MATH-1563: Introducing new implementation of GA functionality (WIP).

Closes #209.

commons-math-examples/examples-ga/examples-ga-tsp/src/main/java/org/apache/commons/math4/examples/ga/tsp/TSPOptimizer.java

@@ -76,7 +76,15 @@ public void optimize(List<City> cities,
         final RealValuedChromosome<List<City>> bestFinal = (RealValuedChromosome<List<City>>) finalPopulation
                 .getFittestChromosome();
 
-        logger.info(bestFinal.decode().toString());
+        StringBuilder schedule = new StringBuilder();
+        schedule.append("Travel Shcedule: " + System.lineSeparator());
+        List<City> bestCities = bestFinal.decode();
+        for (City city : bestCities) {
+            schedule.append("City - " + city.getIndex() + System.lineSeparator());
+        }
+        schedule.append("Total distance - " + Math.abs(bestFinal.evaluate()));
+
+        logger.info(schedule.toString());
     }
 
     private static Population<List<City>> getInitialPopulation(List<City> cities, int populationSize) {
@@ -87,12 +95,9 @@ private static Population<List<City>> getInitialPopulation(List<City> cities, in
                     ChromosomeRepresentationUtils.randomPermutation(cities.size()), decodedChromosome -> {
                 final DistanceMatrix distanceMatrix = DistanceMatrix.getInstance(cities);
                 double totalDistance = 0.0;
-                int index1 = 0;
-                int index2 = 0;
                 for (int j = 0; j < cities.size(); j++) {
-                    index1 = j;
-                    index2 = (j == cities.size() - 1) ? 0 : j + 1;
-                    totalDistance += distanceMatrix.getDistance(cities.get(index1), cities.get(index2));
+                    totalDistance += distanceMatrix.getDistance(decodedChromosome.get(j),
+                            decodedChromosome.get((j == cities.size() - 1) ? 0 : j + 1));
                 }
                 return -totalDistance;
             }, new RandomKeyDecoder<City>(cities)));

commons-math-examples/examples-ga/examples-ga-tsp/src/main/java/org/apache/commons/math4/examples/ga/tsp/legacy/LegacyTSPOptimizer.java

@@ -27,12 +27,18 @@
 import org.apache.commons.math3.genetics.StoppingCondition;
 import org.apache.commons.math3.genetics.TournamentSelection;
 import org.apache.commons.math4.examples.ga.tsp.City;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * This class represents the tsp optimizer based on legacy implementation of
  * Genetic Algorithm.
  */
 public class LegacyTSPOptimizer {
+
+    /** instance of logger. **/
+    private final Logger logger = LoggerFactory.getLogger(LegacyTSPOptimizer.class);
+
     /**
      * Optimizes the TSP problem.
      * @param cities                                  list of cities
@@ -67,9 +73,13 @@ public void optimize(List<City> cities,
         @SuppressWarnings("unchecked")
         final RandomKey<City> bestFinal = (RandomKey<City>) finalPopulation.getFittestChromosome();
 
-        //CHECKSTYLE: stop all
-        System.out.println("best=" + bestFinal.toString());
-        //CHECKSTYLE: resume all
+        StringBuilder schedule = new StringBuilder("Travel Shcedule: " + System.lineSeparator());
+        List<City> bestCities = bestFinal.decode(cities);
+        for (City city : bestCities) {
+            schedule.append("City - " + city.getIndex() + System.lineSeparator());
+        }
+        schedule.append("Total distance - " + Math.abs(bestFinal.fitness()));
+        logger.info(schedule.toString());
     }
 
     private static Population getInitialPopulation(List<City> cities, int populationSize, double elitismRate) {

commons-math-ga/src/main/java/org/apache/commons/math4/ga/AbstractGeneticAlgorithm.java

@@ -42,46 +42,22 @@ public abstract class AbstractGeneticAlgorithm<P> {
 
     /** instance of logger. **/
     private static final Logger LOGGER = LoggerFactory.getLogger(AbstractGeneticAlgorithm.class);
-
     /** the crossover policy used by the algorithm. */
     private final CrossoverPolicy<P> crossoverPolicy;
-
     /** the mutation policy used by the algorithm. */
     private final MutationPolicy<P> mutationPolicy;
-
     /** the selection policy used by the algorithm. */
     private final SelectionPolicy<P> selectionPolicy;
-
+    /** the elitism rate having default value of .25. */
+    private final double elitismRate;
     /**
      * the number of generations evolved to reach {@link StoppingCondition} in the
      * last run.
      */
     private int generationsEvolved;
-
-    /** The elitism rate having default value of .25. */
-    private double elitismRate = .25;
-
-    /** The registry for all interested convergence listeners. **/
+    /** the registry for all interested convergence listeners. **/
     private ConvergenceListenerRegistry<P> convergenceListenerRegistry = new ConvergenceListenerRegistry<>();
 
-    /**
-     * @param crossoverPolicy      The {@link CrossoverPolicy}
-     * @param mutationPolicy       The {@link MutationPolicy}
-     * @param selectionPolicy      The {@link SelectionPolicy}
-     * @param convergenceListeners An optional collection of
-     *                             {@link ConvergenceListener} with variable arity
-     */
-    @SafeVarargs
-    protected AbstractGeneticAlgorithm(final CrossoverPolicy<P> crossoverPolicy,
-            final MutationPolicy<P> mutationPolicy,
-            final SelectionPolicy<P> selectionPolicy,
-            ConvergenceListener<P>... convergenceListeners) {
-        this.crossoverPolicy = crossoverPolicy;
-        this.mutationPolicy = mutationPolicy;
-        this.selectionPolicy = selectionPolicy;
-        updateListenerRigistry(convergenceListeners);
-    }
-
     /**
      * @param crossoverPolicy      The {@link CrossoverPolicy}
      * @param mutationPolicy       The {@link MutationPolicy}
@@ -100,13 +76,7 @@ protected AbstractGeneticAlgorithm(final CrossoverPolicy<P> crossoverPolicy,
         this.mutationPolicy = mutationPolicy;
         this.selectionPolicy = selectionPolicy;
         this.elitismRate = elitismRate;
-        updateListenerRigistry(convergenceListeners);
-    }
 
-    // suppressed warnings as the parameter is annotated as @SafeVarargs in
-    // constructor.
-    @SuppressWarnings("unchecked")
-    private void updateListenerRigistry(ConvergenceListener<P>... convergenceListeners) {
         if (convergenceListeners.length > 0) {
             for (ConvergenceListener<P> convergenceListener : convergenceListeners) {
                 convergenceListenerRegistry.addConvergenceListener(convergenceListener);

commons-math-ga/src/main/java/org/apache/commons/math4/ga/AdaptiveGeneticAlgorithm.java

@@ -53,35 +53,11 @@ public class AdaptiveGeneticAlgorithm<P> extends AbstractGeneticAlgorithm<P> {
 
     /** instance of logger. **/
     private static final Logger LOGGER = LoggerFactory.getLogger(AdaptiveGeneticAlgorithm.class);
-
     /** The crossover rate generator. **/
     private final CrossoverRateGenerator<P> crossoverRateGenerator;
-
     /** The mutation rate generator. **/
     private final MutationRateGenerator<P> mutationRateGenerator;
 
-    /**
-     * @param crossoverPolicy               crossover policy
-     * @param crossoverProbabilityGenerator crossover probability generator
-     * @param mutationPolicy                mutation policy
-     * @param mutationProbabilityGenerator  mutation probability generator
-     * @param selectionPolicy               selection policy
-     * @param convergenceListeners          An optional collection of
-     *                                      {@link ConvergenceListener} with
-     *                                      variable arity
-     */
-    @SafeVarargs
-    public AdaptiveGeneticAlgorithm(CrossoverPolicy<P> crossoverPolicy,
-            CrossoverRateGenerator<P> crossoverProbabilityGenerator,
-            MutationPolicy<P> mutationPolicy,
-            MutationRateGenerator<P> mutationProbabilityGenerator,
-            SelectionPolicy<P> selectionPolicy,
-            ConvergenceListener<P>... convergenceListeners) {
-        super(crossoverPolicy, mutationPolicy, selectionPolicy, convergenceListeners);
-        this.crossoverRateGenerator = crossoverProbabilityGenerator;
-        this.mutationRateGenerator = mutationProbabilityGenerator;
-    }
-
     /**
      * @param crossoverPolicy               crossover policy
      * @param crossoverProbabilityGenerator crossover probability generator
@@ -123,8 +99,7 @@ protected Population<P> nextGeneration(final Population<P> current, final Execut
 
         final int maxOffspringCount = nextGeneration.getPopulationLimit() - nextGeneration.getPopulationSize();
 
-        final Population<P> offsprings = reproduceOffsprings(current, executorService,
-                maxOffspringCount);
+        final Population<P> offsprings = reproduceOffsprings(current, executorService, maxOffspringCount);
 
         LOGGER.debug("Performing adaptive mutation of offsprings.");
 
@@ -139,9 +114,10 @@ private List<Chromosome<P>> mutateChromosomes(final ExecutorService executorServ
             final Population<P> offspringPopulation) {
 
         // recompute the statistics of the offspring population.
-        final PopulationStatisticalSummary<P> offspringPopulationStats = ConstantMutationRateGenerator.class
-                .isAssignableFrom(this.mutationRateGenerator.getClass()) ? null :
-                        new PopulationStatisticalSummaryImpl<>(offspringPopulation);
+        final PopulationStatisticalSummary<P> offspringPopulationStats =
+                mutationRateGenerator instanceof ConstantMutationRateGenerator ?
+                null :
+                new PopulationStatisticalSummaryImpl<>(offspringPopulation);
 
         List<Future<Chromosome<P>>> mutatedChromosomes = new ArrayList<>();
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/GeneticAlgorithm.java

@@ -43,44 +43,15 @@ public class GeneticAlgorithm<P> extends AbstractGeneticAlgorithm<P> {
 
     /** instance of logger. **/
     private static final Logger LOGGER = LoggerFactory.getLogger(GeneticAlgorithm.class);
-
     /** crossover rate string. **/
     private static final String CROSSOVER_RATE = "CROSSOVER_RATE";
-
     /** mutation rate string. **/
     private static final String MUTATION_RATE = "MUTATION_RATE";
-
     /** the rate of crossover for the algorithm. */
     private final double crossoverRate;
-
     /** the rate of mutation for the algorithm. */
     private final double mutationRate;
 
-    /**
-     * Create a new genetic algorithm.
-     * @param crossoverPolicy      The {@link CrossoverPolicy}
-     * @param crossoverRate        The crossover rate as a percentage (0-1
-     *                             inclusive)
-     * @param mutationPolicy       The {@link MutationPolicy}
-     * @param mutationRate         The mutation rate as a percentage (0-1 inclusive)
-     * @param selectionPolicy      The {@link SelectionPolicy}
-     * @param convergenceListeners An optional collection of
-     *                             {@link ConvergenceListener} with variable arity
-     */
-    @SafeVarargs
-    public GeneticAlgorithm(final CrossoverPolicy<P> crossoverPolicy,
-            final double crossoverRate,
-            final MutationPolicy<P> mutationPolicy,
-            final double mutationRate,
-            final SelectionPolicy<P> selectionPolicy,
-            ConvergenceListener<P>... convergenceListeners) {
-        super(crossoverPolicy, mutationPolicy, selectionPolicy, convergenceListeners);
-
-        checkValidity(crossoverRate, mutationRate);
-        this.crossoverRate = crossoverRate;
-        this.mutationRate = mutationRate;
-    }
-
     /**
      * Create a new genetic algorithm.
      * @param crossoverPolicy      The {@link CrossoverPolicy}

commons-math-ga/src/main/java/org/apache/commons/math4/ga/ParallelGeneticAlgorithm.java

@@ -42,7 +42,6 @@ public class ParallelGeneticAlgorithm<P> {
 
     /** instance of logger. **/
     private static final Logger LOGGER = LoggerFactory.getLogger(ParallelGeneticAlgorithm.class);
-
     /** List of algorithm execution configurations to be executed in parallel. **/
     private List<AlgorithmExecutionConfig> algorithmConfigParams = new ArrayList<>();
 
@@ -99,18 +98,15 @@ private List<Population<P>> evolve(ExecutorService executorService) {
         } catch (InterruptedException | ExecutionException e) {
             throw new GeneticIllegalArgumentException(e);
         }
-
         return convergedPopulations;
     }
 
     private final class AlgorithmExecutionConfig {
 
         /** instance of genetic algorithm. **/
         private AbstractGeneticAlgorithm<P> algorithm;
-
         /** initial population to converge. **/
         private Population<P> initialPopulation;
-
         /** stopping condition to decide convergence. **/
         private StoppingCondition<P> stoppingCondition;
 
@@ -121,7 +117,5 @@ private AlgorithmExecutionConfig(AbstractGeneticAlgorithm<P> algorithm,
             this.initialPopulation = initialPopulation;
             this.stoppingCondition = stoppingCondition;
         }
-
     }
-
 }

commons-math-ga/src/main/java/org/apache/commons/math4/ga/chromosome/AbstractChromosome.java

@@ -36,16 +36,12 @@ public abstract class AbstractChromosome<P> implements Chromosome<P> {
 
     /** Value assigned when no fitness has been computed yet. */
     private static final double NO_FITNESS = Double.NEGATIVE_INFINITY;
-
     /** Cached value of the fitness of this chromosome. */
     private double fitness = NO_FITNESS;
-
     /** Fitness function to evaluate fitness of chromosome. **/
     private final FitnessFunction<P> fitnessFunction;
-
     /** decoder to deode the chromosome's genotype representation. **/
     private final Decoder<P> decoder;
-
     /** Id of chromosome. **/
     private final String id;
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/chromosome/BinaryChromosome.java

@@ -35,12 +35,10 @@ public class BinaryChromosome<P> extends AbstractChromosome<P> {
      * maximum allowed length of binary chromosome.
      */
     public static final long MAX_LENGTH = Integer.MAX_VALUE;
-
     /**
      * length of binary chromosome.
      */
     private final long length;
-
     /**
      * binary representation of chromosome.
      */

commons-math-ga/src/main/java/org/apache/commons/math4/ga/chromosome/ChromosomePair.java

@@ -25,7 +25,6 @@ public class ChromosomePair<P> {
 
     /** the first chromosome in the pair. */
     private final Chromosome<P> first;
-
     /** the second chromosome in the pair. */
     private final Chromosome<P> second;
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/chromosome/IntegralValuedChromosome.java

@@ -33,7 +33,6 @@ public class IntegralValuedChromosome<P> extends AbstractListChromosome<Integer,
 
     /** minimum acceptable value of allele. **/
     private final int min;
-
     /** maximum acceptable value of allele. **/
     private final int max;
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/chromosome/RealValuedChromosome.java

@@ -36,7 +36,6 @@ public class RealValuedChromosome<P> extends AbstractListChromosome<Double, P> {
 
     /** minimum acceptable value of allele. **/
     private final double min;
-
     /** maximum acceptable value of allele. **/
     private final double max;
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/convergence/FixedElapsedTime.java

@@ -36,7 +36,6 @@ public class FixedElapsedTime<P> implements StoppingCondition<P> {
 
     /** Maximum allowed time period (in nanoseconds). */
     private final long maxTimePeriod;
-
     /** The predetermined termination time (stopping condition). */
     private long endTime = -1;
 
@@ -73,7 +72,6 @@ public boolean isSatisfied(Population<P> population) {
         if (endTime < 0) {
             endTime = System.nanoTime() + maxTimePeriod;
         }
-
         return System.nanoTime() >= endTime;
     }
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/convergence/FixedGenerationCount.java

@@ -30,9 +30,9 @@
  * @since 2.0
  */
 public class FixedGenerationCount<P> implements StoppingCondition<P> {
+
     /** Number of generations that have passed. */
     private int numGenerations;
-
     /** Maximum number of generations (stopping criteria). */
     private final int maxGenerations;
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/convergence/UnchangedBestFitness.java

@@ -30,13 +30,11 @@ public class UnchangedBestFitness<P> implements StoppingCondition<P> {
 
     /** best fitness of previous generation. **/
     private double lastBestFitness = Double.MIN_VALUE;
-
     /**
      * The configured number of generations for which optimization process will
      * continue with unchanged best fitness value.
      **/
     private final int maxGenerationsWithUnchangedBestFitness;
-
     /** Number of generations the best fitness value has not been changed. **/
     private int generationsHavingUnchangedBestFitness;
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/convergence/UnchangedMeanFitness.java

@@ -31,13 +31,11 @@ public class UnchangedMeanFitness<P> implements StoppingCondition<P> {
 
     /** Mean fitness of previous generation. **/
     private double lastMeanFitness = Double.MIN_VALUE;
-
     /**
      * The configured number of generations for which optimization process will
      * continue with unchanged best fitness value.
      **/
     private final int maxGenerationsWithUnchangedMeanFitness;
-
     /** Number of generations the mean fitness value has not been changed. **/
     private int generationsHavingUnchangedMeanFitness;
 
@@ -66,7 +64,6 @@ public boolean isSatisfied(Population<P> population) {
             this.generationsHavingUnchangedMeanFitness = 0;
             lastMeanFitness = currentMeanFitness;
         }
-
         return false;
     }
 

commons-math-ga/src/main/java/org/apache/commons/math4/ga/crossover/AbstractListChromosomeCrossoverPolicy.java

@@ -65,7 +65,6 @@ private void checkValidity(final Chromosome<P> first, final Chromosome<P> second
             throw new GeneticIllegalArgumentException(GeneticIllegalArgumentException.SIZE_MISMATCH,
                     secondListChromosome.getLength(), length);
         }
-
     }
 
     /**