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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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99
DEC_GUI/DEC-0.0/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("dummy");
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
DEC_GUI/DEC-0.0/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);
};

71
DEC_GUI/DEC-0.0/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);
}
}
PopulationBreedingStrategy* PopulationBreedingStrategy::getInstance(std::string name){
if(name.compare("Verhulst") == 0){
return new VerhulstBreedingStrategy();
}
if(name.compare("inoutbreeding") == 0){
return new InOutBreedingPopulationBreedingStrategy();
}
if(name.compare("kolchan_shindyal_breeding") == 0){
return new KolchShindyalBreedingStrategy();
}
if(name.compare("neutral") == 0){
return new NeutralEvolutionBreedingStrategy();
}
return new PopulationBreedingStrategy();
}

10
DEC_GUI/DEC-0.0/population/BreedingStrategies/PopulationBreedingStrategy.h Normal file
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#pragma once
#include "../Population.h"
class Population;
class PopulationBreedingStrategy {
public:
virtual void breed(Population* pop);
static PopulationBreedingStrategy* getInstance(std::string name);
};

52
DEC_GUI/DEC-0.0/population/BreedingStrategies/VerhulstBreedingStrategy.cpp Normal file
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#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
DEC_GUI/DEC-0.0/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);
};