/**
* Operate on the given chromosome with the given mutation rate.
*
* @param a_chrom chromosome to operate
* @param a_rate mutation rate
* @param a_generator random generator to use (must not be null)
* @return mutated chromosome of null if no mutation has occured.
* @author Audrius Meskauskas
* @author Florian Hafner
* @since 3.3.2
*/
protected IChromosome operate(
final IChromosome a_chrom, final int a_rate, final RandomGenerator a_generator) {
IChromosome chromosome = null;
// ----------------------------------------
for (int j = m_startOffset; j < a_chrom.size(); j++) {
// Ensure probability of 1/currentRate for applying mutation.
// ----------------------------------------------------------
if (a_generator.nextInt(a_rate) == 0) {
if (chromosome == null) {
chromosome = (IChromosome) a_chrom.clone();
// In case monitoring is active, support it.
// -----------------------------------------
if (m_monitorActive) {
chromosome.setUniqueIDTemplate(a_chrom.getUniqueID(), 1);
}
}
Gene[] genes = chromosome.getGenes();
if (m_range == 0) {
m_range = genes.length;
}
Gene[] mutated = operate(a_generator, j, genes);
// setGenes is not required for this operator, but it may
// be needed for the derived operators.
// ------------------------------------------------------
try {
chromosome.setGenes(mutated);
} catch (InvalidConfigurationException cex) {
throw new Error("Gene type not allowed by constraint checker", cex);
}
}
}
return chromosome;
}
/**
* Returns a copy of this Chromosome. The returned instance can evolve independently of this
* instance. Note that, if possible, this method will first attempt to acquire a Chromosome
* instance from the active ChromosomePool (if any) and set its value appropriately before
* returning it. If that is not possible, then a new Chromosome instance will be constructed and
* its value set appropriately before returning.
*
* @return copy of this Chromosome
* @throws IllegalStateException instead of CloneNotSupportedException
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public synchronized Object clone() {
// Before doing anything, make sure that a Configuration object
// has been set on this Chromosome. If not, then throw an
// IllegalStateException.
// ------------------------------------------------------------
if (getConfiguration() == null) {
throw new IllegalStateException(
"The active Configuration object must be set on this "
+ "Chromosome prior to invocation of the clone() method.");
}
IChromosome copy = null;
// Now, first see if we can pull a Chromosome from the pool and just
// set its gene values (alleles) appropriately.
// ------------------------------------------------------------
IChromosomePool pool = getConfiguration().getChromosomePool();
if (pool != null) {
copy = pool.acquireChromosome();
if (copy != null) {
Gene[] genes = copy.getGenes();
for (int i = 0; i < size(); i++) {
genes[i].setAllele(getGene(i).getAllele());
}
}
}
try {
if (copy == null) {
// We couldn't fetch a Chromosome from the pool, so we need to create
// a new one. First we make a copy of each of the Genes. We explicity
// use the Gene at each respective gene location (locus) to create the
// new Gene that is to occupy that same locus in the new Chromosome.
// -------------------------------------------------------------------
int size = size();
if (size > 0) {
Gene[] copyOfGenes = new Gene[size];
for (int i = 0; i < copyOfGenes.length; i++) {
copyOfGenes[i] = getGene(i).newGene();
Object allele = getGene(i).getAllele();
if (allele != null) {
IJGAPFactory factory = getConfiguration().getJGAPFactory();
if (factory != null) {
ICloneHandler cloner = factory.getCloneHandlerFor(allele, allele.getClass());
if (cloner != null) {
try {
allele = cloner.perform(allele, null, this);
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
}
}
copyOfGenes[i].setAllele(allele);
}
// Now construct a new Chromosome with the copies of the genes and
// return it. Also clone the IApplicationData object later on.
// ---------------------------------------------------------------
if (getClass() == Chromosome.class) {
copy = new Chromosome(getConfiguration(), copyOfGenes);
} else {
copy = (IChromosome) getConfiguration().getSampleChromosome().clone();
copy.setGenes(copyOfGenes);
}
} else {
if (getClass() == Chromosome.class) {
copy = new Chromosome(getConfiguration());
} else {
copy = (IChromosome) getConfiguration().getSampleChromosome().clone();
}
}
}
copy.setFitnessValue(m_fitnessValue);
// Clone constraint checker.
// -------------------------
copy.setConstraintChecker(getConstraintChecker());
} catch (InvalidConfigurationException iex) {
throw new IllegalStateException(iex.getMessage());
}
// Also clone the IApplicationData object.
// ---------------------------------------
try {
copy.setApplicationData(cloneObject(getApplicationData()));
} catch (Exception ex) {
throw new IllegalStateException(ex.getMessage());
}
// Clone multi-objective object if necessary and possible.
// -------------------------------------------------------
if (m_multiObjective != null) {
if (getClass() == Chromosome.class) {
try {
((Chromosome) copy).setMultiObjectives((List) cloneObject(m_multiObjective));
} catch (Exception ex) {
throw new IllegalStateException(ex.getMessage());
}
}
}
return copy;
}