/**
* Convenience method that returns a new Chromosome instance with its genes values (alleles)
* randomized. Note that, if possible, this method will acquire a Chromosome instance from the
* active ChromosomePool (if any) and then randomize its gene values before returning it. If a
* Chromosome cannot be acquired from the pool, then a new instance will be constructed and its
* gene values randomized before returning it.
*
* @param a_configuration the configuration to use
* @return randomly initialized Chromosome
* @throws InvalidConfigurationException if the given Configuration instance is invalid
* @throws IllegalArgumentException if the given Configuration instance is null
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public static IChromosome randomInitialChromosome(Configuration a_configuration)
throws InvalidConfigurationException {
// Sanity check: make sure the given configuration isn't null.
// -----------------------------------------------------------
if (a_configuration == null) {
throw new IllegalArgumentException("Configuration instance must not be null");
}
// Lock the configuration settings so that they can't be changed
// from now on.
// -------------------------------------------------------------
a_configuration.lockSettings();
// First see if we can get a Chromosome instance from the pool.
// If we can, we'll randomize its gene values (alleles) and then
// return it.
// -------------------------------------------------------------
IChromosomePool pool = a_configuration.getChromosomePool();
if (pool != null) {
IChromosome randomChromosome = pool.acquireChromosome();
if (randomChromosome != null) {
Gene[] genes = randomChromosome.getGenes();
RandomGenerator generator = a_configuration.getRandomGenerator();
for (int i = 0; i < genes.length; i++) {
genes[i].setToRandomValue(generator);
/** @todo what about Gene's energy? */
}
randomChromosome.setFitnessValueDirectly(FitnessFunction.NO_FITNESS_VALUE);
return randomChromosome;
}
}
// We weren't able to get a Chromosome from the pool, so we have to
// construct a new instance and build it from scratch.
// ------------------------------------------------------------------
IChromosome sampleChromosome = a_configuration.getSampleChromosome();
sampleChromosome.setFitnessValue(FitnessFunction.NO_FITNESS_VALUE);
Gene[] sampleGenes = sampleChromosome.getGenes();
Gene[] newGenes = new Gene[sampleGenes.length];
RandomGenerator generator = a_configuration.getRandomGenerator();
for (int i = 0; i < newGenes.length; i++) {
// We use the newGene() method on each of the genes in the
// sample Chromosome to generate our new Gene instances for
// the Chromosome we're returning. This guarantees that the
// new Genes are setup with all of the correct internal state
// for the respective gene position they're going to inhabit.
// -----------------------------------------------------------
newGenes[i] = sampleGenes[i].newGene();
// Set the gene's value (allele) to a random value.
// ------------------------------------------------
newGenes[i].setToRandomValue(generator);
/** @todo what about Gene's energy? */
}
// Finally, construct the new chromosome with the new random
// genes values and return it.
// ---------------------------------------------------------
return new Chromosome(a_configuration, newGenes);
}
/**
* 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;
}