#include "DerevyankoReport2015.h"
#include "individual/Trait.h"
#include "individual/Phenotype.h"
//#include "population/BreedingStrategies/PopulationBreedingStrategy.h"
#include "population/BreedingStrategies/NeutralEvolutionBreedStrat.h"
#include "processor/Settings.h"

#include <list>
#include <fstream>
#include <cstdio>
#include <ctime>
#include <cstdlib>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/tokenizer.hpp>

using std::string;

std::string DerevyankoReport2015::getInitGene(int type, int num){
	
	// type	- тип человека (0 - кроманьонец, 1 - условный неандерталец)
	// num	- номер гаплогруппы (0-4 - для кроманьонцев, 5-9 - для неандертальцев)
	string initMtDNA = "TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACC";
	initMtDNA += "GCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACT";
	initMtDNA += "TGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCCCCTCATGCTTACAA";
	initMtDNA += "GCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCT";
	initMtDNA += "CACCCACTAGGATATCAACAAACCTACCCATCCTTAACAGTACATGGTACATAAAGCCAT";
	initMtDNA += "TTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCA";
	
	string subSeqs[] = { 
		"AAAAAAAAAA", 
		"TTTTTTTTTT",
		"GGGGGGGGGG",
		"CCCCCCCCCC",
		"AAAAAAAAAA",
		"AAAAATTTTT",
		"TTTTTAAAAA",
		"GGGGGTTTTT",
		"CCCCCGGGGG",
		"GGGGGCCCCC"};

		// Митохондриальная ДНК
		int pos = num*10;
		num = num > 9 ? 9 : num;
		initMtDNA.replace(pos, subSeqs[num].length(), subSeqs[num]);

	return initMtDNA;
}

BisexualPopulation* DerevyankoReport2015::populationFactory(int type, int size){
	BisexualPopulation* ans;

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

	// Фенотип
	Trait trait1(Trait::Discrete, "Age", 20);
	// Пул субстратов
	InnerSubstratesPool* subPool = 0;
	// (END) Пул субстратов

	for(int j = 0; j < size/2; j++){
		// Подготовка инициаторного генома
		Chromosome chrom1("Mitochondrial chromosome");
		string gName = type == 0 ? "mtDna_KR" : "mtDna_Neand";
		int num = 5*type + (j%5);
		Gene gene(Gene::Sequence, gName, getInitGene(type,num));
		chrom1.insertGeneToEnd(gene);
			
		Chromosome chrom2("Numt genome");
		gName = "Numt";
		Gene gene2(Gene::Sequence, gName, "");
		chrom2.insertGeneToEnd(gene2);
	
		std::vector<Chromosome> fGenome;
		std::vector<Chromosome> mGenome;
		fGenome.push_back(chrom1);
		fGenome.push_back(chrom2);
		mGenome.push_back(chrom1);
		mGenome.push_back(chrom2);

		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 DerevyankoReport2015::report2015_01(int argc, char** argv){
	std::vector<std::string> calcScript;
	if(argc > 1){
		calcScript = parseScript(argv[1]);
	}
	else{
		calcScript = parseScript("script.txt");
	}
	// Генерация стартовых популяций
	const int krom = 0; const int neand = 1;
	int popSizeH = Settings::PopulationHomoInitSize;
	int popSizeA = Settings::PopulationAncientInitSize;
	float initBirthRate = Settings::BirthRate;
	float deathRate = Settings::NaturalDeathRate;

	BisexualPopulation* pop_Sapiens = populationFactory(krom, popSizeH);
	NeutralEvolutionBreedingStrategy* breedStrat_Sapiens = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_Sapiens->setBirthRate(initBirthRate);
	breedStrat_Sapiens->setDeathRate(deathRate);
	pop_Sapiens->setBreedingStrategy(breedStrat_Sapiens);

	BisexualPopulation* pop_Ancient = populationFactory(neand, popSizeA);
	NeutralEvolutionBreedingStrategy* breedStrat_Ancient = 
		dynamic_cast<NeutralEvolutionBreedingStrategy*>(PopulationBreedingStrategy::getInstance("neutral"));
	breedStrat_Ancient->setBirthRate(initBirthRate);
	breedStrat_Ancient->setDeathRate(deathRate);
	pop_Ancient->setBreedingStrategy(breedStrat_Ancient);

	///////////////////////////////////////////
	//
	//		Эволюционный процесс
	//
	///////////////////////////////////////////
	//Settings::ProbMtDNARecomb = 1e-4;
	
	// Шаг 1.
	// Вариант 1
	int genPerMigr_H_A = Settings::generationsPerMigration;
	float part_H_to_A = Settings::migrationPartHomoToAncient;
	float part_A_to_H = Settings::migrationPartAncientToHomo;

	unsigned int generation = 0;
	for(unsigned int curLine = 0; curLine < calcScript.size(); curLine++){
		if(calcScript.at(curLine).at(0) == '/' || calcScript.at(curLine).at(0) == '#')
			continue;

		std::vector<std::string > tokensVector; // Search for tokens
		boost::split(tokensVector, calcScript.at(curLine), boost::is_any_of("=") );
		std::string instr = tokensVector.at(0);
		boost::to_lower(instr);
		boost::trim(instr);
		
		// Инструкции

		if(instr == "evolution"){
			int iter = 0;
			sscanf_s(tokensVector.at(1).c_str(),"%d", &iter);
			for(unsigned int i = 0; i < iter; i++, generation++){
				std::cout<<"gen\t"<<generation<<std::endl;
				pop_Sapiens->breedAll();
				//pop_Sapiens->mutationAll();
				// TODO Сделать мутационные стратегии
				pop_Sapiens->mutationDerevyanko2015(1e-6, 1e-8);

				pop_Ancient->breedAll();
				//pop_Ancient->mutationAll();
				pop_Ancient->mutationDerevyanko2015(1e-6, 1e-8);

			}
		}
		else if(instr == "evolution_m"){
			int iter = 0;
			sscanf_s(tokensVector.at(1).c_str(),"%d", &iter);
			for(unsigned int i = 0; i < iter; i++, generation++){
				std::cout<<"gen\t"<<generation<<std::endl;
				pop_Sapiens->breedAll();
				//pop_Sapiens->mutationAll();
		                pop_Sapiens->mutationDerevyanko2015(1e-6, 1e-8);

				pop_Ancient->breedAll();
				//pop_Ancient->mutationAll();
				pop_Ancient->mutationDerevyanko2015(1e-6, 1e-8);
				if(i != 0 && ((i % genPerMigr_H_A) == 0)){
					std::string code = BisexualPopulation::mutualMigration(pop_Sapiens, pop_Ancient, part_H_to_A, part_A_to_H);
					std::cout<<"Migration Sapienti<->Ancient\t"<<code<<"\tIter\t"<<generation<<std::endl;
				}
			}
		}
		else if(instr == "migration"){
			double part_H_to_A = 0.0;
			double part_A_to_H = 0.0;
			sscanf_s(tokensVector.at(1).c_str(),"%lg %lg", &part_H_to_A, &part_A_to_H);
			std::string code = BisexualPopulation::mutualMigration(pop_Sapiens, pop_Ancient, part_H_to_A, part_A_to_H);
			std::cout<<"Migration Sapienti<->Ancient\t"<<code<<"\tIter\t"<<generation<<std::endl;
		}
	} // (END)for(unsigned int curLine = 0; curLine < calcScript.size(); curLine++)


/*	for(generation = 0; generation < 5000; generation++){
		std::cout<<"gen\t"<<generation<<std::endl;
		pop_Sapiens->breedAll();
		pop_Sapiens->mutationAll();
		
		pop_Ancient->breedAll();
		pop_Ancient->mutationAll();

			if(generation != 0 && ((generation % genPerMigr_H_A) == 0)){
				std::string code = BisexualPopulation::mutualMigration(pop_Sapiens, pop_Ancient, part_H_to_A, part_A_to_H);
				std::cout<<"Migration Sapienti<->Ancient\t"<<code<<std::endl;
			}
		}
	}
*/
	// Конец эволюции - вывод статистики в файлы
	std::ofstream file("GenStatistics.pop_Sapiens.fasta");
	pop_Sapiens->putGeneticStatisticsToStream(file);
	file.close();

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

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

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

}

std::vector<std::string> DerevyankoReport2015::parseScript(std::string fileName){
	std::vector<std::string> script;
	std::ifstream file(fileName.c_str());
	std::string str;

	while(getline(file,str)){
		if(str.length() > 2)
			script.push_back(str);
	}
	file.close();

	// process Script
	unsigned int curLine;
	for(curLine = 0; curLine < script.size(); curLine++){
		if(script.at(curLine).at(0) == '/' || script.at(curLine).at(0) == '#')
			continue;

		std::vector<std::string > tokensVector; // Search for tokens
		boost::split(tokensVector, script.at(curLine), boost::is_any_of("=") );

		std::string instr = tokensVector.at(0);
		boost::to_lower(instr);
		boost::trim(instr);
		
		// Инструкции

		if(instr == "model_start"){
			vector<std::string>::const_iterator first = script.begin() + curLine;
			vector<std::string>::const_iterator last = script.end();
			std::vector<std::string> ans(first, last);
			return ans;
		}
		else if(instr == "pop_homo_init"){
			int flag = 0;
			sscanf_s(tokensVector.at(1).c_str(),"%d", &flag);
			if(flag != 0)
				Settings::PopulationHomoInitSize = flag;
		}
		else if(instr == "pop_ancient_init"){
			int flag = 0;
			sscanf_s(tokensVector.at(1).c_str(),"%d", &flag);
			if(flag != 0)
				Settings::PopulationAncientInitSize = flag;
		}
		else if(instr == "generations_per_migration"){
			int flag = Settings::generationsPerMigration;
			sscanf_s(tokensVector.at(1).c_str(),"%d", &flag);
			if(flag != 0)
				Settings::generationsPerMigration = flag;
		}
		else if(instr == "migr_homo_ancient_ratio"){
			double ratio = Settings::migrationPartHomoToAncient;
			sscanf_s(tokensVector.at(1).c_str(),"%lg", &ratio);
			Settings::migrationPartHomoToAncient = ratio;
		}
		else if(instr == "migr_ancient_homo_ratio"){
			double ratio = Settings::migrationPartAncientToHomo;
			sscanf_s(tokensVector.at(1).c_str(),"%lg", &ratio);
			Settings::migrationPartAncientToHomo = ratio;
		}
		else if(instr == "birth" || instr == "birthrate" || instr == "birth_rate" ){
			double rate = Settings::BirthRate;
			sscanf_s(tokensVector.at(1).c_str(),"%lg", &rate);
			Settings::BirthRate = rate;
		}
		else if(instr == "death" || instr == "deathrate" || instr == "death_rate" ){
			double rate = Settings::NaturalDeathRate;
			sscanf_s(tokensVector.at(1).c_str(),"%lg", &rate);
			Settings::NaturalDeathRate = rate;
		}
		else if(instr == "percent_diff_loci" ){
			double value = Settings::percentDiffLoci;
			sscanf_s(tokensVector.at(1).c_str(),"%lg", &value);
			Settings::percentDiffLoci = value;
		}
		else if(instr == "num_loci"){
			int flag = 0;
			sscanf_s(tokensVector.at(1).c_str(),"%d", &flag);
			if(flag != 0)
				Settings::numLoci = flag;
		}
		else if(instr == "prob_recomb" ){
			double value = Settings::ProbMtDNARecomb;
			sscanf_s(tokensVector.at(1).c_str(),"%lg", &value);
			Settings::ProbMtDNARecomb = value;
		}

		
		
		//*****************************
		else if(instr == "breedings"){
			//long int kMax = Settings::KMaxParameter;
			//sscanf_s(tokensVector.at(1).c_str(),"%ld", &kMax);
			std::string strategy = tokensVector.at(1);
			boost::to_lower(strategy);
			boost::trim(strategy);
			Settings::BreedingStrategy = strategy;
		}
	} // (END) for(curLine = 0; curLine < script.size(); curLine++)
	std::vector<std::string> a;
	return a;
}

//void DerevyankoReport2015::parseCalc(std::vector<std::string> script){
//
//}