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This commit is contained in:
Aleksey M. Mukhin
2024-10-03 18:43:04 +07:00
commit f80052961f
186 changed files with 71676 additions and 0 deletions
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54
individual/genome/strategies/KolchShindyal/KolchShindyalBreedingStrategy.cpp Normal file
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#include "KolchShindyalBreedingStrategy.h"
#include "../../../../processor/Settings.h"
#include "../../../Phenotype.h"
#include <algorithm>
#include <iostream>
#include <cstdlib>
#include <ctime>
void KolchShindyalBreedingStrategy::breed(Population *_pop){
// N = const
srand((unsigned int)time(NULL));
// <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>
float deathRate = 0.01f; //Settings::DeathRate
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><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> !!!
// <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);
}
}

8
individual/genome/strategies/KolchShindyal/KolchShindyalBreedingStrategy.h Normal file
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#pragma once
#include "../../../../population/BreedingStrategies/PopulationBreedingStrategy.h"
class KolchShindyalBreedingStrategy : public PopulationBreedingStrategy {
public:
virtual void breed(Population* pop);
};

63
individual/genome/strategies/KolchShindyal/KolchShindyalGenotypeToPhenotypeStrategy.cpp Normal file
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#include "KolchShindyalGenotypeToPhenotypeStrategy.h"
//#include "../GenotypeToPhenotypeStrategy.h"
#include "../../../../processor/Settings.h"
#include <cmath>
void KolchShindyalGenotypeToPhenotypeStrategy::calculatePhenotype(Individual* individ){
Genotype* genotype = individ->genotype;
Phenotype* phenotype = individ->phenotype;
InnerSubstratesPool* substrates = individ->substrateCache;
// Chromosome 1
Chromosome chr1F = individ->genotype->getFatherGenome().getChromosome(0);
Chromosome chr1M = individ->genotype->getMotherGenome().getChromosome(0);
const std::vector<Gene>& genesF = chr1F.getGenesAsVector();
const std::vector<Gene>& genesM = chr1M.getGenesAsVector();
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float c1m = genesM.at(0).getGeneValueCont();
float c2m = genesM.at(1).getGeneValueCont();
float c3m = genesM.at(2).getGeneValueCont();
float c4m = genesM.at(3).getGeneValueCont();
float c5m = genesM.at(4).getGeneValueCont();
float Em = genesM.at(5).getGeneValueCont();
float c1f = genesF.at(0).getGeneValueCont();
float c2f = genesF.at(1).getGeneValueCont();
float c3f = genesF.at(2).getGeneValueCont();
float c4f = genesF.at(3).getGeneValueCont();
float c5f = genesF.at(4).getGeneValueCont();
float Ef = genesF.at(5).getGeneValueCont();
float X = 0;
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
/*
// 1) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <09>) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int feedBackM = genesM.at(6).getGeneValueDiscr();
int feedBackF = genesF.at(6).getGeneValueDiscr();
if( (feedBackF+feedBackM) != 0) {
X = -c2/2 + sqrt( c2*c2/4 + c5*c2/c3*(E+c4));
}
else{
X = c1/c3*(E+c4);
}
// <09>) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>
int feedBackM = genesM.at(6).getGeneValueDiscr();
int feedBackF = genesF.at(6).getGeneValueDiscr();
if( (feedBackF+feedBackM) == 2) {
X = -c2/2 + sqrt( c2*c2/4 + c5*c2/c3*(E+c4));
}
else{
X = c1/c3*(E+c4);
}
// 2) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
*/
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
phenotype->traitsMap["X"].setTraitValue(X);
}

6
individual/genome/strategies/KolchShindyal/KolchShindyalGenotypeToPhenotypeStrategy.h Normal file
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#pragma once
#include "../GenotypeToPhenotypeStrategy.h"
class KolchShindyalGenotypeToPhenotypeStrategy: public GenotypeToPhenotypeStrategy {
public:
virtual void calculatePhenotype(Individual*);
};

16
individual/genome/strategies/KolchShindyal/KolchShindyalPhenToFitnessStrategy.cpp Normal file
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#include "KolchShindyalPhenToFitnessStrategy.h"
#define _USE_MATH_DEFINES
#include <cmath>
#include <math.h>
double KolchShindyalPhenToFitnessStrategy::calculateFitness(Phenotype *phen){
double X = phen->getTraitByName("X").getTraitValueCont();
double Xopt = phen->getTraitByName("Xopt").getTraitValueCont();
double sigmaX = phen->getTraitByName("sigmaX").getTraitValueCont();
double ans = 1/(sqrt(2*M_PI)) * exp(-0.5*pow((X-Xopt)/sigmaX,2.));
return ans;
}

7
individual/genome/strategies/KolchShindyal/KolchShindyalPhenToFitnessStrategy.h Normal file
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#pragma once
#include "../PhenotypeToFitnessStrategy.h"
#include "../../../Phenotype.h"
class KolchShindyalPhenToFitnessStrategy : public PhenotypeToFitnessStrategy {
virtual double calculateFitness(Phenotype* phen);
};