lashin/DEC
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Init version

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

173
individual/genome/strategies/Derevyanko/2015/Derevyanko2015RecombinationStrategy.cpp Normal file
View File

@@ -0,0 +1,173 @@
#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
View File

@@ -0,0 +1,8 @@
#pragma once
#include "../../ChromosomeRearrangementStrategy.h"
class Derevyanko2015RecombinationStrategy : public ChromosomeRearrangementStrategy{
public:
virtual HaploidGenotype buildRecombinantGenotype(const Genotype*);
virtual HaploidGenotype buildRecombinantGenotype(const HaploidGenotype&, const HaploidGenotype&);
};