/*
* This file is part of JGAP.
*
* JGAP offers a dual license model containing the LGPL as well as the MPL.
*
* For licensing 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.*;
import org.jgap.data.config.*;
/**
* 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.
*
* 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 determined by this class if no fixed rate is provided, and is
* calculated based on the size of the Chromosomes in the population. Details
* are specified in the DefaultMutationRateCalculator class.
*
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public class MutationOperator
extends BaseGeneticOperator implements Configurable {
/** String containing the CVS revision. Read out via reflection!*/
private final static String CVS_REVISION = "$Revision: 1.48 $";
/**
* 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;
private MutationOperatorConfigurable m_config = new
MutationOperatorConfigurable();
/**
* 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.
* <p>
* Attention: The configuration used is the one set with the static method
* Genotype.setConfiguration.
*
* @throws InvalidConfigurationException
*
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public MutationOperator()
throws InvalidConfigurationException {
this(Genotype.getStaticConfiguration());
}
/**
* @param a_conf the configuration to use
* @throws InvalidConfigurationException
*
* @author Klaus Meffert
* @since 3.0
*/
public MutationOperator(final Configuration a_conf)
throws InvalidConfigurationException {
super(a_conf);
setMutationRateCalc(new DefaultMutationRateCalculator(a_conf));
}
/**
* Constructs a new instance of this MutationOperator with a specified
* mutation rate calculator, which results in dynamic mutation being turned
* on.
* @param a_config the configuration to use
* @param a_mutationRateCalculator calculator for dynamic mutation rate
* computation
* @throws InvalidConfigurationException
*
* @author Klaus Meffert
* @since 1.1
*/
public MutationOperator(final Configuration a_config,
final IUniversalRateCalculator
a_mutationRateCalculator)
throws InvalidConfigurationException {
super(a_config);
setMutationRateCalc(a_mutationRateCalculator);
}
/**
* Constructs a new instance of this MutationOperator with the given
* mutation rate.
*
* @param a_config the configuration to use
* @param a_desiredMutationRate 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
* @throws InvalidConfigurationException
*
* @author Neil Rotstan
* @since 1.1
*/
public MutationOperator(final Configuration a_config,
final int a_desiredMutationRate)
throws InvalidConfigurationException {
super(a_config);
m_config.m_mutationRate = a_desiredMutationRate;
setMutationRateCalc(null);
}
/**
* @param a_population the population of chromosomes from the current
* evolution prior to exposure to any genetic operators. Chromosomes in this
* array should not be modified. Please notice, that the call in
* Genotype.evolve() to the implementations of GeneticOperator overgoes this
* due to performance issues
* @param a_candidateChromosomes the pool of chromosomes that have been
* mutated
*
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public void operate(final Population a_population,
final List a_candidateChromosomes) {
if (a_population == null || a_candidateChromosomes == null) {
// Population or candidate chromosomes list empty:
// nothing to do.
// -----------------------------------------------
return;
}
if (m_config.m_mutationRate == 0 && m_mutationRateCalc == null) {
// If the mutation rate is set to zero and dynamic mutation rate is
// disabled, then we don't perform any mutation.
// ----------------------------------------------------------------
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 = 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(getConfiguration().getPopulationSize(),
a_population.size());
IGeneticOperatorConstraint constraint = getConfiguration().
getJGAPFactory().getGeneticOperatorConstraint();
//
for (int i = 0; i < size; i++) {
IChromosome chrom = a_population.getChromosome(i);
Gene[] genes = chrom.getGenes();
IChromosome 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(chrom, j);
}
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_config.m_mutationRate) == 0);
}
if (mutate) {
// Verify that crossover allowed.
// ------------------------------
/**@todo move to base class, refactor*/
if (constraint != null) {
List v = new Vector();
v.add(chrom);
if (!constraint.isValid(a_population, v, this)) {
continue;
}
}
// 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 = (IChromosome) chrom.clone();
// ...add it to the candidate pool...
// ----------------------------------
a_candidateChromosomes.add(copyOfChromosome);
// ...then mutate all its genes...
// -------------------------------
genes = copyOfChromosome.getGenes();
// In case monitoring is active, support it.
// -----------------------------------------
if (m_monitorActive) {
copyOfChromosome.setUniqueIDTemplate(chrom.getUniqueID(), 1);
}
}
// Process all atomic elements in the gene. For a StringGene this
// would be as many elements as the string is long , for an
// IntegerGene, it is always one element.
// --------------------------------------------------------------
if (genes[j] instanceof ICompositeGene) {
ICompositeGene compositeGene = (ICompositeGene) genes[j];
if (m_monitorActive) {
compositeGene.setUniqueIDTemplate(chrom.getGene(j).getUniqueID(), 1);
}
for (int k = 0; k < compositeGene.size(); k++) {
mutateGene(compositeGene.geneAt(k), generator);
if (m_monitorActive) {
compositeGene.geneAt(k).setUniqueIDTemplate(
( (ICompositeGene) chrom.getGene(j)).geneAt(k).getUniqueID(),
1);
}
}
}
else {
mutateGene(genes[j], generator);
if (m_monitorActive) {
genes[j].setUniqueIDTemplate(chrom.getGene(j).getUniqueID(), 1);
}
}
}
}
}
}
/**
* Helper: mutate all atomic elements of a gene.
*
* @param a_gene the gene to be mutated
* @param a_generator the generator delivering the amount of mutation
*
* @author Klaus Meffert
* @since 1.1
*/
private void mutateGene(final Gene a_gene, final 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 strength of
* mutation.
*
* @param a_mutationRateCalc MutationRateCalculator
*
* @author Klaus Meffert
* @since 1.1
*/
public void setMutationRateCalc(final IUniversalRateCalculator
a_mutationRateCalc) {
m_mutationRateCalc = a_mutationRateCalc;
if (m_mutationRateCalc != null) {
m_config.m_mutationRate = 0;
}
}
/**
*
* @param a_mutationRate new 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 Klaus Meffert
* @since 3.2.2
*/
public void setMutationRate(int a_mutationRate) {
m_config.m_mutationRate = a_mutationRate;
setMutationRateCalc(null);
}
/**
* Compares this GeneticOperator against the specified object. The result is
* true if and the argument is an instance of this class and is equal wrt the
* data.
*
* @param a_other the object to compare against
* @return true: if the objects are the same, false otherwise
*
* @author Klaus Meffert
* @since 2.6
*/
public boolean equals(final Object a_other) {
try {
return compareTo(a_other) == 0;
} catch (ClassCastException cex) {
return false;
}
}
/**
* Compares the given GeneticOperator to this GeneticOperator.
*
* @param a_other the instance against which to compare this instance
* @return a negative number if this instance is "less than" the given
* instance, zero if they are equal to each other, and a positive number if
* this is "greater than" the given instance
*
* @author Klaus Meffert
* @since 2.6
*/
public int compareTo(Object a_other) {
if (a_other == null) {
return 1;
}
MutationOperator op = (MutationOperator) a_other;
if (m_mutationRateCalc == null) {
if (op.m_mutationRateCalc != null) {
return -1;
}
}
else {
if (op.m_mutationRateCalc == null) {
return 1;
}
else {
}
}
if (m_config.m_mutationRate != op.m_config.m_mutationRate) {
if (m_config.m_mutationRate > op.m_config.m_mutationRate) {
return 1;
}
else {
return -1;
}
}
// Everything is equal. Return zero.
// ---------------------------------
return 0;
}
public int getMutationRate() {
return m_config.m_mutationRate;
}
class MutationOperatorConfigurable
implements java.io.Serializable {
/**
* The current mutation rate used by this MutationOperator, expressed as
* the denominator in the 1 / X ratio. For example, X = 1000 would
* mean that, on average, 1 / 1000 genes would be mutated. A value of zero
* disables mutation entirely.
*/
public int m_mutationRate;
}
}