#include "Population.h"
#include <algorithm>
#include <iostream>
#include <sstream>
#include <cstdlib>
#include <ctime>

BisexualPopulation::~BisexualPopulation(){
	// Тут удалить нафиг всех особей
}
void BisexualPopulation::calculateFitnessAll(){
	// Вызов стратегии фитнесса для всех
}

void BisexualPopulation::breedAll(){
	this->breedingStrategy->breed(this);
}

void BisexualPopulation::selectionAll(){

}

void BisexualPopulation::mutationAll(){
	// !!! Времянка для отчёта по Деревянко
	srand((unsigned int)time(NULL));

	float mutProb = 1 / 1e+6f; // Вероятность мутации - на нуклеотид на поколение
	
	// Тут смысл мутировать только женщин
	std::list<Individual*>::iterator it;
	for(it = this->females.begin(); it != this->females.end(); it++){
		// Хак конкретно для Деревянко 2014
		Chromosome chrom = (*it)->genotype->getMotherGenome().getChromosome(0);
		std::vector<Gene> genes = chrom.getGenesAsVector();
		int wholeSeqLength = 0;
		for(unsigned int i = 0; i < genes.size(); i++){
			wholeSeqLength += genes.at(i).getSequence().size();
		}

		//std::string seq = (*it)->genotype->getRawGene(0,0,0); // Хак конкретно для Деревянко 2013
		int positionToMutate = rand() % (int)(1/mutProb);
		if(positionToMutate < wholeSeqLength){
			std::string seq = genes.at(0).getSequence();
			int geneNum = positionToMutate / seq.size(); // Хак конкретно для Деревянко 2014
			positionToMutate = positionToMutate % seq.size(); // Хак конкретно для Деревянко 2014
			//Gene geneToMutate = genes.at(geneNum);
			int nucl = rand() % 3;
			switch(seq.c_str()[positionToMutate]){
				case 'A':
					if(nucl == 0) seq.replace(positionToMutate,1,"C");
					if(nucl == 1) seq.replace(positionToMutate,1,"G");
					if(nucl == 2) seq.replace(positionToMutate,1,"T");
				break;
				case 'C':
					if(nucl == 0) seq.replace(positionToMutate,1,"A");
					if(nucl == 1) seq.replace(positionToMutate,1,"G");
					if(nucl == 2) seq.replace(positionToMutate,1,"T");
				break;
				case 'G':
					if(nucl == 0) seq.replace(positionToMutate,1,"C");
					if(nucl == 1) seq.replace(positionToMutate,1,"A");
					if(nucl == 2) seq.replace(positionToMutate,1,"T");
				break;
				case 'T':
					if(nucl == 0) seq.replace(positionToMutate,1,"C");
					if(nucl == 1) seq.replace(positionToMutate,1,"G");
					if(nucl == 2) seq.replace(positionToMutate,1,"A");
				break;
			} // (END) switch(...)
			(*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
		} // (END) if (mutate)
	} // (END) for

	// !!! --------------------------------
}

std::string BisexualPopulation::getSatistics(){
	std::string ans;
	return ans;
}

void BisexualPopulation::putGeneticStatisticsToStream(std::ostream& out){
	out<<"Females\n=======\n";
	int i = 1;
	for(std::list<Individual*>::iterator it = females.begin(); it != females.end(); it++){
		
		//out<<"> Female seq mitochondrial"<<(i++)<<"\n";
		out<<(*it)->getGenotype().toSimpleFasta()<<std::endl;
		out<<std::endl;
	}

	out<<"\nMales\n=======\n";
	i = 1;
	for(std::list<Individual*>::iterator it = males.begin(); it != males.end(); it++){
		out<<"> Male seq "<<(i++)<<"\n";
		out<<(*it)->getGenotype().toSimpleFasta()<<std::endl;
		out<<std::endl;
	}	
}

void BisexualPopulation::putGeneticSimpleStatisticsToStream(std::ostream& out){
	out<<"Population statistics:\tMales =\t"<<males.size();
	out<<"\tFemales =\t"<<females.size()<<std::endl;
	//out<<"Genome statistics (mitochondrial DNA sequence):\n\n";
}

void BisexualPopulation::putGeneticMaxModuleStatisticsToStream(std::ostream& out){

}

std::string BisexualPopulation::mutualMigration(BisexualPopulation* p1, BisexualPopulation* p2, float frac1, float frac2){
	std::stringstream ss;

	int sizeP1 = p1->males.size() + p1->females.size();
	int sizeP2 = p2->males.size() + p2->females.size();

	int indsP1toP2 = (int) (frac1*sizeP1)/2;
	int indsP2toP1 = (int) (frac2*sizeP2)/2;

	// Уходят из начала списка, приходят в конец
	std::list<Individual*> malesTemp;
	std::list<Individual*> femalesTemp;

	// P1 -> temp
	// males
	std::list<Individual*>::iterator it1 = p1->males.begin();
	std::list<Individual*>::iterator it2 = it1;
	std::advance(it2, indsP1toP2);
	malesTemp.splice(malesTemp.begin(), p1->males, it1, it2);

	// females
	it1 = p1->females.begin();
	it2 = it1;
	std::advance(it2, indsP1toP2);
	femalesTemp.splice(femalesTemp.begin(), p1->females, it1, it2);
	/////////////////////////////////////////////////////////////

	// P2 -> P1
	// males
	it1 = p2->males.begin();
	it2 = it1;
	std::advance(it2, indsP2toP1);
	p1->males.splice(p1->males.end(), p2->males, it1, it2);

	// females
	it1 = p2->females.begin();
	it2 = it1;
	std::advance(it2, indsP2toP1);
	p1->females.splice(p1->females.end(), p2->females, it1, it2);
	/////////////////////////////////////////////////////////////

	// temp -> P2
	// males
	p2->males.splice(p2->males.end(), malesTemp);

	// females
	p2->females.splice(p2->females.end(), femalesTemp);

	ss<<"Migration:\tP1->P2\t"<<indsP1toP2*2<<"\t\tP2->P1\t"<<indsP2toP1*2<<std::endl;

	return ss.str();
}

BisexualPopulation* BisexualPopulation::createSubpopulation(float frac){
	// Пока делаем тупо - уходят из начала списка

	int malesFounders = (int) (frac*this->males.size());
	int femalesFounders = (int) (frac*this->females.size());

	// Уходят из начала списка, приходят в конец
	std::list<Individual*> malesTemp;
	std::list<Individual*> femalesTemp;

	// P1 -> temp
	// males
	std::list<Individual*>::iterator it1 = this->males.begin();
	std::list<Individual*>::iterator it2 = it1;
	std::advance(it2, malesFounders);
	malesTemp.splice(malesTemp.begin(), this->males, it1, it2);

	// females
	it1 = this->females.begin();
	it2 = it1;
	std::advance(it2, femalesFounders);
	femalesTemp.splice(femalesTemp.begin(), this->females, it1, it2);
	/////////////////////////////////////////////////////////////

	return new BisexualPopulation(malesTemp,femalesTemp, this->breedingStrategy);
}

///////////////////////////////
void BisexualPopulation::mutationDerevyanko2015(double pMutMtDNA, double pMutNumt){
	// !!! Времянка для отчёта по Деревянко
	srand((unsigned int)time(NULL));

	//float mutProb = 1 / 1e+6f; // Вероятность мутации - на нуклеотид на поколение
	
	// По мтДНК смысл мутировать только женщин
	// По нумту - обоих
	std::list<Individual*>::iterator it;
	for(it = this->females.begin(); it != this->females.end(); it++){
		// Хак конкретно для Деревянко 2015
		Chromosome chrom = (*it)->genotype->getMotherGenome().getChromosome(0);
		Chromosome chromNumt = (*it)->genotype->getMotherGenome().getChromosome(1);
		std::vector<Gene> genes = chrom.getGenesAsVector();
		int wholeSeqLength = 0;
		for(unsigned int i = 0; i < genes.size(); i++){
			wholeSeqLength += genes.at(i).getSequence().size();
		}

		int positionToMutate = rand() % (int)(1/pMutMtDNA);
		if(positionToMutate < wholeSeqLength){
			std::string seq = genes.at(0).getSequence();
			int geneNum = positionToMutate / seq.size(); // Хак конкретно для Деревянко 2015
			positionToMutate = positionToMutate % seq.size(); // Хак конкретно для Деревянко 2015
			//Gene geneToMutate = genes.at(geneNum);
			int nucl = rand() % 3;
			switch(seq.c_str()[positionToMutate]){
				case 'A':
					if(nucl == 0) seq.replace(positionToMutate,1,"C");
					if(nucl == 1) seq.replace(positionToMutate,1,"G");
					if(nucl == 2) seq.replace(positionToMutate,1,"T");
				break;
				case 'C':
					if(nucl == 0) seq.replace(positionToMutate,1,"A");
					if(nucl == 1) seq.replace(positionToMutate,1,"G");
					if(nucl == 2) seq.replace(positionToMutate,1,"T");
				break;
				case 'G':
					if(nucl == 0) seq.replace(positionToMutate,1,"C");
					if(nucl == 1) seq.replace(positionToMutate,1,"A");
					if(nucl == 2) seq.replace(positionToMutate,1,"T");
				break;
				case 'T':
					if(nucl == 0) seq.replace(positionToMutate,1,"C");
					if(nucl == 1) seq.replace(positionToMutate,1,"G");
					if(nucl == 2) seq.replace(positionToMutate,1,"A");
				break;
			} // (END) switch(...)
			(*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
		} // (END) if (mutate) 

		// Нумтовая ДНК
		//std::vector<Gene> genes = chromNumt.getGenesAsVector();
		//int wholeSeqLength = 0;
		//for(unsigned int i = 0; i < genes.size(); i++){
		//	wholeSeqLength += genes.at(i).getSequence().size();
		//}

		//int positionToMutate = rand() % (int)(1/pMutNumt);
		//if(positionToMutate < wholeSeqLength){
		//	std::string seq = genes.at(0).getSequence();
		//	int geneNum = positionToMutate / seq.size(); // Хак конкретно для Деревянко 2015
		//	positionToMutate = positionToMutate % seq.size(); // Хак конкретно для Деревянко 2015
		//	//Gene geneToMutate = genes.at(geneNum);
		//	int nucl = rand() % 3;
		//	switch(seq.c_str()[positionToMutate]){
		//		case 'A':
		//			if(nucl == 0) seq.replace(positionToMutate,1,"C");
		//			if(nucl == 1) seq.replace(positionToMutate,1,"G");
		//			if(nucl == 2) seq.replace(positionToMutate,1,"T");
		//		break;
		//		case 'C':
		//			if(nucl == 0) seq.replace(positionToMutate,1,"A");
		//			if(nucl == 1) seq.replace(positionToMutate,1,"G");
		//			if(nucl == 2) seq.replace(positionToMutate,1,"T");
		//		break;
		//		case 'G':
		//			if(nucl == 0) seq.replace(positionToMutate,1,"C");
		//			if(nucl == 1) seq.replace(positionToMutate,1,"A");
		//			if(nucl == 2) seq.replace(positionToMutate,1,"T");
		//		break;
		//		case 'T':
		//			if(nucl == 0) seq.replace(positionToMutate,1,"C");
		//			if(nucl == 1) seq.replace(positionToMutate,1,"G");
		//			if(nucl == 2) seq.replace(positionToMutate,1,"A");
		//		break;
		//	} // (END) switch(...)
		//	(*it)->genotype->doRawMutationSequence(2, 0, geneNum, seq);
		//} // (END) Нумтовая ДНК - пока не мутирует


	} // (END) for

	// !!! --------------------------------

}