOptimizer.java b/...org/apache/commons/math4/examples/genetics/mathfunctions/Dimension2FunctionOptimizer.java
@@ -18,70 +18,86 @@
 package org.apache.commons.math4.examples.genetics.mathfunctions;
 
 import org.apache.commons.math4.examples.genetics.mathfunctions.utils.Constants;
+
 import org.apache.commons.math4.examples.genetics.mathfunctions.utils.GraphPlotter;
-import org.apache.commons.math4.genetics.BinaryChromosome;
-import org.apache.commons.math4.genetics.Chromosome;
 import org.apache.commons.math4.genetics.GeneticAlgorithm;
-import org.apache.commons.math4.genetics.ListPopulation;
-import org.apache.commons.math4.genetics.Population;
+import org.apache.commons.math4.genetics.chromosome.BinaryChromosome;
+import org.apache.commons.math4.genetics.chromosome.Chromosome;
 import org.apache.commons.math4.genetics.convergencecond.StoppingCondition;
 import org.apache.commons.math4.genetics.convergencecond.UnchangedBestFitness;
 import org.apache.commons.math4.genetics.crossover.OnePointCrossover;
 import org.apache.commons.math4.genetics.listener.ConvergenceListenerRegistry;
 import org.apache.commons.math4.genetics.listener.PopulationStatisticsLogger;
 import org.apache.commons.math4.genetics.mutation.BinaryMutation;
+import org.apache.commons.math4.genetics.population.ListPopulation;
+import org.apache.commons.math4.genetics.population.Population;
 import org.apache.commons.math4.genetics.selection.TournamentSelection;
 import org.apache.commons.math4.genetics.utils.ConsoleLogger;
 
 /**
- * 
- *
+ * This class represents an optimizer for a 2-dimensional math function using
+ * genetic algorithm.
  */
 public class Dimension2FunctionOptimizer {
 
+    /**
+     * Optimizes the 2-dimension fitness function.
+     * @param args arguments
+     */
     public static void main(String[] args) {
-        Population<Coordinate> initPopulation = getInitialPopulation();
+        final Population<Coordinate> initPopulation = getInitialPopulation();
 
-        Dimension2FunctionOptimizer optimizer = new Dimension2FunctionOptimizer();
+        final Dimension2FunctionOptimizer optimizer = new Dimension2FunctionOptimizer();
 
-        ConvergenceListenerRegistry<Coordinate> convergenceListenerRegistry = ConvergenceListenerRegistry.getInstance();
-        convergenceListenerRegistry.addConvergenceListener(new PopulationStatisticsLogger<Coordinate>("UTF-8"));
+        final ConvergenceListenerRegistry<Coordinate> convergenceListenerRegistry = ConvergenceListenerRegistry
+                .getInstance();
+        convergenceListenerRegistry
+                .addConvergenceListener(new PopulationStatisticsLogger<Coordinate>(Constants.ENCODING));
         convergenceListenerRegistry
                 .addConvergenceListener(new GraphPlotter("Convergence Stats", "generation", "fitness"));
 
         optimizer.optimize(initPopulation);
     }
 
+    /**
+     * Optimizes the population.
+     * @param initial The {@link Population}
+     */
     public void optimize(Population<Coordinate> initial) {
 
         // initialize a new genetic algorithm
-        GeneticAlgorithm<Coordinate> ga = new GeneticAlgorithm<Coordinate>(new OnePointCrossover<Integer, Coordinate>(),
+        final GeneticAlgorithm<Coordinate> ga = new GeneticAlgorithm<>(new OnePointCrossover<Integer, Coordinate>(),
                 Constants.CROSSOVER_RATE, new BinaryMutation<Coordinate>(), Constants.AVERAGE_MUTATION_RATE,
                 new TournamentSelection<Coordinate>(Constants.TOURNAMENT_SIZE), Constants.ELITISM_RATE);
 
         // stopping condition
-        StoppingCondition<Coordinate> stopCond = new UnchangedBestFitness<Coordinate>(
+        final StoppingCondition<Coordinate> stopCond = new UnchangedBestFitness<>(
                 Constants.GENERATION_COUNT_WITH_UNCHANGED_BEST_FUTNESS);
 
         // run the algorithm
-        Population<Coordinate> finalPopulation = ga.evolve(initial, stopCond);
+        final Population<Coordinate> finalPopulation = ga.evolve(initial, stopCond);
 
         // best chromosome from the final population
-        Chromosome<Coordinate> bestFinal = finalPopulation.getFittestChromosome();
-        ConsoleLogger consoleLogger = ConsoleLogger.getInstance("UTF-8");
+        final Chromosome<Coordinate> bestFinal = finalPopulation.getFittestChromosome();
+        final ConsoleLogger consoleLogger = ConsoleLogger.getInstance(Constants.ENCODING);
         consoleLogger.log("*********************************************");
         consoleLogger.log("***********Optimization Result***************");
-        consoleLogger.log("*********************************************");
 
         consoleLogger.log(bestFinal.toString());
 
     }
 
+    /**
+     * Generates an initial population.
+     * @return initial population
+     */
     private static Population<Coordinate> getInitialPopulation() {
-        Population<Coordinate> population = new ListPopulation<>(Constants.POPULATION_SIZE);
+        final Population<Coordinate> population = new ListPopulation<>(Constants.POPULATION_SIZE);
+        final Dimension2FitnessFunction fitnessFunction = new Dimension2FitnessFunction();
+        final Dimension2Decoder decoder = new Dimension2Decoder();
         for (int i = 0; i < Constants.POPULATION_SIZE; i++) {
             population.addChromosome(BinaryChromosome.<Coordinate>randomChromosome(Constants.CHROMOSOME_LENGTH,
-                    new Dimension2FitnessFunction(), new Dimension2Decoder()));
+                    fitnessFunction, decoder));
         }
         return population;
     }