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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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59
individual/AbstractIndividual.h Normal file
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#pragma once
/*
*/
#include "../environment/AbstractEnvironment.h"
#include "genome/AbstractGenome.h"
#include "InnerSubstratesPool.h"
#include "genome/strategies/PhenotypeToFitnessStrategy.h"
class Phenotype;
class GenotypeToPhenotypeStrategy;
class Individual {
public:
enum Gender { male, female, hermaphrodite };
friend class GenotypeToPhenotypeStrategy;
friend class InOutBreedingGenotypeToPhenotypeStrategy;
friend class KolchShindyalGenotypeToPhenotypeStrategy;
friend class BisexualPopulation; // <20> <20><><EFBFBD><EFBFBD> <20><> MutationStrategy !!!
protected:
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
GenotypeToPhenotypeStrategy* genToPhenStrategy;
PhenotypeToFitnessStrategy* phenToFitStrategy;
ChromosomeRearrangementStrategy* recombinationStrategy;
////
//Environment* currentEnvironment;
Region* region;
unsigned int age;
Gender gender;
Genotype* genotype;
InnerSubstratesPool* substrateCache ; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
Phenotype* phenotype;
double fitness;
/////////////////
public:
Individual(const Individual& father, const Individual& mother); // <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
Individual(Genotype* gType, Phenotype* pType, InnerSubstratesPool* sub, Gender _gender = hermaphrodite, Region* reg = 0);
virtual ~Individual();
virtual const Genotype& getGenotype() const { return *genotype;}
virtual const Phenotype& getPhenotype() const {return *phenotype;}
//virtual void setEnvironment(Environment* env) { currentEnvironment = env; }
virtual void setRegion(Region* _region) {};
virtual void setGenToPhenStrategy(GenotypeToPhenotypeStrategy* s){ genToPhenStrategy = s;}
virtual void setPhenToFitnessStrategy(PhenotypeToFitnessStrategy* p) { if(phenToFitStrategy != 0) {delete phenToFitStrategy;} phenToFitStrategy = p;}
virtual void calculateFitness();
virtual void calculatePhenotype();
virtual double getFitness() const { return fitness; }
Gender getGender() const { return gender; }
virtual bool operator<(const Individual* _ind) const { return this->fitness < _ind->fitness;}
};
//bool compareOnFitness(const Individual& a, const Individual& b);
bool compareOnFitness(const Individual* a, const Individual* b);

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#include "AbstractIndividual.h"
#include "genome/strategies/GenotypeToPhenotypeStrategy.h"
#include <iostream>
Individual::Individual(const Individual& father, const Individual& mother)
{
this->genToPhenStrategy = GenotypeToPhenotypeStrategies::getInstance("inoutbreeding");
this->phenToFitStrategy = PhenotypeToFitnessStrategy::getInstance("inoutbreeding");
this->recombinationStrategy = RecombinationStrategies::getInstance("Simple recombination");
genotype = new Genotype(
father.getGenotype().recombinantHaploidGenotype(recombinationStrategy),
mother.getGenotype().recombinantHaploidGenotype(recombinationStrategy));
// <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>
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
this->substrateCache = new InnerSubstratesPool();
phenotype= new Phenotype(father.getPhenotype());
this->age = 0;
this->calculateFitness();
}
Individual::Individual(Genotype* gType, Phenotype* pType, InnerSubstratesPool* sub, Gender _gender, Region* _reg):
genotype(gType), phenotype(pType), substrateCache(sub),
gender(_gender), region(_reg)
{
this->genToPhenStrategy = GenotypeToPhenotypeStrategies::getInstance("inoutbreeding");
this->phenToFitStrategy = PhenotypeToFitnessStrategy::getInstance("inoutbreeding");
this->recombinationStrategy = RecombinationStrategies::getInstance("Simple recombination");
this->age = 0;
//this->calculateFitness();
//this->phenotype
}
Individual::~Individual(){
// std::cerr<<"Destructor works"<<std::endl;
delete this->genotype;
delete this->phenotype;
//delete this->genToPhenStrategy;
//delete this->phenToFitStrategy;
//delete this->recombinationStrategy;
if(this->substrateCache != 0)
delete this->substrateCache;
}
/*bool compareOnFitness(const Individual& a, const Individual& b){
return a.getFitness() < b.getFitness();
}*/
bool compareOnFitness(const Individual* a, const Individual* b){
return a->getFitness() < b->getFitness();
}
void Individual::calculateFitness(){
this->genToPhenStrategy->calculatePhenotype(this);
this->fitness = this->phenToFitStrategy->calculateFitness(this->phenotype);
}
void Individual::calculatePhenotype(){
this->genToPhenStrategy->calculatePhenotype(this);
}

1
individual/InnerSubstratesPool.cpp Normal file
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#include "InnerSubstratesPool.h"

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individual/InnerSubstratesPool.h Normal file
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#pragma once
#include <vector>
#include <map>
#include <string>
using std::vector;
using std::map;
class InnerSubstratesPool {
protected:
std::vector<float> subConcentrations; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::map<std::string, int> subNamesMap; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>)
// P.S. <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>...
std::vector<float> regConcentrations; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::map<std::string, int> regNamesMap; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> (<28><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>)
public:
InnerSubstratesPool(){};
InnerSubstratesPool(const vector<float>& _subs, const map<std::string, int>& _subNames)
: subConcentrations(_subs), subNamesMap(_subNames){}
InnerSubstratesPool(const vector<float>& _subs, const map<std::string, int>& _subNames,
const vector<float>& _regs, const map<std::string, int>& _regNames)
: subConcentrations(_subs), subNamesMap(_subNames),
regConcentrations(_regs), regNamesMap(_regNames){}
virtual void utilizeSubstrate(int num, float count) { subConcentrations.at(num) -= count; }
virtual void utilizeRegulator(int num, float count) { regConcentrations.at(num) -= count; }
virtual void utilizeSubstrate(std::string name, float count) { subConcentrations.at(subNamesMap[name]) -= count; }
virtual void utilizeRegulator(std::string name, float count) { subConcentrations.at(regNamesMap[name]) -= count; }
virtual void addSubstrate(int num, float count) { subConcentrations.at(num) += count; }
virtual void addRegulator(int num, float count) { regConcentrations.at(num) += count; }
virtual void addSubstrate(std::string name, float count) { subConcentrations.at(subNamesMap[name]) += count; }
virtual void addRegulator(std::string name, float count) { subConcentrations.at(regNamesMap[name]) += count; }
};

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#include "Phenotype.h"
#include <iostream>
#include <sstream>
Phenotype::Phenotype(Trait _trait){
this->traitsMap[_trait.getName()] = _trait;
}
void Phenotype::addTrait(Trait _trait){
std::map<std::string,Trait>::iterator it;
it = this->traitsMap.find(_trait.getName());
if(it == this->traitsMap.end()){
this->traitsMap[_trait.getName()] = _trait;
}
else{
std::cerr<<"Phenotype.cpp(16): already has the trait: "<<it->first<<std::endl;
}
}
std::ostream& operator << (std::ostream& os, const Phenotype& p){
std::map<std::string,Trait>::const_iterator it;
for(it = p.traitsMap.begin(); it != p.traitsMap.end(); it++){
os<<(it->first)<<"\t"<<(it->second.getTraitValueCont())<<"\t";
}
return os;
}
std::string Phenotype::toSimpleString() const {
std::stringstream os;
std::map<std::string,Trait>::const_iterator it;
for(it = this->traitsMap.begin(); it != this->traitsMap.end(); it++){
os<<(it->second.getTraitValueCont())<<"\t";
}
return os.str();
}

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individual/Phenotype.h Normal file
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#pragma once
#include "Trait.h"
#include <vector>
#include <map>
#include <string>
class Phenotype {
friend class GenotypeToPhenotypeStrategy;
friend class InOutBreedingGenotypeToPhenotypeStrategy;
friend class KolchShindyalGenotypeToPhenotypeStrategy;
friend class PhenotypeToFitnessStrategy;
friend std::ostream& operator << (std::ostream& os, const Phenotype& p);
protected:
//std::vector<Trait> traits;
std::map<std::string, Trait> traitsMap;
public:
Phenotype() { };
Phenotype(const std::map<std::string, Trait>& _tm) : traitsMap(_tm) {}
Phenotype(Trait _trait);
Trait getTraitByName(std::string name) const {return this->traitsMap.find(name)->second;};
void addTrait(Trait _trait);
std::string toSimpleString() const;
};

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individual/Trait.cpp Normal file
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#include "Trait.h"
#include <iostream>
//Trait::Trait(const Trait& _t)
//{
// *this = _t;
//}
Trait::Trait(Trait::idType _ID, std::string _name, float value):
ID(_ID), name(_name), traitValueCont(value), traitType(Continious)
{}
Trait::Trait(Trait::idType _ID, std::string _name, int value):
ID(_ID), name(_name), traitValueDiscr(value), traitType(Discrete)
{}
void Trait::setTraitValue(float _value){
if(this->traitType == Continious){
this->traitValueCont = _value;
return;
}
/*throw*/std::cerr<<"Trait.cpp(17) Warning: can't assign float value to discrete trait\n";
}
void Trait::setTraitValue(int _value){
if(this->traitType == Discrete){
this->traitValueDiscr = _value;
return;
}
/*throw*/std::cerr<<"Trait.cpp(25) Warning: can't assign int value to continious trait\n";
}

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#pragma once
#include <string>
class Trait {
public:
enum TraitType { Continious, Discrete };
typedef unsigned int idType;
protected:
TraitType traitType; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
idType ID; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::string name; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float traitValueCont; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int traitValueDiscr; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
public:
Trait(){};
Trait(idType _ID, std::string _name, float value);
Trait(idType _ID, std::string _name, int value);
TraitType getTraitType() const { return traitType; }
idType getID() const { return ID; }
std::string getName() const { return name; }
float getTraitValueCont() const { return traitValueCont; }
int getTraitValueDiscr() const { return traitValueDiscr; }
void setName(const std::string& _name) { name = _name; }
void setID(idType _ID) { ID = _ID; }
void setTraitValue(float _value);
void setTraitValue(int _value);
};

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individual/genome/AbstractGenome.h Normal file
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#pragma once
#include "Chromosome.h"
#include "strategies/ChromosomeRearrangementStrategy.h"
#include "strategies\Derevyanko\2015\Derevyanko2015RecombinationStrategy.h"
#include <vector>
#include <iostream>
/*
*/
class ChromosomeRearrangementStrategy; // forward declaration
class Derevyanko2015RecpmbinationStrategy;
class Genotype;
class HaploidGenotype {
friend class Genotype;
friend class ChromosomeRearrangementStrategy;
friend class Derevyanko2015RecpmbinationStrategy;
friend std::ostream& operator << (std::ostream& os, const Genotype& g);
protected:
std::vector<Chromosome> chromosomes;
public:
const Chromosome& getChromosome(unsigned int i) const { return this->chromosomes.at(i);}
public:
HaploidGenotype(const std::vector<Chromosome>& _chrom) : chromosomes(_chrom){};
};
class Genotype {
friend class ChromosomeRearrangementStrategy;
friend class Derevyanko2015RecpmbinationStrategy;
friend std::ostream& operator<< (std::ostream& os, const Genotype& g);
protected:
HaploidGenotype fatherGenome;
HaploidGenotype motherGenome;
public:
Genotype(const std::vector<Chromosome>& _fGenome, const std::vector<Chromosome>& _mGenome) : fatherGenome(HaploidGenotype(_fGenome)), motherGenome(HaploidGenotype(_mGenome)) {};
Genotype(const HaploidGenotype& _fGenome, const HaploidGenotype& _mGenome) : fatherGenome(_fGenome), motherGenome(_mGenome) {};
Genotype(const Genotype& _fDiplGenome, const Genotype& _mDiplGenome);
HaploidGenotype recombinantHaploidGenotype(ChromosomeRearrangementStrategy*) const;
const HaploidGenotype& getFatherGenome() const { return this->fatherGenome;}
const HaploidGenotype& getMotherGenome() const { return this->motherGenome;}
std::string toSimpleString() const;
std::string toSimpleFasta(bool onlyMother = true) const;
std::string toMaxModuleAB() const;
std::string getRawGene(unsigned int fatherMother, unsigned int chromoNum, unsigned int geneNum) const;
void doRawMutationSequence(unsigned int fatherMother, unsigned int chromoNum, unsigned int geneNum, std::string newSeq);
};
//!!!!!!!!!!
class PolyploidGenotype {
};

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#include "Chromosome.h"
void Chromosome::insertGene(Gene gene, int pos){
std::vector<Gene>::iterator it = this->genes.begin();
this->genes.insert(it+pos, gene);
}
void Chromosome::insertGeneToEnd(Gene gene, int pos){
std::vector<Gene>::iterator it = this->genes.end();
this->genes.insert(it-pos, gene);
}

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individual/genome/Chromosome.h Normal file
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#pragma once
#include <string>
#include <vector>
#include "Gene.h"
/*
<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
*/
class Chromosome {
friend class ChromosomeRearrangementStrategy;
friend class Derevyanko2015RecpmbinationStrategy;
friend class Genotype;
protected:
std::string name;
std::vector<Gene> genes;
public:
Chromosome(std::string _name) : name(_name) {};
Chromosome(std::string _name, Gene gene) : name(_name), genes(1, gene) {};
Chromosome(std::string _name, const std::vector<Gene>& _genes) : name(_name), genes(_genes) {};
void insertGene(Gene gene, int pos = 0);
void insertGeneToEnd(Gene gene, int pos = 0);
std::string getName() const { return name;}
const std::vector<Gene>& getGenesAsVector() const { return genes;}
};

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#include "Gene.h"
#include <iostream>
Gene::Gene(idType _ID, std::string _name, float value):
ID(_ID), name(_name), geneValueCont(value), geneType(Continious)
{}
Gene::Gene(idType _ID, std::string _name, int value):
ID(_ID), name(_name), geneValueDiscr(value), geneType(Discrete)
{}
Gene::Gene(idType _ID, std::string _name, std::string _seq):
ID(_ID), name(_name), sequence(_seq), geneType(Sequence)
{}
void Gene::setGeneValue(float _value){
if(this->geneType == Continious){
this->geneValueCont = _value;
return;
}
/*throw*/std::cerr<<"Gene.cpp(17) Warning: can't assign float value to discrete Gene\n";
}
void Gene::setGeneValue(int _value){
if(this->geneType == Discrete){
this->geneValueDiscr = _value;
return;
}
/*throw*/std::cerr<<"Gene.cpp(25) Warning: can't assign int value to continious Gene\n";
}
void Gene::setGeneValue(std::string _seq){
if(this->geneType == Sequence){
this->sequence = _seq;
return;
}
/*throw*/std::cerr<<"Gene.cpp(37) Warning: can't assign numerical value to sequence Gene\n";
}

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#pragma once
#include <string>
/*
<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD>, <20><><EFBFBD>
<EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> "<22><><EFBFBD> <20><><EFBFBD><EFBFBD>" (<28><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>),
<EFBFBD> <20><><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><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><>
1) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
2) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20>/<2F><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
3) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20>/<2F><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
4) <20><><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> (<28> <20>.<2E>. <20> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>???)
5) <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20>.<2E>.
*/
class Gene {
friend class Derevyanko2015RecpmbinationStrategy;
public:
enum GeneType { Continious, Discrete, Sequence };
typedef unsigned int idType;
protected:
GeneType geneType; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
idType ID; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::string name; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
float geneValueCont;// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int geneValueDiscr; // <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
std::string sequence;
public:
Gene(idType _ID, std::string _name, float value);
Gene(idType _ID, std::string _name, int value);
Gene(idType _ID, std::string _name, std::string seq);
GeneType getGeneType() const { return geneType; }
idType getID() const { return ID; }
std::string getName() const { return name; }
float getGeneValueCont() const { return geneValueCont; }
int getGeneValueDiscr() const { return geneValueDiscr; }
std::string getSequence()const { return sequence; }
void setName(const std::string& _name) { name = _name; }
void setID(idType _ID) { ID = _ID; }
void setGeneValue(float _value);
void setGeneValue(int _value);
void setGeneValue(std::string _seq);
};

119
individual/genome/Genotype.cpp Normal file
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#include "AbstractGenome.h"
#include <iostream>
#include <sstream>
#include <cmath>
//Genotype::Genotype(const Genotype& _fDiplGenome, const Genotype& _mDiplGenome){
//}
HaploidGenotype Genotype::recombinantHaploidGenotype(ChromosomeRearrangementStrategy* strategy) const {
return strategy->buildRecombinantGenotype(this);
}
std::ostream& operator<< (std::ostream& os, const Genotype& g){
os<<"F";
for(unsigned int i = 0; i < g.fatherGenome.chromosomes.size(); i++){
os<<"ch"<<(i+1)<<":";
const std::vector<Gene> genesF = g.fatherGenome.chromosomes.at(i).getGenesAsVector();
const std::vector<Gene> genesM = g.motherGenome.chromosomes.at(i).getGenesAsVector();
for(unsigned int j = 0; j < genesF.size(); j++){
os<<"\t";
os<<genesF.at(j).getName();//<<", ";
if(genesF.at(j).getGeneType() == Gene::Continious){
os<<"\t"<<genesF.at(j).getGeneValueCont();//<<"\t";
os<<"\t"<<genesM.at(j).getGeneValueCont();//<<"\t";
}
else{
os<<"\t"<<genesF.at(j).getGeneValueDiscr();//<<"\t";
os<<"\t"<<genesM.at(j).getGeneValueDiscr();//<<"\t";
}
os<<"\t";
}
}
return os;
}
std::string Genotype::toSimpleString() const {
std::stringstream os;
for(unsigned int i = 0; i < this->fatherGenome.chromosomes.size(); i++){
const std::vector<Gene> genesF = this->fatherGenome.chromosomes.at(i).getGenesAsVector();
const std::vector<Gene> genesM = this->motherGenome.chromosomes.at(i).getGenesAsVector();
for(unsigned int j = 0; j < genesF.size(); j++){
if(genesF.at(j).getGeneType() == Gene::Continious){
os<<genesF.at(j).getGeneValueCont()<<"\t";
os<<genesM.at(j).getGeneValueCont()<<"\t";
}
else{
os<<genesF.at(j).getGeneValueDiscr()<<"\t";
os<<genesM.at(j).getGeneValueDiscr()<<"\t";
}
//os<<"\t";
}
}
return os.str();
}
std::string Genotype::toMaxModuleAB() const {
std::stringstream os;
for(unsigned int i = 0; i < this->fatherGenome.chromosomes.size(); i++){
const std::vector<Gene> genesF = this->fatherGenome.chromosomes.at(i).getGenesAsVector();
const std::vector<Gene> genesM = this->motherGenome.chromosomes.at(i).getGenesAsVector();
for(unsigned int j = 0; j < genesF.size(); j++){
if(genesF.at(j).getGeneType() == Gene::Continious){
if(fabs(genesF.at(j).getGeneValueCont()) > fabs(genesM.at(j).getGeneValueCont())){
os<<genesF.at(j).getGeneValueCont()<<"\t";
}
else{
os<<genesM.at(j).getGeneValueCont()<<"\t";
}
}
else{
os<<genesF.at(j).getGeneValueDiscr()<<"\t";
os<<genesM.at(j).getGeneValueDiscr()<<"\t";
}
//os<<"\t";
}
}
return os.str();
}
std::string Genotype::getRawGene(unsigned int fatherMother, unsigned int chromoNum, unsigned int geneNum) const{
const HaploidGenotype* genome = (fatherMother == 0) ? &(this->fatherGenome) : &(this->motherGenome);
return genome->getChromosome(chromoNum).getGenesAsVector().at(geneNum).getSequence();
}
void Genotype::doRawMutationSequence(unsigned int fatherMother, unsigned int chromoNum, unsigned int geneNum, std::string newSeq){
if(fatherMother==2){
this->fatherGenome.chromosomes.at(chromoNum).genes.at(geneNum).setGeneValue(newSeq);
this->motherGenome.chromosomes.at(chromoNum).genes.at(geneNum).setGeneValue(newSeq);
}
}
std::string Genotype::toSimpleFasta(bool onlyMother) const {
std::stringstream os;
for(unsigned int i = 0; i < this->motherGenome.chromosomes.size(); i++){
const std::vector<Gene> genesF = this->fatherGenome.chromosomes.at(i).getGenesAsVector();
const std::vector<Gene> genesM = this->motherGenome.chromosomes.at(i).getGenesAsVector();
os<<"> "<<this->motherGenome.chromosomes.at(i).getName()<<"\n";
for(unsigned int j = 0; j < genesM.size(); j++){
if(genesM.at(i).getGeneType() == Gene::Sequence){
os<<genesM.at(j).getSequence();
}
else if(genesM.at(j).getGeneType() == Gene::Continious){
os<<genesF.at(j).getGeneValueCont()<<"\t";
os<<genesM.at(j).getGeneValueCont()<<"\t";
}
else{
os<<genesF.at(j).getGeneValueDiscr()<<"\t";
os<<genesM.at(j).getGeneValueDiscr()<<"\t";
}
//os<<"\t";
}
}
return os.str();
}

87
individual/genome/strategies/ChromosomeRearrangementStrategy.cpp Normal file
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#include "ChromosomeRearrangementStrategy.h"
#include "Derevyanko\2015\Derevyanko2015RecombinationStrategy.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);
}
std::map<std::string, ChromosomeRearrangementStrategy*> RecombinationStrategies::_strategies;
ChromosomeRearrangementStrategy* RecombinationStrategies::getInstance(std::string _name){
if(_strategies.find(_name) == _strategies.end()){
if(_name.compare("D2015") == 0){
ChromosomeRearrangementStrategy* s = new Derevyanko2015RecombinationStrategy();
}
else{
ChromosomeRearrangementStrategy* s = new ChromosomeRearrangementStrategy();
}
_strategies[_name] = s;
}
return _strategies[_name];
}

20
individual/genome/strategies/ChromosomeRearrangementStrategy.h Normal file
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#pragma once
#include "../AbstractGenome.h"
#include <map>
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 {
static std::map<std::string, ChromosomeRearrangementStrategy*> _strategies;
public:
static ChromosomeRearrangementStrategy* getInstance(std::string _name);
};

173
individual/genome/strategies/Derevyanko/2015/Derevyanko2015RecombinationStrategy.cpp Normal file
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#include "Derevyanko2015RecombinationStrategy.h"
#include <cstdlib>
#include <ctime>
HaploidGenotype Derevyanko2015RecombinationStrategy::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));
// int flag = rand() % 2;
const std::vector<Gene>* first;
const std::vector<Gene>* second;
first = &fGenome->at(0).genes;
second= &mGenome->at(0).genes;
double pNumt = 1e-2;
double pHybr = 1e-5;
bool sameSpecies = true;
if(first->at(0).getName().compare(second->at(0).getName()) != 0){
sameSpecies = false;
pHybr = 1e-2;
}
Chromosome childChromosome(mGenome->at(0).name);
Chromosome numtChromosome(mGenome->at(1).name);
std::string numtName = mGenome->at(1).genes.at(0).getName();
std::string numtSeq = mGenome->at(1).genes.at(0).sequence;
int flag = rand() % (int)(1/pHybr);
if(flag == 0){
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int bound1 = rand() % first->at(0).sequence.length;
int bound2 = rand() % first->at(0).sequence.length;
// <20><><EFBFBD><EFBFBD> <20>1><3E>2, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD>
std::string seq;
if(bound1 > bound2){
seq = first->at(0).sequence;
seq.replace(bound2, bound1-bound2,
second->at(0).sequence.substr(bound2, bound1-bound2));
}
else{
seq = second->at(0).sequence;
seq.replace(bound1, bound2-bound1,
first->at(0).sequence.substr(bound1, bound2-bound1));
}
std::string gName = second->at(0).getName();
Gene gene(Gene::Sequence, gName, seq);
childChromosome.insertGeneToEnd(gene);
std::cerr<<"Recombination occured:\t"<<seq<<"\n";
if(!sameSpecies){
// <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int flagNumt = rand() % (int)(1/pNumt);
if(flagNumt == 0){
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD>
int bound1 = rand() % first->at(0).sequence.length;
int bound2 = rand() % first->at(0).sequence.length;
std::string numtAdd = (bound1 < bound2) ?
first->at(0).sequence.substr(bound1, bound2-bound1) :
first->at(0).sequence.substr(bound2, bound1-bound2);
numtSeq += numtAdd;
std::cerr<<"New numt occured:\t"<<numtSeq<<"\n";
}
}
}
else{
childChromosome.insertGeneToEnd(second->at(0));
}
Gene geneNumt(Gene::Sequence, numtName, numtSeq);
numtChromosome.insertGeneToEnd(geneNumt);
chromosomes.push_back(childChromosome);
chromosomes.push_back(numtChromosome);
return HaploidGenotype(chromosomes);
}
HaploidGenotype Derevyanko2015RecombinationStrategy::
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;
// 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));
// int flag = rand() % 2;
const std::vector<Gene>* first;
const std::vector<Gene>* second;
first = &fGenome->at(0).genes;
second= &mGenome->at(0).genes;
double pNumt = 1e-2;
double pHybr = 1e-5;
bool sameSpecies = true;
if(first->at(0).getName().compare(second->at(0).getName()) != 0){
sameSpecies = false;
pHybr = 1e-2;
}
Chromosome childChromosome(mGenome->at(0).name);
Chromosome numtChromosome(mGenome->at(1).name);
std::string numtName = mGenome->at(1).genes.at(0).getName();
std::string numtSeq = mGenome->at(1).genes.at(0).sequence;
int flag = rand() % (int)(1/pHybr);
if(flag == 0){
// <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int bound1 = rand() % first->at(0).sequence.length;
int bound2 = rand() % first->at(0).sequence.length;
// <20><><EFBFBD><EFBFBD> <20>1><3E>2, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD>, <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> - <20><><EFBFBD><EFBFBD>
std::string seq;
if(bound1 > bound2){
seq = first->at(0).sequence;
seq.replace(bound2, bound1-bound2,
second->at(0).sequence.substr(bound2, bound1-bound2));
}
else{
seq = second->at(0).sequence;
seq.replace(bound1, bound2-bound1,
first->at(0).sequence.substr(bound1, bound2-bound1));
}
std::string gName = second->at(0).getName();
Gene gene(Gene::Sequence, gName, seq);
childChromosome.insertGeneToEnd(gene);
std::cerr<<"Recombination occured:\t"<<seq<<"\n";
if(!sameSpecies){
// <20><><EFBFBD><EFBFBD> <20><> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD>
int flagNumt = rand() % (int)(1/pNumt);
if(flagNumt == 0){
// <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD> <20><><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD><EFBFBD> <20> <20><><EFBFBD><EFBFBD>
int bound1 = rand() % first->at(0).sequence.length;
int bound2 = rand() % first->at(0).sequence.length;
std::string numtAdd = (bound1 < bound2) ?
first->at(0).sequence.substr(bound1, bound2-bound1) :
first->at(0).sequence.substr(bound2, bound1-bound2);
numtSeq += numtAdd;
std::cerr<<"New numt occured:\t"<<numtSeq<<"\n";
}
}
}
else{
childChromosome.insertGeneToEnd(second->at(0));
}
Gene geneNumt(Gene::Sequence, numtName, numtSeq);
numtChromosome.insertGeneToEnd(geneNumt);
chromosomes.push_back(childChromosome);
chromosomes.push_back(numtChromosome);
return HaploidGenotype(chromosomes);
}

8
individual/genome/strategies/Derevyanko/2015/Derevyanko2015RecombinationStrategy.h Normal file
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#pragma once
#include "../../ChromosomeRearrangementStrategy.h"
class Derevyanko2015RecombinationStrategy : public ChromosomeRearrangementStrategy{
public:
virtual HaploidGenotype buildRecombinantGenotype(const Genotype*);
virtual HaploidGenotype buildRecombinantGenotype(const HaploidGenotype&, const HaploidGenotype&);
};

44
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);
}
}
std::map<std::string, GenotypeToPhenotypeStrategy*> GenotypeToPhenotypeStrategies::_strategies;
GenotypeToPhenotypeStrategy* GenotypeToPhenotypeStrategies::getInstance(std::string _name){
if(_strategies.find(_name) == _strategies.end()){
GenotypeToPhenotypeStrategy* s = 0;
if(_name.compare("inoutbreeding") == 0){
s = new InOutBreedingGenotypeToPhenotypeStrategy();
}
else if(_name.compare("kolchan_shindyal_gen_to_phen") == 0){
s = new KolchShindyalGenotypeToPhenotypeStrategy();
}
else {
// default
s = new GenotypeToPhenotypeStrategy();;
}
_strategies[_name] = s;
}
return _strategies[_name];
}

23
individual/genome/strategies/GenotypeToPhenotypeStrategy.h Normal file
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#pragma once
#include "../../AbstractIndividual.h"
#include "../AbstractGenome.h"
#include "../../Phenotype.h"
#include <map>
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 {
static std::map<std::string, GenotypeToPhenotypeStrategy*> _strategies;
public:
static GenotypeToPhenotypeStrategy* getInstance(std::string _name);
};

11
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
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
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
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);
};

101
individual/genome/strategies/InOutBreeding/InOutBreeginGenToPhenStrategy.cpp Normal file
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#include "../GenotypeToPhenotypeStrategy.h"
#include "../../../../processor/Settings.h"
#include <cmath>
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 - (fabs(a*a*a) + 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
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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@@ -0,0 +1,8 @@
#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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@@ -0,0 +1,6 @@
#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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@@ -0,0 +1,7 @@
#pragma once
#include "../PhenotypeToFitnessStrategy.h"
#include "../../../Phenotype.h"
class KolchShindyalPhenToFitnessStrategy : public PhenotypeToFitnessStrategy {
virtual double calculateFitness(Phenotype* phen);
};

36
individual/genome/strategies/PhenotypeToFitnessStrategy.cpp Normal file
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@@ -0,0 +1,36 @@
#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);
}
std::map<std::string, PhenotypeToFitnessStrategy*> PhenotypeToFitnessStrategy::_strategies;
PhenotypeToFitnessStrategy* PhenotypeToFitnessStrategy::getInstance(std::string _name){
if(_strategies.find(_name) == _strategies.end()){
PhenotypeToFitnessStrategy* s = 0;
if(_name.compare("inoutbreeding") == 0){
s = new InOutBreedingPhenToFitStrategy();
}
else if(_name.compare("kolch_shindyal_phen_to_fit") == 0){
s = new KolchShindyalPhenToFitnessStrategy();
}
else {
s = new PhenotypeToFitnessStrategy();
}
_strategies[_name] = s;
}
return _strategies[_name];
}

12
individual/genome/strategies/PhenotypeToFitnessStrategy.h Normal file
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#pragma once
#include <string>
#include <map>
class Phenotype;
class PhenotypeToFitnessStrategy {
static std::map<std::string, PhenotypeToFitnessStrategy*> _strategies;
public:
static PhenotypeToFitnessStrategy* getInstance(std::string);
virtual double calculateFitness(Phenotype* phen);
};