#pragma once

#include "Chromosome.h"
#include "strategies/ChromosomeRearrangementStrategy.h"
#include <vector>
#include <iostream>
/*

*/
class ChromosomeRearrangementStrategy; // forward declaration
class Genotype;

class HaploidGenotype {
	friend class Genotype;
	friend class ChromosomeRearrangementStrategy;
	friend std::ostream& operator << (std::ostream& os, const Genotype& g);
    friend class Processor;
protected:
	std::vector<Chromosome> chromosomes;

public:
	const Chromosome& getChromosome(unsigned int i) const { return this->chromosomes.at(i);}
	
public:
	HaploidGenotype(const std::vector<Chromosome>& _chrom) : chromosomes(_chrom){};
	
};

class Genotype {
	friend class ChromosomeRearrangementStrategy;
	friend std::ostream& operator<< (std::ostream& os, const Genotype& g);
    friend class Processor;
protected:
	HaploidGenotype fatherGenome;
	HaploidGenotype motherGenome;

public:
	Genotype(const std::vector<Chromosome>& _fGenome, const std::vector<Chromosome>& _mGenome) : fatherGenome(HaploidGenotype(_fGenome)), motherGenome(HaploidGenotype(_mGenome)) {};
	Genotype(const HaploidGenotype& _fGenome, const HaploidGenotype& _mGenome) : fatherGenome(_fGenome), motherGenome(_mGenome) {};
	Genotype(const Genotype& _fDiplGenome, const Genotype& _mDiplGenome);
	HaploidGenotype recombinantHaploidGenotype(ChromosomeRearrangementStrategy*) const;
	const HaploidGenotype& getFatherGenome() const { return this->fatherGenome;}
	const HaploidGenotype& getMotherGenome() const { return this->motherGenome;}
	std::string toSimpleString() const;
	std::string toSimpleFasta(bool onlyMother = true) const;
	std::string toMaxModuleAB() const;

	std::string getRawGene(unsigned int fatherMother, unsigned int chromoNum, unsigned int geneNum) const;
	void doRawMutationSequence(unsigned int fatherMother, unsigned int chromoNum, unsigned int geneNum, std::string newSeq);
};


//!!!!!!!!!!
class PolyploidGenotype {

};