Init version

DEC_GUI/DEC-0.0/individual/genome/AbstractGenome.h

@@ -0,0 +1,56 @@
+#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 {
+
+};