/**
* Prints a single Chromosome
*
* @param cd the Chromosome
* @return
*/
public String print(Chromosome cd) {
String s = "";
s += "-----\n";
s += "objectives: [";
for (int i = 0; i < cd.getObjectives().length; i++) {
s += cd.getObjectives()[i] + ",";
}
s += "]\n";
s += "genes: [";
for (int i = 0; i < cd.getGenes().size(); i++) {
Gene curr = cd.getGene(i);
if (curr instanceof DoubleGene) {
DoubleGene double_curr = (DoubleGene) curr;
s += double_curr.doubleValue() + ",";
} else if (curr instanceof IntegerGene) {
IntegerGene int_curr = (IntegerGene) curr;
s += int_curr.intValue() + ",";
} else {
s += curr.toString() + ",";
}
}
s += "]\n";
return s;
}
public Object clone() {
Chromosome clone = new Chromosome();
clone.genes = new Vector<Gene>();
for (Gene curr : genes) {
clone.genes.add((Gene) curr.clone());
}
return clone;
}
/**
* Initializes a chromosome based on the sample chromosome's gene set. The genes of this
* chromosome are generated randomly in the range specified in the gene set.
*
* @param sample the sample chromosome.
*/
public Chromosome(Chromosome sample) {
genes = new Vector<Gene>();
Vector<Gene> sample_genes = sample.getGenes();
for (Gene curr : sample_genes) {
genes.add(curr.generate());
}
}
public boolean isDuplicate(Chromosome chrom1, Chromosome chrom2) {
boolean duplicate = true;
// check gene by gene
for (int g = 0; g < chrom1.getGenes().size(); g++) {
if (chrom1.getGene(g) instanceof IntegerGene) {
IntegerGene i_gene = (IntegerGene) chrom1.getGene(g);
IntegerGene j_gene = (IntegerGene) chrom2.getGene(g);
if (i_gene.intValue() != j_gene.intValue()) duplicate = false;
} else if (chrom1.getGene(g) instanceof DoubleGene) {
DoubleGene i_gene = (DoubleGene) chrom1.getGene(g);
DoubleGene j_gene = (DoubleGene) chrom2.getGene(g);
// compute 1% of range in gene set
double max_difference = (i_gene.upperBound() - i_gene.lowerBound()) * .01;
if (Math.abs(i_gene.doubleValue() - j_gene.doubleValue()) > max_difference)
duplicate = false;
} else if (!chrom1.getGene(g).equals(chrom2.getGene(g))) {
duplicate = false;
}
}
return duplicate;
}
public Vector<Chromosome> select(Vector<Chromosome> from, int num) {
// ** FIRST, evaluate any new chromosomes
// check for duplicates from
for (int i = 0; i < from.size(); i++) {
for (int j = i + 1; j < from.size(); j++) {
Chromosome i_chrom = from.get(i);
Chromosome j_chrom = from.get(j);
if (isDuplicate(i_chrom, j_chrom)) {
// remove j_chrom
from.remove(j);
j--;
continue;
}
}
}
for (Chromosome curr : from) {
if (curr.getObjectives() == null) {
curr.setObjectives(eval.getFitness(curr));
}
}
// ** SECOND, we want to add chromosomes to elite set and swap
// copy from from to clone_from
Vector<ChromDominance> clone_from = new Vector<ChromDominance>();
for (Chromosome curr : from) {
clone_from.add(new ChromDominance(curr));
}
// remove bad chromosomes
// duplicate-checking with elite set now included in goodChromosome()
for (int i = 0; i < clone_from.size(); i++) {
Chromosome chrom = clone_from.get(i).chrom;
if (!goodChromosome(chrom)) {
clone_from.remove(i);
i--;
continue;
}
}
// check to see if elite set is not full
if (elite.size() < elite_size) {
// move from clone_from to elite
for (int i = 0; i < clone_from.size(); i++) {
elite.add(clone_from.get(i));
}
// check if its still less
if (elite.size() < elite_size) {
if (num_select != 0) {
num = num_select;
}
return callSelector(from, num);
} else {
// now evaluate dominance counts within elite set
for (int i = 0; i < elite.size(); i++) {
for (int j = i + 1; j < elite.size(); j++) {
ChromDominance i_chrom = elite.get(i);
ChromDominance j_chrom = elite.get(j);
if (eval.isFitter(i_chrom.chrom, j_chrom.chrom)) {
j_chrom.dominance++;
} else if (eval.isFitter(j_chrom.chrom, i_chrom.chrom)) {
i_chrom.dominance++;
}
}
}
}
}
// compare for dominance counts within clone_from
for (int i = 0; i < clone_from.size(); i++) {
for (int j = i + 1; j < clone_from.size(); j++) {
Chromosome i_chrom = clone_from.get(i).chrom;
Chromosome j_chrom = clone_from.get(j).chrom;
if (eval.isFitter(i_chrom, j_chrom)) {
ChromDominance cd = clone_from.get(j);
cd.dominance++;
} else if (eval.isFitter(j_chrom, i_chrom)) {
ChromDominance cd = clone_from.get(i);
cd.dominance++;
}
}
}
// compare for dominance counts between clone_from and elite
for (int i = 0; i < clone_from.size(); i++) {
for (int j = 0; j < elite_size; j++) {
Chromosome i_chrom = clone_from.get(i).chrom;
Chromosome j_chrom = elite.get(j).chrom;
if (eval.isEquivalent(i_chrom, j_chrom)) {
ChromDominance cd = clone_from.get(i);
cd.dominance++; // keep elite set individual if not comparable
}
if (eval.isFitter(i_chrom, j_chrom)) {
ChromDominance cd = elite.get(j);
cd.dominance++;
} else if (eval.isFitter(j_chrom, i_chrom)) {
ChromDominance cd = clone_from.get(i);
cd.dominance++;
}
}
}
// switch between the sets, best -> elite set
for (int i = 0; i < clone_from.size(); i++) {
for (int j = 0; j < elite.size(); j++) {
ChromDominance i_chrom = clone_from.get(i);
ChromDominance j_chrom = elite.get(j);
if (i_chrom.dominance < j_chrom.dominance) {
clone_from.remove(i);
elite.remove(j);
clone_from.add(j_chrom);
elite.add(i_chrom);
i--;
break;
}
}
}
// find num_changed
int num_changed = 0; // number of chromosomes that are different now
for (int i = 0; i < elite.size(); i++) {
ChromDominance chrom = elite.get(i);
if (chrom.changed) {
num_changed++;
chrom.changed = false;
}
}
if (num_changed <= thresh_percent * elite_size) {
// comparison of threshold evolutions to max
// is done in MultiConnector
thresh_evolutions++;
} else {
thresh_evolutions = 0; // reset if not within threshold
}
// sort the elite set
EliteSorter es = new EliteSorter();
Collections.sort(elite, es);
// calculate average objectives in the elite set
double[] avg_objectives = new double[eval.getOptimal().length];
for (int i = 0; i < elite.size(); i++) {
double[] cd_objectives = elite.get(i).chrom.getObjectives();
for (int j = 0; j < cd_objectives.length; j++) {
avg_objectives[j] += cd_objectives[j];
}
}
for (int i = 0; i < avg_objectives.length; i++) {
avg_objectives[i] = avg_objectives[i] / elite.size();
}
// calculate change in average objectives
if (last_avg_objectives != null) {
for (int i = 0; i < avg_objectives.length; i++) {
objective_change[i] = avg_objectives[i] / last_avg_objectives[i];
}
} else {
objective_change = new double[avg_objectives.length];
}
last_avg_objectives = avg_objectives;
// copy from new clone_from to a Vector<Chromosome>
Vector<Chromosome> clone_chroms = new Vector<Chromosome>();
for (int i = 0; i < clone_from.size(); i++) {
clone_chroms.add(clone_from.get(i).chrom);
}
// copy from elite to clone_chroms
for (int i = 0; i < elite.size(); i++) {
clone_chroms.add(elite.get(i).chrom);
}
if (num_select != 0) {
num = num_select;
}
if (merge) {
return callSelector(clone_chroms, num);
} else {
return callSelector(from, num);
}
}