#include "DerevyankoReport.h"
#include "individual/Trait.h"
#include "individual/Phenotype.h"
//#include "population/BreedingStrategies/PopulationBreedingStrategy.h"
#include "population/BreedingStrategies/NeutralEvolutionBreedStrat.h"

#include <list>
#include <fstream>

using std::string;

BisexualPopulation* DerevyankoReport::populationFactory(int size, std::string initMtGenome){
	BisexualPopulation* ans;

	std::list<Individual*> males;
	std::list<Individual*> females;

	Gene gene1(Gene::Sequence, "mtDna1", initMtGenome);
	Chromosome chrom1("Mitochondrial chromosome");
	chrom1.insertGeneToEnd(gene1);
		
	std::vector<Chromosome> fGenome;
	std::vector<Chromosome> mGenome;
	fGenome.push_back(chrom1);
	mGenome.push_back(chrom1);
	
	// Фенотип
	Trait trait1(Trait::Discrete, "Age", 20);
	// Пул субстратов
	InnerSubstratesPool* subPool = 0;
	// (END) Пул субстратов

	for(int i = 0; i < size/2; i++){
		Genotype* genotype = new Genotype(fGenome, mGenome);
		Phenotype* phenotype = new Phenotype(trait1);
		males.push_back(new Individual(genotype, phenotype, subPool, Individual::male, 0));
		
		genotype = new Genotype(fGenome, mGenome);
		phenotype = new Phenotype(trait1);
		females.push_back(new Individual(genotype, phenotype, subPool, Individual::female, 0));
	}

	ans = new BisexualPopulation(males,females);
	return ans;
}
void DerevyankoReport::reportRFBR2013_01(){
	
	// Митохондриальная ДНК (популяция f)
	string initMtDNA = "TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACC";
	initMtDNA += "GCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACT";
	initMtDNA += "TGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCCCCTCATGCTTACAA";
	initMtDNA += "GCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCT";
	initMtDNA += "CACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCAT";
	initMtDNA += "TTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCA";

	// Мутантная мтДНК (популяция G)
	string initMtDNA_G = initMtDNA;
	initMtDNA_G.replace(60,1,"T");
	initMtDNA_G.replace(120,1,"A");
	initMtDNA_G.replace(180,1,"C");
	initMtDNA_G.replace(240,1,"G");
	
	// Генерация стартовых популяций
	//
	int basePopSize = 5000;
	float initBirthRate = 0.25f;
	float deltaBirthRate = 0.0002f;
	BisexualPopulation* pop_f = populationFactory(basePopSize, initMtDNA);
	NeutralEvolutionBreedingStrategy* breedStrat_f = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_f->setBirthRate(initBirthRate);
	breedStrat_f->setDeathRate(initBirthRate-deltaBirthRate);
	pop_f->setBreedingStrategy(breedStrat_f);

	BisexualPopulation* pop_G = populationFactory(basePopSize, initMtDNA_G);
	NeutralEvolutionBreedingStrategy* breedStrat_G = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_G->setBirthRate(initBirthRate);
	breedStrat_G->setDeathRate(initBirthRate-deltaBirthRate);
	pop_G->setBreedingStrategy(breedStrat_G);

	///////////////////////////////////////////
	//
	//		Эволюционный процесс
	//
	///////////////////////////////////////////

	unsigned int generation;

	// Шаг 1.
	// Вариант 1
	int genPerMigr_f_G = 100;
	float part_f_to_G = 0.01f;
	float part_G_to_f = 0.01f;
	std::cout<<"Variant 1"<<std::endl;

	// Вариант 2
	//int genPerMigr_f_G = 1000;
	//float part_f_to_G = 0.1f;
	//float part_G_to_f = 0.1f;
	//std::cout<<"Variant 2"<<std::endl;

	for(generation = 0; generation < 7000; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_f->breedAll();
		pop_f->mutationAll();
		
		pop_G->breedAll();
		pop_G->mutationAll();

		if(generation != 0 && ((generation % genPerMigr_f_G) == 0)){
			std::string code = BisexualPopulation::mutualMigration(pop_f, pop_G, part_f_to_G, part_G_to_f);
			std::cout<<"Migration f<->G\t"<<code<<std::endl;
		}
	}

	// Шаг 2.
	// Вычленение популяции e и её жизнь (10 поколений) f нас больше не интересует
	float fraction_e_founder = 0.5f;
	BisexualPopulation* pop_e = pop_f->createSubpopulation(fraction_e_founder);
	std::cout<<"pop_e has been created"<<std::endl;

	for(; generation < 7010; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_e->breedAll();
		pop_e->mutationAll();

		pop_G->breedAll();
		pop_G->mutationAll();
	}

	// Шаг 3.
	// Разделение популяции е на F и d
	// Далее эволюция 50 поколений
	// мажорная ветка - это популяция d, ей остаётся 90% популяции
	float fraction_F_founder = 0.1f;
	BisexualPopulation* pop_F = pop_e->createSubpopulation(fraction_F_founder);
	std::cout<<"pop_F has been created"<<std::endl;
	
	BisexualPopulation* pop_d = pop_e; // Остаток становится d
	NeutralEvolutionBreedingStrategy* breedStrat_d = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_d->setBirthRate(initBirthRate);
	breedStrat_d->setDeathRate(initBirthRate-deltaBirthRate*2);
	pop_d->setBreedingStrategy(breedStrat_d);
	std::cout<<"pop_e -> pop_d\tPop dynamics coeffs have been changed:\td =\t";
	std::cout<<(initBirthRate-deltaBirthRate*2)<<std::endl;

	for(; generation < 7060; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_d->breedAll();
		pop_d->mutationAll();

		pop_F->breedAll();
		pop_F->mutationAll();

		pop_G->breedAll();
		pop_G->mutationAll();
	}

	// Шаг 4.
	// Разделение популяции d на E и c
	// Далее эволюция 100 поколений
	// мажорная ветка - это популяция c, ей остаётся 90% популяции
	float fraction_E_founder = 0.1f;
	BisexualPopulation* pop_E = pop_d->createSubpopulation(fraction_E_founder);
	std::cout<<"pop_E has been created"<<std::endl;
	
	BisexualPopulation* pop_c = pop_d; // Остаток становится c
	NeutralEvolutionBreedingStrategy* breedStrat_c = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_c->setBirthRate(initBirthRate);
	breedStrat_c->setDeathRate(initBirthRate-deltaBirthRate*2.5f);
	pop_c->setBreedingStrategy(breedStrat_c);
	std::cout<<"pop_d -> pop_c\tPop dynamics coeffs have been changed:\td =\t";
	std::cout<<(initBirthRate-deltaBirthRate*2.5f)<<std::endl;

	for(; generation < 7160; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_c->breedAll();
		pop_c->mutationAll();

		pop_E->breedAll();
		pop_E->mutationAll();

		pop_F->breedAll();
		pop_F->mutationAll();

		pop_G->breedAll();
		pop_G->mutationAll();
	}

	// Шаг 5.
	// Разделение популяции c на D и b
	// Далее эволюция 100 поколений
	// мажорная ветка - это популяция b, ей остаётся 90% популяции
	float fraction_D_founder = 0.1f;
	BisexualPopulation* pop_D = pop_c->createSubpopulation(fraction_D_founder);
	std::cout<<"pop_D has been created"<<std::endl;
	
	BisexualPopulation* pop_b = pop_c; // Остаток становится b
	NeutralEvolutionBreedingStrategy* breedStrat_b = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_b->setBirthRate(initBirthRate);
	breedStrat_b->setDeathRate(initBirthRate-deltaBirthRate*3.f);
	pop_b->setBreedingStrategy(breedStrat_b);
	std::cout<<"pop_c -> pop_b\tPop dynamics coeffs have been changed:\td =\t";
	std::cout<<(initBirthRate-deltaBirthRate*3.f)<<std::endl;

	for(; generation < 7260; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_b->breedAll();
		pop_b->mutationAll();

		pop_D->breedAll();
		pop_D->mutationAll();

		pop_E->breedAll();
		pop_E->mutationAll();

		pop_F->breedAll();
		pop_F->mutationAll();

		pop_G->breedAll();
		pop_G->mutationAll();
	}

	// Шаг 6.
	// Разделение популяции b на C и a
	// Далее эволюция 200 поколений
	// мажорная ветка - это популяция a, ей остаётся 90% популяции
	float fraction_C_founder = 0.1f;
	BisexualPopulation* pop_C = pop_b->createSubpopulation(fraction_C_founder);
	std::cout<<"pop_C has been created"<<std::endl;
	
	BisexualPopulation* pop_a = pop_b; // Остаток становится b
	NeutralEvolutionBreedingStrategy* breedStrat_a = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_a->setBirthRate(initBirthRate);
	breedStrat_a->setDeathRate(initBirthRate-deltaBirthRate*3.5f);
	pop_a->setBreedingStrategy(breedStrat_a);
	std::cout<<"pop_b -> pop_a\tPop dynamics coeffs have been changed:\td =\t";
	std::cout<<(initBirthRate-deltaBirthRate*3.5f)<<std::endl;

	for(; generation < 7460; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_a->breedAll();
		pop_a->mutationAll();

		pop_C->breedAll();
		pop_C->mutationAll();

		pop_D->breedAll();
		pop_D->mutationAll();

		pop_E->breedAll();
		pop_E->mutationAll();

		pop_F->breedAll();
		pop_F->mutationAll();

		pop_G->breedAll();
		pop_G->mutationAll();
	}

	// Шаг 7.
	// Разделение популяции a на A и B
	// Далее эволюция 2540 поколений
	// полумажорная ветка - это популяция A, ей остаётся 50% популяции,
	// но чуть меньшая смертность.
	// На протяжении эволюции миграции между A и B, а также из A в C, D, E, F (G выводится из эволюции)
	float fraction_B_founder = 0.5f;
	BisexualPopulation* pop_B = pop_a->createSubpopulation(fraction_B_founder);
	std::cout<<"pop_B has been created"<<std::endl;
	
	BisexualPopulation* pop_A = pop_a; // Остаток становится A
	NeutralEvolutionBreedingStrategy* breedStrat_A = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_A->setBirthRate(initBirthRate);
	breedStrat_A->setDeathRate(initBirthRate-deltaBirthRate*4.f);
	pop_A->setBreedingStrategy(breedStrat_A);
	std::cout<<"pop_a -> pop_A\tPop dynamics coeffs have been changed:\td =\t";
	std::cout<<(initBirthRate-deltaBirthRate*4.f)<<std::endl;

	// Вариант 1
	int genPerMigr_A_B = 100;
	int genPerMigr_A_C = 150;
	int genPerMigr_A_D = 200;
	int genPerMigr_A_E = 250;
	int genPerMigr_A_F = 300;

	float part_A_to_B = 0.01f;
	float part_B_to_A = 0.01f;
	float part_A_to_C = 0.005f;
	float part_A_to_D = 0.005f;
	float part_A_to_E = 0.005f;
	float part_A_to_F = 0.005f;

	for(; generation < 10001; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_A->breedAll();
		pop_A->mutationAll();

		pop_B->breedAll();
		pop_B->mutationAll();

		pop_C->breedAll();
		pop_C->mutationAll();

		pop_D->breedAll();
		pop_D->mutationAll();

		pop_E->breedAll();
		pop_E->mutationAll();

		pop_F->breedAll();
		pop_F->mutationAll();

		if((generation % genPerMigr_A_B) == 0){
			std::string code = BisexualPopulation::mutualMigration(pop_A, pop_B, part_A_to_B, part_B_to_A);
			std::cout<<"Migration A<->B\t"<<code<<std::endl;
		}
		if((generation % genPerMigr_A_C) == 0){
			std::string code = BisexualPopulation::mutualMigration(pop_A, pop_C, part_A_to_C, 0.f);
			std::cout<<"Migration A->C\t"<<code<<std::endl;
		}
		if((generation % genPerMigr_A_D) == 0){
			std::string code = BisexualPopulation::mutualMigration(pop_A, pop_D, part_A_to_D, 0.f);
			std::cout<<"Migration A->D\t"<<code<<std::endl;
		}
		if((generation % genPerMigr_A_E) == 0){
			std::string code = BisexualPopulation::mutualMigration(pop_A, pop_E, part_A_to_E, 0.f);
			std::cout<<"Migration A->E\t"<<code<<std::endl;
		}
		if((generation % genPerMigr_A_F) == 0){
			std::string code = BisexualPopulation::mutualMigration(pop_A, pop_F, part_A_to_F, 0.f);
			std::cout<<"Migration A->F\t"<<code<<std::endl;
		}
	}

	// Конец эволюции - вывод статистики в файлы
	std::ofstream file("GenStatistics.pop_A.fasta");
	pop_A->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_A.txt");
	pop_A->putGeneticSimpleStatisticsToStream(file);
	file.close();

	////////////////////////////////////////
	file.open("GenStatistics.pop_B.fasta");
	pop_B->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_B.txt");
	pop_B->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////

	////////////////////////////////////////
	file.open("GenStatistics.pop_C.fasta");
	pop_C->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_C.txt");
	pop_C->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////

	////////////////////////////////////////
	file.open("GenStatistics.pop_D.fasta");
	pop_D->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_D.txt");
	pop_D->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////

	////////////////////////////////////////
	file.open("GenStatistics.pop_E.fasta");
	pop_E->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_E.txt");
	pop_E->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////

	////////////////////////////////////////
	file.open("GenStatistics.pop_F.fasta");
	pop_F->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_F.txt");
	pop_F->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////

	////////////////////////////////////////
	file.open("GenStatistics.pop_G.fasta");
	pop_G->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_G.txt");
	pop_G->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////

	////////////////////////////////////////
	file.open("GenStatistics.pop_flittle.fasta");
	pop_f->putGeneticStatisticsToStream(file);
	file.close();

	file.open("GenStatistics.pop_flittle.txt");
	pop_f->putGeneticSimpleStatisticsToStream(file);
	file.close();
	////////////////////////////////////////
}