/**
* @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 selected for the next
* evolved population
* @author Audrius Meskauskas
* @author Klaus Meffert
* @since 3.3.2
*/
public void operate(final Population a_population, List a_candidateChromosomes) {
// this was a private variable, now it is local reference.
final IUniversalRateCalculator m_mutationRateCalc = getMutationRateCalc();
// If the mutation rate is set to zero and dynamic mutation rate is
// disabled, then we don't perform any mutation.
// ----------------------------------------------------------------
if (getMutationRate() == 0 && m_mutationRateCalc == null) {
return;
}
// Determine the mutation rate. If dynamic rate is enabled, then
// calculate it based upon the number of genes in the chromosome.
// Otherwise, go with the mutation rate set upon construction.
// --------------------------------------------------------------
int currentRate;
if (m_mutationRateCalc != null) {
currentRate = m_mutationRateCalc.calculateCurrentRate();
} else {
currentRate = getMutationRate();
}
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 = a_population.size();
for (int i = 0; i < size; i++) {
IChromosome x = a_population.getChromosome(i);
// This returns null if not mutated:
IChromosome xm = operate(x, currentRate, generator);
if (xm != null) {
a_candidateChromosomes.add(xm);
}
}
}
/**
* Marshall a Genotype instance into an XML Element representation, including its population of
* Chromosome instances as sub-elements. This may be useful in scenarios where representation as
* an entire Document is undesirable, such as when the representation of this Genotype is to be
* combined with other elements in a single Document.
*
* @param a_subject the genotype to represent as an XML element
* @param a_xmlDocument a Document instance that will be used to create the Element instance. Note
* that the element will NOT be added to the document by this method
* @return an Element object representing the given Genotype
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Element representGenotypeAsElement(
final Genotype a_subject, final Document a_xmlDocument) {
Population population = a_subject.getPopulation();
// Start by creating the genotype element and its size attribute,
// which represents the number of chromosomes present in the
// genotype.
// --------------------------------------------------------------
Element genotypeTag = a_xmlDocument.createElement(GENOTYPE_TAG);
genotypeTag.setAttribute(SIZE_ATTRIBUTE, Integer.toString(population.size()));
// Next, add nested elements for each of the chromosomes in the
// genotype.
// ------------------------------------------------------------
for (int i = 0; i < population.size(); i++) {
Element chromosomeElement =
representChromosomeAsElement(population.getChromosome(i), a_xmlDocument);
genotypeTag.appendChild(chromosomeElement);
}
return genotypeTag;
}
public boolean needsToRun(Run run, int generation) {
Population pop = getPopulationFor(run, generation);
int count = run.getIntProperty(GenetikConstants.POPULATION, Integer.MAX_VALUE, true);
int scoreCount = 0;
for (int i = 0, max = pop.size(); i < max; i++) {
Individual ind = pop.get(i);
if (ind.hasFitness() && ind.hasScores()) {
scoreCount++;
}
}
return scoreCount != count;
}