mutationoperator.java

用java语言写的遗传算法库

/*
 * This file is part of JGAP.
 *
 * JGAP offers a dual license model containing the LGPL as well as the MPL.
 *
 * For licencing information please see the file license.txt included with JGAP
 * or have a look at the top of class org.jgap.Chromosome which representatively
 * includes the JGAP license policy applicable for any file delivered with JGAP.
 */
package org.jgap.impl;

import java.util.*;
import org.jgap.*;

/**
 * The mutation operator runs through the genes in each of the Chromosomes
 * in the population and mutates them in statistical accordance to the
 * given mutation rate. Mutated Chromosomes are then added to the list of
 * candidate Chromosomes destined for the natural selection process.
 * <p>
 * This MutationOperator supports both fixed and dynamic mutation rates.
 * A fixed rate is one specified at construction time by the user. A dynamic
 * rate is one determined by this class if no fixed rate is provided, and is
 * calculated based on the size of the Chromosomes in the population such
 * that, on average, one gene will be mutated for every ten Chromosomes
 * processed by this operator.
 *
 * @author Neil Rotstan
 * @author Klaus Meffert
 * @since 1.0
 */
public class MutationOperator
    implements GeneticOperator {
  /** String containing the CVS revision. Read out via reflection!*/
  private final static String CVS_REVISION = "$Revision: 1.17 $";

  /**
   * The current mutation rate used by this MutationOperator, expressed as
   * the denominator in the 1 / X ratio. For example, a value of 1000 would
   * mean that, on average, 1 / 1000 genes would be mutated. A value of zero
   * disabled mutation entirely.
   */
  protected int m_mutationRate;

  /**
   * Calculator for dynamically determining the mutation rate. If set to
   * null the value of m_mutationRate will be used.
   * Replaces the previously used boolean m_dynamicMutationRate
   */
  private IUniversalRateCalculator m_mutationRateCalc;

  /**
   * Constructs a new instance of this MutationOperator without a specified
   * mutation rate, which results in dynamic mutation being turned on. This
   * means that the mutation rate will be automatically determined by this
   * operator based upon the number of genes present in the chromosomes.
   *
   * @author Neil Rotstan
   * @since 1.0
   */
  public MutationOperator() {
    setMutationRateCalc(new DefaultMutationRateCalculator());
  }

  /**
   * Constructs a new instance of this MutationOperator with a specified
   * mutation rate calculator, which results in dynamic mutation being turned
   * on.
   * @param a_mutationRateCalculator calculator for dynamic mutation rate
   *        computation
   *
   * @author Klaus Meffert
   * @since 1.1
   */
  public MutationOperator(IUniversalRateCalculator a_mutationRateCalculator) {
    setMutationRateCalc(a_mutationRateCalculator);
  }

  /**
   * Constructs a new instance of this MutationOperator with the given
   * mutation rate.
   *
   * @param a_desiredMutationRate The desired rate of mutation, expressed
   *                              as the denominator of the 1 / X fraction.
   *                              For example, 1000 would result in 1/1000
   *                              genes being mutated on average. A mutation
   *                              rate of zero disables mutation entirely.
   *
   * @author Neil Rotstan
   * @since 1.1
   */
  public MutationOperator(int a_desiredMutationRate) {
    m_mutationRate = a_desiredMutationRate;
    setMutationRateCalc(null);
  }

  /**
   * The operate method will be invoked on each of the genetic operators
   * referenced by the current Configuration object during the evolution
   * phase. Operators are given an opportunity to run in the order that
   * they are added to the Configuration. Implementations of this method
   * may reference the population of Chromosomes as it was at the beginning
   * of the evolutionary phase and/or they may instead reference the
   * candidate Chromosomes, which are the results of prior genetic operators.
   * In either case, only Chromosomes added to the list of candidate
   * chromosomes will be considered for natural selection. Implementations
   * should never modify the original population, but should first make copies
   * of the Chromosomes selected for modification and operate upon the copies.
   *
   * @param a_population The population of chromosomes from the current
   *                     evolution prior to exposure to any genetic operators.
   *                     Chromosomes in this array should never be modified.
   * @param a_candidateChromosomes The pool of chromosomes that are candidates
   *                               for the next evolved population. Only these
   *                               chromosomes will go to the natural
   *                               phase, so it's important to add any
   *                               modified copies of Chromosomes to this
   *                               list if it's desired for them to be
   *                               considered for natural selection.
   *
   * @author Neil Rotstan
   * @author Klaus Meffert
   * @since 1.0
   */
  public void operate(final Population a_population,
                      final List a_candidateChromosomes) {
    // If the mutation rate is set to zero and dynamic mutation rate is
    // disabled, then we don't perform any mutation.
    // ----------------------------------------------------------------
    if (m_mutationRate == 0 && m_mutationRateCalc == null) {
      return;
    }
    // Determine the mutation rate. If dynamic rate is enabled, then
    // calculate it using the IUniversalRateCalculator instance.
    // Otherwise, go with the mutation rate set upon construction.
    // --------------------------------------------------------------
    boolean mutate = false;

    RandomGenerator generator = Genotype.getConfiguration().getRandomGenerator();

    // It would be inefficient to create copies of each Chromosome just
    // to decide whether to mutate them. Instead, we only make a copy
    // once we've positively decided to perform a mutation.
    // ----------------------------------------------------------------
    int size = Math.min(Genotype.getConfiguration().getPopulationSize(),
                        a_population.size());
    for (int i = 0; i < size; i++) {
      Gene[] genes = a_population.getChromosome(i).getGenes();
      Chromosome copyOfChromosome = null;
      // For each Chromosome in the population...
      // ----------------------------------------
      for (int j = 0; j < genes.length; j++) {

        if (m_mutationRateCalc != null) {
          // If it's a dynamic mutation rate then let the calculator decide
          // whether the current gene should be mutated
          mutate = m_mutationRateCalc.toBePermutated();
        }
        else {
          // Else non-dynamic so just mutate based on the the current rate.
          // In fact we use a rate of 1/m_mutationRate
          mutate = (generator.nextInt(m_mutationRate) == 0);
        }

        if (mutate) {
          // Now that we want to actually modify the Chromosome,
          // let's make a copy of it (if we haven't already) and
          // add it to the candidate chromosomes so that it will
          // be considered for natural selection during the next
          // phase of evolution. Then we'll set the gene's value
          // to a random value as the implementation of our
          // "mutation" of the gene.
          // ---------------------------------------------------
          if (copyOfChromosome == null) {
            // ...take a copy of it...
            // -----------------------
            copyOfChromosome = (Chromosome) a_population.getChromosome(i).clone();
            // ...add it to the candidate pool...
            // ----------------------------------
            a_candidateChromosomes.add(copyOfChromosome);
            // ...then mutate all its genes...
            // -------------------------------
            genes = copyOfChromosome.getGenes();

          }
          // Process all atomic elements in the gene. For a StringGene this
          // would be the length of the string, for an IntegerGene, it is
          // always one element
          // --------------------------------------------------------------
          if (genes[j] instanceof CompositeGene) {
            CompositeGene compositeGene = (CompositeGene) genes[j];
            for (int k = 0; k < compositeGene.size(); k++) {
              mutateGene(compositeGene.geneAt(k), generator);
            }
          }
          else {
            mutateGene(genes[j], generator);
          }
        }
      }
    }
  }

  /**
   * Helper: mutate all atomic elements of a gene
   * @param a_gene the gene to be mutated
   * @param a_generator the generator delivering amount of mutation
   *
   * @author Klaus Meffert
   * @since 1.1
   */
  private void mutateGene(Gene a_gene, RandomGenerator a_generator) {
    for (int k = 0; k < a_gene.size(); k++) {
      // Retrieve value between 0 and 1 (not included) from
      // generator. Then map this value to range -1 and 1
      // (-1 included, 1 not)
      // --------------------------------------------------
      double percentage = -1 + a_generator.nextDouble() * 2;
      // Mutate atomic element by calculated percentage
      // ----------------------------------------------
      a_gene.applyMutation(k, percentage);
    }
  }

  /**
   * @return the MutationRateCalculator used
   *
   * @author Klaus Meffert
   * @since 1.1
   */
  public IUniversalRateCalculator getMutationRateCalc() {
    return m_mutationRateCalc;
  }

  /**
   * Sets the MutationRateCalculator to be used for determining the strengt of
   * mutation
   * @param m_mutationRateCalc MutationRateCalculator
   *
   * @author Klaus Meffert
   * @since 1.1
   */
  public void setMutationRateCalc(IUniversalRateCalculator m_mutationRateCalc) {
    this.m_mutationRateCalc = m_mutationRateCalc;
    if (m_mutationRateCalc != null) {
      m_mutationRate = 0;
    }
  }
}