hivpopulation.h

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#ifndef HIVPOPULATION_H_
#define HIVPOPULATION_H_

#include <string>
#include <fstream>
#include <sstream>
#include <iomanip>
#include <boost/algorithm/string.hpp>

#include "ffpopsim_highd.h"

#define HIVPOP_VERBOSE 0
#define HIVPOP_BADARG -1354341
#define NOTHING 1e-10
#define HIVGENOME 10000

// HIV genes
#define ENV_START 7000
#define ENV_END 8000


struct hivgene {
        unsigned int start;
        unsigned int end;
        hivgene(unsigned int start_in=0, unsigned int end_in=HIVGENOME);
};

class hivpopulation : public haploid_highd {
public:
        // constructors/destructors
        hivpopulation(int N=0, int rng_seed=0, double mutation_rate=3e-5, double coinfection_rate=1e-2, double crossover_rate=1e-3);
        virtual ~hivpopulation();

        // genes
        hivgene env;

        // treatment (set/get)
        void set_treatment(double t){treatment=t; update_traits(); update_fitness();}
        double get_treatment() {return treatment;}

        // stream I/O
        int read_replication_coefficients(istream &model);
        int read_resistance_coefficients(istream &model);
        int write_genotypes(ostream &out_genotypes, int sample_size, string gt_label="", int start=0, int length=0);

protected:
        // fitness landscape
        virtual void calc_individual_fitness_from_traits(clone_t *tempgt);

private:
        //random number generator
        double treatment;
        gsl_rng* rng;
        int seed;

};

#endif /* HIVPOPULATION_H_ */