Init version

2024-10-03 18:43:04 +07:00
commit f80052961f
186 changed files with 71676 additions and 0 deletions
--- a/individual/genome/Genotype.cpp
+++ b/individual/genome/Genotype.cpp
@@ -0,0 +1,119 @@
+#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();
+}