int main()
{
srand(time(NULL));
Population population;
for (int i = 0; i < POPULATION_COUNT; ++i) {
Individual ind;
Chromosome chromosome(targetString.size());
chromosome.randomize();
float fitness = evaluate(chromosome);
ind.setChromosome(chromosome);
ind.setFitness(fitness);
population.addIndividual(ind);
}
population.sortPopulation();
std::string solution = "";
Individual bestInd;
int generationCount = 0;
int nth = 64;
for (int i = 0; i < GENERATION_COUNT; ++i) {
generationCount++;
evolve(population);
population.sortPopulation();
if (bestInd < population[0]) {
bestInd = population[0];
}
if (i % nth == 0) {
std::cout << "Generation: " << generationCount << std::endl;
std::cout << "Best individual: " << bestInd << std::endl;
}
if (bestInd.getFitness() >= 1){
break;
}
}
std::cout << std::endl;
std::cout << "Solved on generation " << generationCount << '!' << std::endl;
std::cout << bestInd << std::endl << std::endl;
std::cout << "Press enter to exit";
std::cin.get();
return 0;
}
void eStrategy::initialize() {
for(size_t indiv = 0; indiv < CONF_SIZE_POP; indiv++) {
chromosome::data_block genes, sigmas;
for(size_t gene = 0; gene < CONF_DIM; gene++) {
sigmas.push_back(frand());
genes.push_back(frand() * (CONF_BOUND_UPPER - CONF_BOUND_LOWER) + CONF_BOUND_LOWER);
}
auto c = chromosome(genes, sigmas);
c.set_fitness(this->eval(c));
this->parent_pop.push_back(c);
}
this->sort_population();
}
chromosome eStrategy::xover_and_mut(const chromosome* const p1, const chromosome* const p2) const {
p1->validate(), p2->validate();
assert(p1->sigmas.size() == p2->sigmas.size() && p1->sigmas.size() == CONF_DIM);
double prob = frand();
auto sp = p1;
if(prob > 0.5) sp = p2;
chromosome::data_block new_sigmas, new_genes;
if(prob < CONF_PROB_MUT) {
double step = exp(PARAM_TAW_PRIME * normrnd() + CONST_STEP_GLOB);
auto xd = normrnd();
for(size_t index = 0; index < sp->sigmas.size(); index++) {
auto s = sp->sigmas.at(index) * step;
if(s < CONF_RANGE_SIGMA && s > -CONF_RANGE_SIGMA)
s = s / abs(s) * CONF_RANGE_SIGMA;
new_sigmas.push_back(s);
auto g = sp->genes.at(index) + s * xd;
if(g > CONF_BOUND_UPPER) g = CONF_BOUND_UPPER;
else if(g < CONF_BOUND_LOWER) g = CONF_BOUND_LOWER;
new_genes.push_back(g);
}
assert(new_genes.size() == new_sigmas.size());
} else if((1 - prob) < CONF_PROB_XOVER) {
double rp = frand(), rq = frand();
for(size_t index = 0; index < sp->genes.size(); index++) {
auto g = (p1->genes.at(index) * rp + p2->genes.at(index) * rq);
if(g > CONF_BOUND_UPPER) g = CONF_BOUND_UPPER;
else if(g < CONF_BOUND_LOWER) g = CONF_BOUND_LOWER;
new_genes.push_back(g);
if(frand() < 0.5) new_sigmas.push_back(p1->sigmas.at(index));
else new_sigmas.push_back(p2->sigmas.at(index));
}
}
auto c = chromosome(new_genes, new_sigmas);
if(this->eval(c) < sp->get_fitness())
return c;
return chromosome(*sp);
}
void reader::read_infercars(const ProblemInstance& cfg, std::vector<Genome>& genome) {
std::ifstream input(cfg.get_blk_file().c_str());
if(!input) {
std::cerr << "Unable to open " << cfg.get_blk_file() << std::endl;
exit(1);
}
std::string gene;
std::vector<std::string> chromosome(cfg.get_count_genomes());
std::vector<std::string> sign(cfg.get_count_genomes());
std::vector<int> start_block(cfg.get_count_genomes());
std::vector<int> end_block(cfg.get_count_genomes());
std::vector<int> count_block(cfg.get_count_genomes());
while(!input.eof()) {
std::string line;
std::getline(input, line);
line = reader::trim(line);
if (line.empty()) {
if (gene.empty()) {
continue;
}
bool ambig = false;
for(int i = 0; i < count_block.size(); ++i) {
if (count_block[i] != 1) {
ambig = true;
break;
}
}
if (ambig) {
std::clog << "Ambiguous block: " << gene << std::endl;
continue;
}
for(int i = 0; i < count_block.size(); ++i) {
if (count_block[i] == 1) {
int sign_ = (sign[i] == "+")? +1: -1;
genome[i].insert(gene, chromosome[i], (start_block[i] + end_block[i]) / 2, sign_, std::min(start_block[i], end_block[i]), std::max(start_block[i], end_block[i]));
}
}
gene.clear();
} else if (line[0] == '#') {
continue;
} else if(line[0] == '>') {
gene = line.substr(1);
std::fill(count_block.begin(), count_block.end(), 0);
} else {
line[line.find(".")] = ' ';
line[line.find(":")] = ' ';
line[line.find("-")] = ' ';
std::istringstream istr(line);
std::string genome_name;
istr >> genome_name;
if (!cfg.member_name(genome_name)) {
std::cerr << "Unknown genome name: " << genome_name << std::endl;
continue;
}
size_t k = cfg.get_number(genome_name);
istr >> chromosome[k] >> start_block[k] >> end_block[k] >> sign[k];
++count_block[k];
}
}
input.close();
}
