#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();
}