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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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74
DEC_GUI/DEC-0.0/individual/genome/strategies/ChromosomeRearrangementStrategy.cpp Normal file
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#include "ChromosomeRearrangementStrategy.h"
#include <cstdlib>
#include <ctime>
HaploidGenotype ChromosomeRearrangementStrategy::buildRecombinantGenotype(const Genotype* parentGenotype){
std::vector<Chromosome> chromosomes;
const std::vector<Chromosome>* fGenome = &parentGenotype->fatherGenome.chromosomes;
const std::vector<Chromosome>* mGenome = &parentGenotype->motherGenome.chromosomes;
//srand((unsigned int)time(NULL));
for (unsigned int i = 0; i < fGenome->size(); i++){
int flag = rand() % 2;
const std::vector<Gene>* first;
const std::vector<Gene>* second;
if(flag == 0){
first = &fGenome->at(i).genes;
second= &mGenome->at(i).genes;
}
else{
first = &mGenome->at(i).genes;
second= &fGenome->at(i).genes;
}
Chromosome childChromosome(fGenome->at(i).name, *first);
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> "<22><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>"
int bound = rand() % first->size();
for(unsigned int j = bound; j < first->size(); j++){
childChromosome.genes.at(j) = second->at(j);
}
chromosomes.push_back(childChromosome);
}
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD>. <20> <20> <20>),
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
return HaploidGenotype(chromosomes);
}
HaploidGenotype ChromosomeRearrangementStrategy::
buildRecombinantGenotype(const HaploidGenotype& fatherGenome, const HaploidGenotype& motherGenome){
std::vector<Chromosome> chromosomes;
const std::vector<Chromosome> fGenome = fatherGenome.chromosomes;
const std::vector<Chromosome> mGenome = motherGenome.chromosomes;
//srand((unsigned int)time(NULL));
for (unsigned int i = 0; i < fGenome.size(); i++){
int flag = rand() % 2;
std::vector<Gene> first;
std::vector<Gene> second;
if(flag == 0){
first = fGenome.at(i).genes;
second= mGenome.at(i).genes;
}
else{
first = mGenome.at(i).genes;
second= fGenome.at(i).genes;
}
Chromosome childChromosome(fGenome.at(i).name, first);
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> "<22><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>"
int bound = rand() % first.size();
for(unsigned int j = bound; j < first.size(); j++){
childChromosome.genes.at(j) = second.at(j);
}
chromosomes.push_back(childChromosome);
}
// <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD>. <20> <20> <20>),
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
return HaploidGenotype(chromosomes);
}
ChromosomeRearrangementStrategy* RecombinationStrategies::getInstance(std::string _name){
return new ChromosomeRearrangementStrategy();
}

17
DEC_GUI/DEC-0.0/individual/genome/strategies/ChromosomeRearrangementStrategy.h Normal file
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#pragma once
#include "../AbstractGenome.h"
class HaploidGenotype;
class Genotype;
class ChromosomeRearrangementStrategy {
public:
virtual HaploidGenotype buildRecombinantGenotype(const Genotype*);
virtual HaploidGenotype buildRecombinantGenotype(const HaploidGenotype&, const HaploidGenotype&);
};
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
class RecombinationStrategies {
public:
static ChromosomeRearrangementStrategy* getInstance(std::string _name);
};

35
DEC_GUI/DEC-0.0/individual/genome/strategies/GenotypeToPhenotypeStrategy.cpp Normal file
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#include "GenotypeToPhenotypeStrategy.h"
#include "KolchShindyal/KolchShindyalGenotypeToPhenotypeStrategy.h"
#include <cmath>
void GenotypeToPhenotypeStrategy::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();
for(unsigned int i = 0; i < genesF.size(); i++){
float geneVal = std::min(
genesF.at(i).getGeneValueCont(),
genesM.at(i).getGeneValueCont());
phenotype->traitsMap[genesF.at(i).getName()].setTraitValue(geneVal);
}
}
GenotypeToPhenotypeStrategy* GenotypeToPhenotypeStrategies::getInstance(std::string _name){
if(_name.compare("inoutbreeding") == 0){
return new InOutBreedingGenotypeToPhenotypeStrategy();
}
if(_name.compare("kolchan_shindyal_gen_to_phen") == 0){
return new KolchShindyalGenotypeToPhenotypeStrategy();
}
// default
return new GenotypeToPhenotypeStrategy();
}

21
DEC_GUI/DEC-0.0/individual/genome/strategies/GenotypeToPhenotypeStrategy.h Normal file
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#pragma once
#include "../../AbstractIndividual.h"
#include "../AbstractGenome.h"
#include "../../Phenotype.h"
class GenotypeToPhenotypeStrategy {
public:
virtual void calculatePhenotype(Individual*);
//virtual void calculatePhenotype(const Genotype*, Phenotype*);
//Phenotype* calculatePhenotype(const Genotype*);
};
class InOutBreedingGenotypeToPhenotypeStrategy : public GenotypeToPhenotypeStrategy {
public:
virtual void calculatePhenotype(Individual*);
};
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
class GenotypeToPhenotypeStrategies {
public:
static GenotypeToPhenotypeStrategy* getInstance(std::string _name);
};

11
DEC_GUI/DEC-0.0/individual/genome/strategies/InOutBreeding/InOutBreedingPhenToFitStrategy.cpp Normal file
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#include "InOutBreedingPhenToFitStrategy.h"
#include "../../../Phenotype.h"
double InOutBreedingPhenToFitStrategy::calculateFitness(Phenotype *phen){
double ans = 0.0;
ans = phen->getTraitByName("coadaptive").getTraitValueCont();
//float coef = phen->getTraitByName("disease")
return ans;
}

7
DEC_GUI/DEC-0.0/individual/genome/strategies/InOutBreeding/InOutBreedingPhenToFitStrategy.h Normal file
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#pragma once
#include "../PhenotypeToFitnessStrategy.h"
class InOutBreedingPhenToFitStrategy : public PhenotypeToFitnessStrategy {
virtual double calculateFitness(Phenotype* phen);
};

85
DEC_GUI/DEC-0.0/individual/genome/strategies/InOutBreeding/InOutBreedingPopulationBreedingStrategy.cpp Normal file
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#include "InOutBreedingPopulationBreedingStrategy.h"
#include "../../../../processor/Settings.h"
#include "../../../Phenotype.h"
#include <algorithm>
#include <iostream>
#include <cstdlib>
#include <ctime>
void InOutBreedingPopulationBreedingStrategy::breed(Population *_pop){
// N = const
AsexualPopulation* pop = dynamic_cast<AsexualPopulation*>(_pop);
if(pop == NULL){
std::cerr<<"Wrong dynamic cast to AsexualPopulation\n";
return;
}
srand((unsigned int)time(NULL));
int offsprings = Settings::OffspringsMean;
std::vector<Individual*> newIndivids;
long int inds;
for(inds = pop->individs.size();inds >=2; inds -= 2){
int motherIndex = rand()%inds;
int fatherIndex = rand()%inds;
if(fatherIndex == motherIndex){
fatherIndex = (fatherIndex+1)%inds;
}
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
for(int i = 0; i < offsprings; i++){
Individual* ind = new Individual(*(pop->individs.at(motherIndex)), *(pop->individs.at(fatherIndex)));
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
ind->calculatePhenotype();
Phenotype phen = ind->getPhenotype();
float coadapt = phen.getTraitByName("coadaptive").getTraitValueCont();
float disease = phen.getTraitByName("disease").getTraitValueCont();
if(disease > Settings::DiseaseThreshold){ // <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float probSurvive = 1.f;
if(coadapt < Settings::CoadaptiveThreshold){ // TODO: <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>
probSurvive = Settings::CoadaptiveMinimumP;
}
else{
probSurvive = (1-Settings::CoadaptiveMinimumP)/(Settings::CoadaptiveMaximumTrait-Settings::CoadaptiveThreshold);
probSurvive *= coadapt - Settings::CoadaptiveMaximumTrait;
probSurvive += 1;
}
int order = 1000;
int prob = rand()%order;
if(prob < order*probSurvive){
// <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>.
newIndivids.push_back(ind);
}
}
} // (END) for(int i = 0; i < offsprings; i++)
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
delete pop->individs.at(motherIndex);
delete pop->individs.at(fatherIndex);
if(motherIndex > fatherIndex){
pop->individs.erase(pop->individs.begin()+motherIndex);
pop->individs.erase(pop->individs.begin()+fatherIndex);
}
else{
pop->individs.erase(pop->individs.begin()+fatherIndex);
pop->individs.erase(pop->individs.begin()+motherIndex);
}
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
if(newIndivids.size() >= Settings::KMaxParameter){
for(unsigned int i = 0; i < pop->individs.size(); i++){
delete pop->individs.at(i);
}
pop->individs.clear();
break;
}
} // (END) for(inds = pop->individs.size();inds >=2; inds -= 2)
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
pop->individs.insert(pop->individs.begin(), newIndivids.begin(), newIndivids.end());
}

8
DEC_GUI/DEC-0.0/individual/genome/strategies/InOutBreeding/InOutBreedingPopulationBreedingStrategy.h Normal file
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#pragma once
#include "../../../../population/BreedingStrategies/PopulationBreedingStrategy.h"
class InOutBreedingPopulationBreedingStrategy : public PopulationBreedingStrategy {
public:
virtual void breed(Population* pop);
};

102
DEC_GUI/DEC-0.0/individual/genome/strategies/InOutBreeding/InOutBreeginGenToPhenStrategy.cpp Normal file
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#include "../GenotypeToPhenotypeStrategy.h"
#include "../../../../processor/Settings.h"
#include <cmath>
#include <qmath.h>
void InOutBreedingGenotypeToPhenotypeStrategy::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><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float a1 = genesF.at(0).getGeneValueCont();
float a2 = genesM.at(0).getGeneValueCont();
float b1 = genesF.at(1).getGeneValueCont();
float b2 = genesM.at(1).getGeneValueCont();
// (END) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::vector<float> diseaseAllelesF(4);
std::vector<float> diseaseAllelesM(4);
for(unsigned int i = 0; i < diseaseAllelesF.size(); i++){
diseaseAllelesF.at(i) = genesF.at(i+2).getGeneValueCont();
diseaseAllelesM.at(i) = genesM.at(i+2).getGeneValueCont();
}
// (END) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float trait1 = 0, trait2 = 0;
float a, b;
// 1) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD>
if(Settings::CoadaptiveGenesInteraction == "onechromosome"){
// 1.1 <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
a = a1;
b = b1;
}
else if(Settings::CoadaptiveGenesInteraction == "mean"){
// 1.2 <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
a = 0.5f*(a1+a2);
b = 0.5f*(b1+b2);
}
else{ // Settings::CoadaptiveGenesInteraction == "maxmodule"
// 1.3 <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
a = std::fabs(a1) >= std::fabs(a2) ? a1 : a2;
b = std::fabs(b1) >= std::fabs(b2) ? b1 : b2;
}
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> 1
trait1 = std::max(a*b - (std::fabs(a*a*a) + std::fabs(b*b*b))/20, 0.0f);
//trait1 = std::max(a*b - (a*a*a*a + b*b*b*b)/250, 0.0f);
// 2) <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
if(Settings::DiseaseGenesInteraction == "add1"){
// 2.1<EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float sum1 = 0.0f, sum2 = 0.0f;
for(unsigned int i = 0; i < diseaseAllelesF.size(); i++){
sum1 += diseaseAllelesF.at(i);
sum2 += diseaseAllelesM.at(i);
}
trait2 = std::max(sum1,sum2);
}
else if(Settings::DiseaseGenesInteraction == "addmax"){
// 2.1<EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD>)
for(unsigned int i = 0; i < diseaseAllelesF.size(); i++){
trait2 += std::max(diseaseAllelesF.at(i), diseaseAllelesM.at(i));
}
}
else if(Settings::DiseaseGenesInteraction == "mult"){
// 2.2 <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
for(unsigned int i = 0; i < diseaseAllelesF.size(); i++){
trait2 *= std::max(diseaseAllelesF.at(i), diseaseAllelesM.at(i));
}
}
else if(Settings::DiseaseGenesInteraction == "meanadd"){
// 2.3<EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>)
for(unsigned int i = 0; i < diseaseAllelesF.size(); i++){
trait2 += diseaseAllelesF.at(i) + diseaseAllelesM.at(i);
}
trait2 /= 2.0f;
}
else{// if(Settings::DiseaseGenesInteraction == "meanmult"){
// 2.3<EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>)
for(unsigned int i = 0; i < diseaseAllelesF.size(); i++){
trait2 *= (diseaseAllelesF.at(i) + diseaseAllelesM.at(i))/2;
}
}
// <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["coadaptive"].setTraitValue(trait1);
phenotype->traitsMap["disease"].setTraitValue(trait2);
}

54
DEC_GUI/DEC-0.0/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
DEC_GUI/DEC-0.0/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
DEC_GUI/DEC-0.0/individual/genome/strategies/KolchShindyal/KolchShindyalGenotypeToPhenotypeStrategy.cpp Normal file
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@@ -0,0 +1,63 @@
#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
DEC_GUI/DEC-0.0/individual/genome/strategies/KolchShindyal/KolchShindyalGenotypeToPhenotypeStrategy.h Normal file
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@@ -0,0 +1,6 @@
#pragma once
#include "../GenotypeToPhenotypeStrategy.h"
class KolchShindyalGenotypeToPhenotypeStrategy: public GenotypeToPhenotypeStrategy {
public:
virtual void calculatePhenotype(Individual*);
};

14
DEC_GUI/DEC-0.0/individual/genome/strategies/KolchShindyal/KolchShindyalPhenToFitnessStrategy.cpp Normal file
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@@ -0,0 +1,14 @@
#include "KolchShindyalPhenToFitnessStrategy.h"
#define _USE_MATH_DEFINES
#include <cmath>
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
DEC_GUI/DEC-0.0/individual/genome/strategies/KolchShindyal/KolchShindyalPhenToFitnessStrategy.h Normal file
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@@ -0,0 +1,7 @@
#pragma once
#include "../PhenotypeToFitnessStrategy.h"
#include "../../../Phenotype.h"
class KolchShindyalPhenToFitnessStrategy : public PhenotypeToFitnessStrategy {
virtual double calculateFitness(Phenotype* phen);
};

26
DEC_GUI/DEC-0.0/individual/genome/strategies/PhenotypeToFitnessStrategy.cpp Normal file
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@@ -0,0 +1,26 @@
#include "PhenotypeToFitnessStrategy.h"
#include "../../Phenotype.h"
#include "InOutBreeding/InOutBreedingPhenToFitStrategy.h"
#include "KolchShindyal/KolchShindyalPhenToFitnessStrategy.h"
#include <cmath>
double PhenotypeToFitnessStrategy::calculateFitness(Phenotype *phen){
double ans = 0.0;
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::map<std::string, Trait>::iterator it;
for(it = phen->traitsMap.begin(); it != phen->traitsMap.end(); it++){
float trait = it->second.getTraitValueCont();
ans += trait*trait;
}
return std::pow(ans,0.5);
}
PhenotypeToFitnessStrategy* PhenotypeToFitnessStrategy::getInstance(std::string name){
if(name.compare("inoutbreeding") == 0){
return new InOutBreedingPhenToFitStrategy();
}
if(name.compare("kolch_shindyal_phen_to_fit") == 0){
return new KolchShindyalPhenToFitnessStrategy();
}
return new PhenotypeToFitnessStrategy();
}

10
DEC_GUI/DEC-0.0/individual/genome/strategies/PhenotypeToFitnessStrategy.h Normal file
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@@ -0,0 +1,10 @@
#pragma once
#include <string>
class Phenotype;
class PhenotypeToFitnessStrategy {
public:
static PhenotypeToFitnessStrategy* getInstance(std::string);
virtual double calculateFitness(Phenotype* phen);
};