/**
* 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);
}
/**
* 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;
}
boolean checkAlleles(IChromosome chrom, int j, int nextInt) {
Gene[] newgene = chrom.getGenes();
Integer[] alleles = new Integer[j];
for (int i = 0; i < j; i++) {
alleles[i] = (Integer) newgene[i].getAllele();
}
if (Arrays.asList(alleles).contains(new Integer(nextInt))) {
return true;
}
return false;
}
/**
* Marshall a Chromosome instance to an XML Element representation, including its contained Genes
* as sub-elements. This may be useful in scenarios where representation as an entire Document is
* undesirable, such as when the representation of this Chromosome is to be combined with other
* elements in a single Document.
*
* @param a_subject the chromosome 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 Chromosome
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Element representChromosomeAsElement(
final IChromosome a_subject, final Document a_xmlDocument) {
// Start by creating an element for the chromosome and its size
// attribute, which represents the number of genes in the chromosome.
// ------------------------------------------------------------------
Element chromosomeElement = a_xmlDocument.createElement(CHROMOSOME_TAG);
chromosomeElement.setAttribute(SIZE_ATTRIBUTE, Integer.toString(a_subject.size()));
// Next create the genes element with its nested gene elements,
// which will contain string representations of the alleles.
// --------------------------------------------------------------
Element genesElement = representGenesAsElement(a_subject.getGenes(), a_xmlDocument);
// Add the new genes element to the chromosome element and then
// return the chromosome element.
// -------------------------------------------------------------
chromosomeElement.appendChild(genesElement);
return chromosomeElement;
}
/**
* Compares the given Chromosome to this Chromosome. This chromosome is considered to be "less
* than" the given chromosome if it has a fewer number of genes or if any of its gene values
* (alleles) are less than their corresponding gene values in the other chromosome.
*
* @param other the Chromosome against which to compare this chromosome
* @return a negative number if this chromosome is "less than" the given chromosome, zero if they
* are equal to each other, and a positive number if this chromosome is "greater than" the
* given chromosome
* @author Neil Rotstan
* @author Klaus Meffert
* @since 1.0
*/
public int compareTo(Object other) {
// First, if the other Chromosome is null, then this chromosome is
// automatically the "greater" Chromosome.
// ---------------------------------------------------------------
if (other == null) {
return 1;
}
int size = size();
IChromosome otherChromosome = (IChromosome) other;
Gene[] otherGenes = otherChromosome.getGenes();
// If the other Chromosome doesn't have the same number of genes,
// then whichever has more is the "greater" Chromosome.
// --------------------------------------------------------------
if (otherChromosome.size() != size) {
return size() - otherChromosome.size();
}
// Next, compare the gene values (alleles) for differences. If
// one of the genes is not equal, then we return the result of its
// comparison.
// ---------------------------------------------------------------
for (int i = 0; i < size; i++) {
int comparison = getGene(i).compareTo(otherGenes[i]);
if (comparison != 0) {
return comparison;
}
}
// Compare current fitness value.
// ------------------------------
if (m_fitnessValue != otherChromosome.getFitnessValueDirectly()) {
FitnessEvaluator eval = getConfiguration().getFitnessEvaluator();
if (eval != null) {
if (eval.isFitter(m_fitnessValue, otherChromosome.getFitnessValueDirectly())) {
return 1;
} else {
return -1;
}
} else {
// undetermined order, but unequal!
// --------------------------------
return -1;
}
}
if (m_compareAppData) {
// Compare application data.
// -------------------------
if (getApplicationData() == null) {
if (otherChromosome.getApplicationData() != null) {
return -1;
}
} else if (otherChromosome.getApplicationData() == null) {
return 1;
} else {
if (getApplicationData() instanceof Comparable) {
try {
return ((Comparable) getApplicationData())
.compareTo(otherChromosome.getApplicationData());
} catch (ClassCastException cex) {
/** @todo improve */
return -1;
}
} else {
return getApplicationData()
.getClass()
.getName()
.compareTo(otherChromosome.getApplicationData().getClass().getName());
}
}
}
// Everything is equal. Return zero.
// ---------------------------------
return 0;
}
/**
* 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;
}
protected void doCrossover(
IChromosome firstMate,
IChromosome secondMate,
List a_candidateChromosomes,
RandomGenerator generator) {
Gene[] firstGenes = firstMate.getGenes();
Gene[] secondGenes = secondMate.getGenes();
int locus = generator.nextInt(firstGenes.length);
// Swap the genes.
// ---------------
Gene gene1, gene11;
Gene gene2, gene22;
Integer firstAllele, firstAllele1;
Integer secondAllele, secondAllele1;
for (int j = locus; j < firstGenes.length; j++) {
gene1 = firstGenes[j];
gene2 = secondGenes[j];
firstAllele = (Integer) gene1.getAllele();
secondAllele = (Integer) gene2.getAllele();
if (payload[firstAllele] != null && payload[secondAllele] != null) {
if (!checkAlleles(firstMate, j, secondAllele)) gene1.setAllele(secondAllele);
if (!checkAlleles(secondMate, j, firstAllele)) gene2.setAllele(firstAllele);
}
if (payload[firstAllele] == null && payload[secondAllele] == null) {
if (payload[64 + firstAllele].getPair() != payload[64 + secondAllele].getPair()) continue;
if (payload[64 + firstAllele].getPair() == 1) {
if (!checkAlleles(firstMate, j, secondAllele)
&& !checkAlleles(secondMate, j, firstAllele)) {
if (chkonepair(j) || chktwopair(j + 1)) {
System.out.println("Crossover.. something wrong");
}
gene11 = firstGenes[j + 1];
firstAllele1 = (Integer) gene11.getAllele();
gene22 = secondGenes[j + 1];
secondAllele1 = (Integer) gene22.getAllele();
if (!checkAlleles(firstMate, j + 1, secondAllele1)) {
gene1.setAllele(secondAllele);
gene11.setAllele(secondAllele1);
}
if (!checkAlleles(secondMate, j + 1, firstAllele1)) {
gene2.setAllele(firstAllele);
gene22.setAllele(firstAllele1);
}
}
} else if (payload[64 + firstAllele].getPair() == 2) {
if (!checkAlleles(firstMate, j, secondAllele)
&& !checkAlleles(secondMate, j, firstAllele)) {
gene11 = firstGenes[j - 1];
firstAllele1 = (Integer) gene11.getAllele();
gene22 = secondGenes[j - 1];
secondAllele1 = (Integer) gene22.getAllele();
if (!checkAlleles(firstMate, j - 1, secondAllele1)) {
gene1.setAllele(secondAllele);
gene11.setAllele(secondAllele1);
}
if (!checkAlleles(secondMate, j - 1, firstAllele1)) {
gene2.setAllele(firstAllele);
gene22.setAllele(firstAllele1);
}
}
} else {
System.out.println("...Invalid Configuration Exception...");
}
}
}
// Add the modified chromosomes to the candidate pool so that
// they'll be considered for natural selection during the next
// phase of evolution.
// -----------------------------------------------------------
a_candidateChromosomes.add(firstMate);
a_candidateChromosomes.add(secondMate);
}