Developed the new genetic algorithm module following the JIRA MATH-1563.

commons-math-examples/examples-ga/examples-ga-math-functions/pom.xml

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+<?xml version="1.0"?>
+<!--
+   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>
+        <groupId>org.apache.commons</groupId>
+        <artifactId>examples-ga</artifactId>
+        <version>4.0-SNAPSHOT</version>
+    </parent>
+    <artifactId>examples-ga-math-functions</artifactId>
+
+    <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.ga.mathfunctions</commons.osgi.symbolicName>
+        <commons.osgi.export>org.apache.commons.math4.examples.ga.mathfunctions</commons.osgi.export>
+        <!-- Java 9+ -->
+        <commons.automatic.module.name>org.apache.commons.math4.examples.ga.mathfunctions</commons.automatic.module.name>
+        <!-- Workaround to avoid duplicating config files. -->
+        <math.parent.dir>${basedir}/../../..</math.parent.dir>
+
+        <uberjar.name>examples-ga-mathfunctions</uberjar.name>
+        <project.mainClass>org.apache.commons.math4.examples.ga.mathfunctions.Dimension2FunctionOptimizer</project.mainClass>
+    </properties>
+
+</project>

commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dim2GraphPlotter.java

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+/*
+ * 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.ga.mathfunctions.dimension2;
+
+import java.awt.BorderLayout;
+import java.util.List;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import org.apache.commons.math4.ga.internal.stats.PopulationStatisticalSummaryImpl;
+import org.apache.commons.math4.ga.listener.ConvergenceListener;
+import org.apache.commons.math4.ga.population.Population;
+import org.apache.commons.math4.ga.stats.PopulationStatisticalSummary;
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+/**
+ * This class represents the graph plotter during optimization.
+ */
+public class Dim2GraphPlotter extends JFrame implements ConvergenceListener<Dimension2Coordinate> {
+
+    /**
+     * Generated serialversionId.
+     */
+    private static final long serialVersionUID = -5683904006424006584L;
+
+    /** collection of 2-D series. **/
+    private final XYSeriesCollection dataset = new XYSeriesCollection();
+
+    /**
+     * constructor.
+     * @param plotSubject subject of plot
+     * @param xAxisLabel  x axis label
+     * @param yAxisLabel  y axis label
+     */
+    public Dim2GraphPlotter(String plotSubject, String xAxisLabel, String yAxisLabel) {
+        super(plotSubject);
+
+        final JPanel chartPanel = createChartPanel(plotSubject, xAxisLabel, yAxisLabel);
+        add(chartPanel, BorderLayout.CENTER);
+
+        setSize(640, 480);
+        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        setLocationRelativeTo(null);
+
+        setVisible(true);
+    }
+
+    /**
+     * Adds data point to graph.
+     * @param graphName  name of graph
+     * @param generation generation, to be plotted along x axis
+     * @param value      value, to be plotted along y axis
+     */
+    private void addDataPoint(String graphName, int generation, double value) {
+        XYSeries series = null;
+
+        if (!containsGraph(graphName)) {
+            series = new XYSeries(graphName);
+            dataset.addSeries(series);
+        } else {
+            series = dataset.getSeries(graphName);
+        }
+        series.add(generation, value);
+
+        setVisible(true);
+    }
+
+    /**
+     * Checks if the graph with the given name already exists.
+     * @param graphName name of the graph
+     * @return true/false
+     */
+    @SuppressWarnings("unchecked")
+    private boolean containsGraph(String graphName) {
+        final List<XYSeries> seriesList = dataset.getSeries();
+        if (seriesList == null || seriesList.isEmpty()) {
+            return false;
+        }
+        for (XYSeries series : seriesList) {
+            if (series.getKey().compareTo(graphName) == 0) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    /**
+     * Creates chart panel.
+     * @param chartTitle chart title
+     * @param xAxisLabel x axis label
+     * @param yAxisLabel y axis label
+     * @return panel
+     */
+    private JPanel createChartPanel(String chartTitle, String xAxisLabel, String yAxisLabel) {
+
+        final boolean showLegend = true;
+        final boolean createURL = false;
+        final boolean createTooltip = false;
+
+        final JFreeChart chart = ChartFactory.createXYLineChart(chartTitle, xAxisLabel, yAxisLabel, dataset,
+                PlotOrientation.VERTICAL, showLegend, createTooltip, createURL);
+        final XYPlot plot = chart.getXYPlot();
+        final XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
+
+        plot.setRenderer(renderer);
+
+        return new ChartPanel(chart);
+
+    }
+
+    /**
+     * {@inheritDoc}
+     */
+    @Override
+    public void notify(int generation, Population<Dimension2Coordinate> population) {
+        PopulationStatisticalSummary<Dimension2Coordinate> populationStatisticalSummary =
+                new PopulationStatisticalSummaryImpl<>(population);
+        this.addDataPoint("Average", generation, populationStatisticalSummary.getMeanFitness());
+        this.addDataPoint("Best", generation, populationStatisticalSummary.getMaxFitness());
+    }
+
+}

commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dimension2Coordinate.java

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+/*
+ * 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.ga.mathfunctions.dimension2;
+
+/**
+ * This class represents the coordinate of the problem domain i.e. the phenotype of chromosome.
+ */
+public class Dimension2Coordinate {
+
+    /** coordinate of first dimension. **/
+    private final double x;
+
+    /** coordinate of second dimension. **/
+    private final double y;
+
+    /**
+     * constructor.
+     * @param x coordinate of first dimension
+     * @param y coordinate of second dimension
+     */
+    public Dimension2Coordinate(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 + "]";
+    }
+
+}

commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dimension2Decoder.java

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+/*
+ * 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.ga.mathfunctions.dimension2;
+
+import java.util.List;
+
+import org.apache.commons.math4.ga.chromosome.AbstractListChromosome;
+import org.apache.commons.math4.ga.chromosome.BinaryChromosome;
+import org.apache.commons.math4.ga.decoder.AbstractListChromosomeDecoder;
+
+/**
+ * Decoder to convert chromosome's binary genotype to phenotype
+ * {@link Dimension2Coordinate}.
+ */
+public class Dimension2Decoder extends AbstractListChromosomeDecoder<Integer, Dimension2Coordinate> {
+
+    /**
+     * decode the binary representation of chromosome to
+     * {@link Dimension2Coordinate}.
+     * @param chromosome The {@link AbstractListChromosome}
+     */
+    @Override
+    protected Dimension2Coordinate decode(AbstractListChromosome<Integer, Dimension2Coordinate> chromosome) {
+        final BinaryChromosome<Dimension2Coordinate> binaryChromosome =
+                (BinaryChromosome<Dimension2Coordinate>) chromosome;
+        final List<Integer> alleles = binaryChromosome.getRepresentation();
+
+        final StringBuilder allelesStr = new StringBuilder();
+        for (Integer allele : alleles) {
+            allelesStr.append(Integer.toBinaryString(allele));
+        }
+
+        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 Dimension2Coordinate(x, y);
+    }
+
+}

commons-math-examples/examples-ga/examples-ga-math-functions/src/main/java/org/apache/commons/math4/examples/ga/mathfunctions/dimension2/Dimension2FitnessFunction.java

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+/*
+ * 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.ga.mathfunctions.dimension2;
+
+import org.apache.commons.math4.ga.fitness.FitnessFunction;
+
+/**
+ * This class represents the mathematical fitness function for optimizing a 2
+ * dimension mathematical function.
+ */
+public class Dimension2FitnessFunction implements FitnessFunction<Dimension2Coordinate> {
+
+    /**
+     * Computes the fitness value based on the decoded chromosome.
+     * @param coordinate The {@link Dimension2Coordinate}
+     * @return the fitness value
+     */
+    @Override
+    public double compute(Dimension2Coordinate coordinate) {
+        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);
+    }
+
+}