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Init version

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This commit is contained in:
Aleksey M. Mukhin
2024-10-03 18:43:04 +07:00
commit f80052961f
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287
population/BisexualPopulation.cpp Normal file
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#include "Population.h"
#include <algorithm>
#include <iostream>
#include <sstream>
#include <cstdlib>
#include <ctime>
BisexualPopulation::~BisexualPopulation(){
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
}
void BisexualPopulation::calculateFitnessAll(){
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD>
}
void BisexualPopulation::breedAll(){
this->breedingStrategy->breed(this);
}
void BisexualPopulation::selectionAll(){
}
void BisexualPopulation::mutationAll(){
// !!! <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
srand((unsigned int)time(NULL));
float mutProb = 1 / 1e+6f; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::list<Individual*>::iterator it;
for(it = this->females.begin(); it != this->females.end(); it++){
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2014
Chromosome chrom = (*it)->genotype->getMotherGenome().getChromosome(0);
std::vector<Gene> genes = chrom.getGenesAsVector();
int wholeSeqLength = 0;
for(unsigned int i = 0; i < genes.size(); i++){
wholeSeqLength += genes.at(i).getSequence().size();
}
//std::string seq = (*it)->genotype->getRawGene(0,0,0); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2013
int positionToMutate = rand() % (int)(1/mutProb);
if(positionToMutate < wholeSeqLength){
std::string seq = genes.at(0).getSequence();
int geneNum = positionToMutate / seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2014
positionToMutate = positionToMutate % seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2014
//Gene geneToMutate = genes.at(geneNum);
int nucl = rand() % 3;
switch(seq.c_str()[positionToMutate]){
case 'A':
if(nucl == 0) seq.replace(positionToMutate,1,"C");
if(nucl == 1) seq.replace(positionToMutate,1,"G");
if(nucl == 2) seq.replace(positionToMutate,1,"T");
break;
case 'C':
if(nucl == 0) seq.replace(positionToMutate,1,"A");
if(nucl == 1) seq.replace(positionToMutate,1,"G");
if(nucl == 2) seq.replace(positionToMutate,1,"T");
break;
case 'G':
if(nucl == 0) seq.replace(positionToMutate,1,"C");
if(nucl == 1) seq.replace(positionToMutate,1,"A");
if(nucl == 2) seq.replace(positionToMutate,1,"T");
break;
case 'T':
if(nucl == 0) seq.replace(positionToMutate,1,"C");
if(nucl == 1) seq.replace(positionToMutate,1,"G");
if(nucl == 2) seq.replace(positionToMutate,1,"A");
break;
} // (END) switch(...)
(*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
} // (END) if (mutate)
} // (END) for
// !!! --------------------------------
}
std::string BisexualPopulation::getSatistics(){
std::string ans;
return ans;
}
void BisexualPopulation::putGeneticStatisticsToStream(std::ostream& out){
out<<"Females\n=======\n";
int i = 1;
for(std::list<Individual*>::iterator it = females.begin(); it != females.end(); it++){
//out<<"> Female seq mitochondrial"<<(i++)<<"\n";
out<<(*it)->getGenotype().toSimpleFasta()<<std::endl;
out<<std::endl;
}
out<<"\nMales\n=======\n";
i = 1;
for(std::list<Individual*>::iterator it = males.begin(); it != males.end(); it++){
out<<"> Male seq "<<(i++)<<"\n";
out<<(*it)->getGenotype().toSimpleFasta()<<std::endl;
out<<std::endl;
}
}
void BisexualPopulation::putGeneticSimpleStatisticsToStream(std::ostream& out){
out<<"Population statistics:\tMales =\t"<<males.size();
out<<"\tFemales =\t"<<females.size()<<std::endl;
//out<<"Genome statistics (mitochondrial DNA sequence):\n\n";
}
void BisexualPopulation::putGeneticMaxModuleStatisticsToStream(std::ostream& out){
}
std::string BisexualPopulation::mutualMigration(BisexualPopulation* p1, BisexualPopulation* p2, float frac1, float frac2){
std::stringstream ss;
int sizeP1 = p1->males.size() + p1->females.size();
int sizeP2 = p2->males.size() + p2->females.size();
int indsP1toP2 = (int) (frac1*sizeP1)/2;
int indsP2toP1 = (int) (frac2*sizeP2)/2;
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD>
std::list<Individual*> malesTemp;
std::list<Individual*> femalesTemp;
// P1 -> temp
// males
std::list<Individual*>::iterator it1 = p1->males.begin();
std::list<Individual*>::iterator it2 = it1;
std::advance(it2, indsP1toP2);
malesTemp.splice(malesTemp.begin(), p1->males, it1, it2);
// females
it1 = p1->females.begin();
it2 = it1;
std::advance(it2, indsP1toP2);
femalesTemp.splice(femalesTemp.begin(), p1->females, it1, it2);
/////////////////////////////////////////////////////////////
// P2 -> P1
// males
it1 = p2->males.begin();
it2 = it1;
std::advance(it2, indsP2toP1);
p1->males.splice(p1->males.end(), p2->males, it1, it2);
// females
it1 = p2->females.begin();
it2 = it1;
std::advance(it2, indsP2toP1);
p1->females.splice(p1->females.end(), p2->females, it1, it2);
/////////////////////////////////////////////////////////////
// temp -> P2
// males
p2->males.splice(p2->males.end(), malesTemp);
// females
p2->females.splice(p2->females.end(), femalesTemp);
ss<<"Migration:\tP1->P2\t"<<indsP1toP2*2<<"\t\tP2->P1\t"<<indsP2toP1*2<<std::endl;
return ss.str();
}
BisexualPopulation* BisexualPopulation::createSubpopulation(float frac){
// <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int malesFounders = (int) (frac*this->males.size());
int femalesFounders = (int) (frac*this->females.size());
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD>
std::list<Individual*> malesTemp;
std::list<Individual*> femalesTemp;
// P1 -> temp
// males
std::list<Individual*>::iterator it1 = this->males.begin();
std::list<Individual*>::iterator it2 = it1;
std::advance(it2, malesFounders);
malesTemp.splice(malesTemp.begin(), this->males, it1, it2);
// females
it1 = this->females.begin();
it2 = it1;
std::advance(it2, femalesFounders);
femalesTemp.splice(femalesTemp.begin(), this->females, it1, it2);
/////////////////////////////////////////////////////////////
return new BisexualPopulation(malesTemp,femalesTemp, this->breedingStrategy);
}
///////////////////////////////
void BisexualPopulation::mutationDerevyanko2015(double pMutMtDNA, double pMutNumt){
// !!! <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
srand((unsigned int)time(NULL));
//float mutProb = 1 / 1e+6f; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><> <20><><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD>
std::list<Individual*>::iterator it;
for(it = this->females.begin(); it != this->females.end(); it++){
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2015
Chromosome chrom = (*it)->genotype->getMotherGenome().getChromosome(0);
Chromosome chromNumt = (*it)->genotype->getMotherGenome().getChromosome(1);
std::vector<Gene> genes = chrom.getGenesAsVector();
int wholeSeqLength = 0;
for(unsigned int i = 0; i < genes.size(); i++){
wholeSeqLength += genes.at(i).getSequence().size();
}
int positionToMutate = rand() % (int)(1/pMutMtDNA);
if(positionToMutate < wholeSeqLength){
std::string seq = genes.at(0).getSequence();
int geneNum = positionToMutate / seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2015
positionToMutate = positionToMutate % seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2015
//Gene geneToMutate = genes.at(geneNum);
int nucl = rand() % 3;
switch(seq.c_str()[positionToMutate]){
case 'A':
if(nucl == 0) seq.replace(positionToMutate,1,"C");
if(nucl == 1) seq.replace(positionToMutate,1,"G");
if(nucl == 2) seq.replace(positionToMutate,1,"T");
break;
case 'C':
if(nucl == 0) seq.replace(positionToMutate,1,"A");
if(nucl == 1) seq.replace(positionToMutate,1,"G");
if(nucl == 2) seq.replace(positionToMutate,1,"T");
break;
case 'G':
if(nucl == 0) seq.replace(positionToMutate,1,"C");
if(nucl == 1) seq.replace(positionToMutate,1,"A");
if(nucl == 2) seq.replace(positionToMutate,1,"T");
break;
case 'T':
if(nucl == 0) seq.replace(positionToMutate,1,"C");
if(nucl == 1) seq.replace(positionToMutate,1,"G");
if(nucl == 2) seq.replace(positionToMutate,1,"A");
break;
} // (END) switch(...)
(*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
} // (END) if (mutate)
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD>
//std::vector<Gene> genes = chromNumt.getGenesAsVector();
//int wholeSeqLength = 0;
//for(unsigned int i = 0; i < genes.size(); i++){
// wholeSeqLength += genes.at(i).getSequence().size();
//}
//int positionToMutate = rand() % (int)(1/pMutNumt);
//if(positionToMutate < wholeSeqLength){
// std::string seq = genes.at(0).getSequence();
// int geneNum = positionToMutate / seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2015
// positionToMutate = positionToMutate % seq.size(); // <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 2015
// //Gene geneToMutate = genes.at(geneNum);
// int nucl = rand() % 3;
// switch(seq.c_str()[positionToMutate]){
// case 'A':
// if(nucl == 0) seq.replace(positionToMutate,1,"C");
// if(nucl == 1) seq.replace(positionToMutate,1,"G");
// if(nucl == 2) seq.replace(positionToMutate,1,"T");
// break;
// case 'C':
// if(nucl == 0) seq.replace(positionToMutate,1,"A");
// if(nucl == 1) seq.replace(positionToMutate,1,"G");
// if(nucl == 2) seq.replace(positionToMutate,1,"T");
// break;
// case 'G':
// if(nucl == 0) seq.replace(positionToMutate,1,"C");
// if(nucl == 1) seq.replace(positionToMutate,1,"A");
// if(nucl == 2) seq.replace(positionToMutate,1,"T");
// break;
// case 'T':
// if(nucl == 0) seq.replace(positionToMutate,1,"C");
// if(nucl == 1) seq.replace(positionToMutate,1,"G");
// if(nucl == 2) seq.replace(positionToMutate,1,"A");
// break;
// } // (END) switch(...)
// (*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
//} // (END) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> - <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
} // (END) for
// !!! --------------------------------
}

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population/BreedingStrategies/NeutralEvolutionBreedStrat.cpp Normal file
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#include "NeutralEvolutionBreedStrat.h"
#include "../../individual/Phenotype.h"
#include "../../processor/Settings.h"
#include <algorithm>
#include <iostream>
#include <cstdlib>
#include <ctime>
void NeutralEvolutionBreedingStrategy::breed(Population* _pop){
BisexualPopulation* pop = dynamic_cast<BisexualPopulation*>(_pop);
if(pop == NULL){
std::cerr<<"Wrong dynamic cast to BisexualPopulation\n";
return;
}
int numMales = pop->males.size();
int numFemales = pop->females.size();
int inds = numMales + numFemales;
srand((unsigned int)time(NULL));
//srand(0);
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int toDie = int (inds * deathRate);
for(int i = 0; i < toDie; i++){
int indToDie = rand() % (inds-i);
if(indToDie < numMales){
std::list<Individual*>::iterator it = pop->males.begin();
std::advance(it,indToDie); // it += indToDie;
delete *it;
pop->males.erase(it);
numMales--;
}
else{
std::list<Individual*>::iterator it = pop->females.begin();
std::advance(it,indToDie-numMales); // it += indToDie;
delete *it;
pop->females.erase(it);
numFemales--;
}
}
//std::cout<<"PopulationBreedingStrategy::breed: "<<toDie<<" individs have died\n";
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int toBorn = int (inds * birthRate);
numMales = pop->males.size();
numFemales = pop->females.size();
inds = numMales + numFemales;
for(int i = 0; i < toBorn; i++) {
int fatherNum = rand() % numMales;
int motherNum = rand() % numFemales;
int gender = rand() % 2;
std::list<Individual*>::iterator itFather = pop->males.begin();
std::advance(itFather, fatherNum);
std::list<Individual*>::iterator itMother = pop->females.begin();
std::advance(itMother, motherNum);
Genotype* genotype;
double prob = Settings::ProbMtDNARecomb;
if(prob > 0.0){
int invProb = (int)(1/prob);
int recombine = rand() % invProb;
if(recombine == 0){
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
//std::cerr<<"Recomb\n";
ChromosomeRearrangementStrategy* recombinator = RecombinationStrategies::getInstance("D2015");
HaploidGenotype recombGenotype = recombinator->buildRecombinantGenotype(
(*itFather)->getGenotype().getMotherGenome(), (*itMother)->getGenotype().getMotherGenome());
genotype = new Genotype(recombGenotype, recombGenotype);
}
else{
genotype = new Genotype(
(*itMother)->getGenotype().getMotherGenome(), (*itMother)->getGenotype().getMotherGenome());
}
}
else{
genotype = new Genotype(
(*itMother)->getGenotype().getMotherGenome(), (*itMother)->getGenotype().getMotherGenome());
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
}
Phenotype* phenotype= new Phenotype((*itFather)->getPhenotype());
Individual* ind = new Individual(genotype, phenotype, 0, Individual::Gender(gender));
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
if(gender == 0){
pop->males.push_back(ind);
}
else{
pop->females.push_back(ind);
}
}
}

12
population/BreedingStrategies/NeutralEvolutionBreedStrat.h Normal file
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#pragma once
#include "PopulationBreedingStrategy.h"
class NeutralEvolutionBreedingStrategy : public PopulationBreedingStrategy {
float birthRate;
float deathRate;
public:
void setBirthRate(float b) {birthRate = b;}
void setDeathRate(float d) {deathRate = d;}
virtual void breed(Population* pop);
};

81
population/BreedingStrategies/PopulationBreedingStrategy.cpp Normal file
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#include "PopulationBreedingStrategy.h"
#include "VerhulstBreedingStrategy.h"
#include "NeutralEvolutionBreedStrat.h"
#include "../../individual/genome/strategies/InOutBreeding/InOutBreedingPopulationBreedingStrategy.h"
#include "../../individual/genome/strategies/KolchShindyal/KolchShindyalBreedingStrategy.h"
#include "../../processor/Settings.h"
//#include <vector>
#include <algorithm>
#include <iostream>
#include <cstdlib>
#include <ctime>
void PopulationBreedingStrategy::breed(Population* _pop){
float deathRate = Settings::NaturalDeathRate;//0.01f; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>
AsexualPopulation* pop = dynamic_cast<AsexualPopulation*>(_pop);
if(pop == NULL){
std::cerr<<"Wrong dynamic cast to AsexualPopulation\n";
return;
}
std::sort(pop->individs.begin(), pop->individs.end(), compareOnFitness);
int inds = pop->individs.size();
// <20><> <20><><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> SelectionAll
// <20> <20><><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>-<2D><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int toDie = int (inds * deathRate);
std::vector<Individual*>::iterator start = pop->individs.begin();
std::vector<Individual*>::iterator end = pop->individs.begin()+toDie;
//advance(end,toDie);
for(std::vector<Individual*>::iterator it = start; it != end; it++){
delete *it;
}
pop->individs.erase(start, end);
std::cout<<"PopulationBreedingStrategy::breed: "<<toDie<<" individs have died\n";
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float birthRate = Settings::BirthRate;//0.02f;
int toBorn = int (inds * birthRate);
inds = pop->individs.size();
srand((unsigned int)time(NULL));
for(int i = 0; i < toBorn; i++) {
int male = rand() % inds;
int female = rand() % inds;
female = (female != male ? female : (female + 1) % inds);
Individual* ind = new Individual(*(pop->individs.at(male)), *(pop->individs.at(female)));
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
pop->individs.push_back(ind);
}
}
std::map<std::string, PopulationBreedingStrategy*> PopulationBreedingStrategy::_strategies;
PopulationBreedingStrategy* PopulationBreedingStrategy::getInstance(std::string _name){
if(_strategies.find(_name) == _strategies.end()){
PopulationBreedingStrategy* s = 0;
if(_name.compare("Verhulst") == 0){
s = new VerhulstBreedingStrategy();
}
else if(_name.compare("inoutbreeding") == 0){
s = new InOutBreedingPopulationBreedingStrategy();
}
else if(_name.compare("kolchan_shindyal_breeding") == 0){
s = new KolchShindyalBreedingStrategy();
}
else if(_name.compare("neutral") == 0){
s = new NeutralEvolutionBreedingStrategy();
}
else {
s = new PopulationBreedingStrategy();
}
_strategies[_name] = s;
}
return _strategies[_name];
}

12
population/BreedingStrategies/PopulationBreedingStrategy.h Normal file
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#pragma once
#include "../Population.h"
#include <map>
class Population;
class PopulationBreedingStrategy {
static std::map<std::string, PopulationBreedingStrategy*> _strategies;
public:
virtual void breed(Population* pop);
static PopulationBreedingStrategy* getInstance(std::string name);
};

52
population/BreedingStrategies/VerhulstBreedingStrategy.cpp Normal file
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@@ -0,0 +1,52 @@
#include "VerhulstBreedingStrategy.h"
#include "../../processor/Settings.h"
#include <algorithm>
#include <iostream>
#include <cstdlib>
#include <ctime>
void VerhulstBreedingStrategy::breed(Population *_pop) {
// <09><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// rX * (1 - X/K) = rX - (r/K)X^2
double birthRate = Settings::BirthRate;// 0.03;
double r = 1 + birthRate;
double K = _pop->region->getCapacity();
AsexualPopulation* pop = dynamic_cast<AsexualPopulation*>(_pop);
if(pop == NULL){
std::cerr<<"Wrong dynamic cast to AsexualPopulation\n";
return;
}
long int inds = pop->individs.size();
long int toDie = long int (inds*inds * r/K + 0.5); // 0.5 - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>-<2D><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
long int toBorn = long int (inds*birthRate + 0.5); // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>
std::sort(pop->individs.begin(), pop->individs.end(), compareOnFitness);
std::vector<Individual*>::iterator start = pop->individs.begin();
std::vector<Individual*>::iterator end = pop->individs.begin()+toDie;
for(std::vector<Individual*>::iterator it = start; it != end; it++){
delete *it;
}
pop->individs.erase(start, end);
std::cout<<"VerhulstBreedingStrategy::breed: "<<toDie<<" individs have died\n";
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
inds = pop->individs.size();
srand((unsigned int)time(NULL));
for(long int i = 0; i < toBorn; i++) {
int male = rand() % inds;
int female = rand() % inds;
female = (female != male ? female : (female + 1) % inds);
Individual* ind = new Individual(*(pop->individs.at(male)), *(pop->individs.at(female)));
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
pop->individs.push_back(ind);
}
}

7
population/BreedingStrategies/VerhulstBreedingStrategy.h Normal file
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#pragma once
#include "PopulationBreedingStrategy.h"
class VerhulstBreedingStrategy : public PopulationBreedingStrategy {
public:
virtual void breed(Population* pop);
};

159
population/Population.cpp Normal file
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@@ -0,0 +1,159 @@
#include "Population.h"
#include "../individual/Phenotype.h"
#include <cstdlib>
#include <sstream>
#include <algorithm>
AsexualPopulation::~AsexualPopulation(){
// TODO : <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD>
}
AsexualPopulation::AsexualPopulation(int size, PopulationBreedingStrategy* _strategy) :
Population(_strategy), individs(size/*, 0*/)
{
srand(0);
int RANGE = 1000;
float gValue;
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
for(int i = 0; i < size; i++){
// <20><><EFBFBD><EFBFBD><EFBFBD>
std::vector<Chromosome> fGenome;
std::vector<Chromosome> mGenome;
// <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
gValue = (rand()%RANGE + 1) / (float) RANGE;
Gene geneF1(Gene::Continious, "X", gValue);
gValue = (rand()%RANGE + 1) / (float) RANGE;
Gene geneF2(Gene::Continious, "Y", gValue);
gValue = (rand()%RANGE + 1) / (float) RANGE;
Gene geneF3(Gene::Continious, "Z", gValue);
Chromosome chromF("Chrom 1"); // <20><><EFBFBD><EFBFBD>
chromF.insertGeneToEnd(geneF1);
chromF.insertGeneToEnd(geneF2);
chromF.insertGeneToEnd(geneF3);
gValue = (rand()%RANGE + 1) / (float) RANGE;
Gene geneM1(Gene::Continious, "X", gValue);
gValue = (rand()%RANGE + 1) / (float) RANGE;
Gene geneM2(Gene::Continious, "Y", gValue);
gValue = (rand()%RANGE + 1) / (float) RANGE;
Gene geneM3(Gene::Continious, "Z", gValue);
Chromosome chromM("Chrom 1"); // <20><><EFBFBD><EFBFBD>
chromM.insertGeneToEnd(geneM1);
chromM.insertGeneToEnd(geneM2);
chromM.insertGeneToEnd(geneM3);
fGenome.push_back(chromF);
mGenome.push_back(chromM);
Genotype* genotype = new Genotype(fGenome, mGenome);
// (END) <20><><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
Trait trait1(Trait::Continious, "X", 0.0f);
Trait trait2(Trait::Continious, "Y", 0.0f);
Trait trait3(Trait::Continious, "Z", 0.0f);
Phenotype* phenotype = new Phenotype(trait1);
phenotype->addTrait(trait2);
phenotype->addTrait(trait3);
// (END) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
InnerSubstratesPool* subPool = 0;
// (END) <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
this->individs.at(i) = new Individual(genotype, phenotype, subPool, Individual::hermaphrodite, 0);
} // (END) for(int i = 0; i < size; i++)
}
void AsexualPopulation::calculateFitnessAll(){
for(unsigned int i = 0; i < this->individs.size(); i++){
this->individs.at(i)->calculateFitness();
}
}
void AsexualPopulation::breedAll(){
this->breedingStrategy->breed(this);
}
void AsexualPopulation::selectionAll(){
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> breedAll
}
void AsexualPopulation::mutationAll(){
}
void AsexualPopulation::setRegion(Region *_region){
this->region = _region;
for(unsigned int i = 0; i < this->individs.size(); i++){
this->individs.at(i)->setRegion(_region);
}
}
std::string AsexualPopulation::getSatistics(){
std::stringstream ans;
long int pSize = this->individs.size();
ans<<"Population size\t"<<pSize<<"\t";
//////////////////////////
double totalFitness = 0.0;
double best = 0.0;
double worst= 1000.0;
for(int i = 0; i < pSize; i++){
double fitness = this->individs.at(i)->getFitness();
best = fitness > best ? fitness : best;
worst= fitness < worst? fitness : worst;
totalFitness += fitness;
}
ans<<"Average fitness\t"<<(totalFitness/pSize);
ans<<"\tBest\t"<<(best);
ans<<"\tWorst\t"<<(worst);
return ans.str();
}
void AsexualPopulation::putGeneticStatisticsToStream(std::ostream &out){
out<<"Population size:\t"<<this->individs.size()<<std::endl;
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
//sort(this->individs.begin(),this->individs.end());
for(unsigned int i = 0; i < this->individs.size(); i++){
out<<(i+1)<<"\t";
out<<"Fitness:\t"<<(this->individs.at(i)->getFitness());
out<<"\t";
out<<"Genotype:\t"<<(this->individs.at(i)->getGenotype());
out<<"\t";
out<<"Phenotype:\t"<<(this->individs.at(i)->getPhenotype());
out<<std::endl;
}
}
void AsexualPopulation::putGeneticSimpleStatisticsToStream(std::ostream &out){
for(unsigned int i = 0; i < this->individs.size(); i++){
out<<(i+1)<<"\t"<<(this->individs.at(i)->getFitness());
out<<"\t"<<(this->individs.at(i)->getGenotype().toSimpleString());
//out<<"\t";
out<<(this->individs.at(i)->getPhenotype().toSimpleString());
out<<std::endl;
}
}
void AsexualPopulation::putGeneticMaxModuleStatisticsToStream(std::ostream &out){
for(unsigned int i = 0; i < this->individs.size(); i++){
out<<(i+1)<<"\t"<<(this->individs.at(i)->getFitness());
out<<"\t"<<(this->individs.at(i)->getGenotype().toMaxModuleAB());
//out<<"\t";
//out<<(this->individs.at(i)->getPhenotype().toSimpleString());
out<<std::endl;
}
}

84
population/Population.h Normal file
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#pragma once
#include <list>
#include <vector>
#include "../individual/AbstractIndividual.h"
#include "BreedingStrategies/PopulationBreedingStrategy.h"
#include "../environment/AbstractEnvironment.h"
class PopulationBreedingStrategy;
class Population {
friend class PopulationBreedingStrategy;
friend class VerhulstBreedingStrategy;
protected:
PopulationBreedingStrategy* breedingStrategy;
Region* region;
public:
Population(PopulationBreedingStrategy* _strategy) : breedingStrategy(_strategy){}
virtual ~Population() {};
virtual void setBreedingStrategy(PopulationBreedingStrategy* _strategy) { breedingStrategy = _strategy;}
virtual void setRegion(Region* _region) { region = _region;}
virtual void calculateFitnessAll() = 0;
virtual void breedAll() = 0;
virtual void selectionAll() = 0;
virtual void mutationAll() = 0;
virtual std::string getSatistics() = 0;
virtual void putGeneticStatisticsToStream(std::ostream& out) = 0;
virtual void putGeneticSimpleStatisticsToStream(std::ostream& out) = 0;
virtual void putGeneticMaxModuleStatisticsToStream(std::ostream& out) = 0;
};
class AsexualPopulation : public Population {
friend class PopulationBreedingStrategy;
friend class VerhulstBreedingStrategy;
friend class InOutBreedingPopulationBreedingStrategy;
friend class KolchShindyalBreedingStrategy;
protected:
std::vector<Individual*> individs;
public:
AsexualPopulation(const std::vector<Individual*>& _inds, PopulationBreedingStrategy* _strategy = 0) : Population(_strategy), individs(_inds) {};
AsexualPopulation(int size, PopulationBreedingStrategy* _strategy = 0);
virtual ~AsexualPopulation();
virtual void setRegion(Region* _region);
virtual void calculateFitnessAll();
virtual void breedAll();
virtual void selectionAll();
virtual void mutationAll();
virtual std::string getSatistics();
virtual void putGeneticStatisticsToStream(std::ostream& out);
virtual void putGeneticSimpleStatisticsToStream(std::ostream& out);
virtual void putGeneticMaxModuleStatisticsToStream(std::ostream& out);
};
//////////////////////////////////////////////
//////////////////////////////////////////////
//////////////////////////////////////////////
class BisexualPopulation : public Population {
friend class NeutralEvolutionBreedingStrategy;
protected:
std::list<Individual*> males;
std::list<Individual*> females;
public:
BisexualPopulation(const std::list<Individual*>& _males,
const std::list<Individual*>& _females, PopulationBreedingStrategy* _strategy = 0) :
Population(_strategy), males(_males), females(_females) {}
virtual ~BisexualPopulation();
//virtual void setRegion(Region* _region);
virtual void calculateFitnessAll();
virtual void breedAll();
virtual void selectionAll();
virtual void mutationAll();
virtual std::string getSatistics();
virtual void putGeneticStatisticsToStream(std::ostream& out);
virtual void putGeneticSimpleStatisticsToStream(std::ostream& out);
virtual void putGeneticMaxModuleStatisticsToStream(std::ostream& out);
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
static std::string mutualMigration(BisexualPopulation* p1, BisexualPopulation* p2, float frac1, float frac2 = -1.f);
BisexualPopulation* createSubpopulation(float frac);
void mutationDerevyanko2015(double pMutMtDNA, double pMutNumt);
};