#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){
		// Рекомбинируем митохондриалку
		int bound1 = rand() % first->at(0).sequence.length;
		int bound2 = rand() % first->at(0).sequence.length;
		
		// Если б1>б2, основа - папа, наоборот - мама
		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){
			// Тест на нумтизацию
			int flagNumt = rand() % (int)(1/pNumt);
			if(flagNumt == 0){
			// Кусок мужской мтДНК копируется в нумт
				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){
		// Рекомбинируем митохондриалку
		int bound1 = rand() % first->at(0).sequence.length;
		int bound2 = rand() % first->at(0).sequence.length;
		
		// Если б1>б2, основа - папа, наоборот - мама
		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){
			// Тест на нумтизацию
			int flagNumt = rand() % (int)(1/pNumt);
			if(flagNumt == 0){
			// Кусок мужской мтДНК копируется в нумт
				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);

}