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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
186 changed files with 71676 additions and 0 deletions
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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);
}