go_fish_data_struct.h

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/* go_fish_data_struct.h
 *
 * Author: David Lawrie
 * Subset of go_fish.cuh: GO_Fish data structures
 */

#ifndef GO_FISH_DATA_H_
#define GO_FISH_DATA_H_

#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <sstream>
#include <cstring>

namespace Spectrum_details{ class transfer_allele_trajectories; } //for passing data to SPECTRUM functions

namespace GO_Fish{

/* ----- sim result output ----- */
struct mutID{
    int origin_generation;  
    int origin_population;  
    int origin_threadID; 
    int reserved;  
    inline mutID();

    inline mutID(int origin_generation, int origin_population, int origin_threadID, int reserved);

    inline std::string toString();
    inline std::string toString() const;
};

struct allele_trajectories{
    //----- initialization parameters -----
    struct sim_constants{
        int seed1;  
        int seed2;  
        int num_generations;  
        float num_sites;  
        int num_populations;  
        bool init_mse;  
        int prev_sim_sample;  
        int compact_interval;  
        int device;  
        inline sim_constants();
    };

    sim_constants sim_input_constants;  
    //----- end -----
 
    inline allele_trajectories();
 
    inline allele_trajectories(const allele_trajectories & in);
 
    inline allele_trajectories & operator=(allele_trajectories in);
 
    inline sim_constants last_run_constants();
 
    inline int num_sites();
 
    inline int num_populations();
 
    inline int num_time_samples();
 
    inline int maximal_num_mutations();
 
    inline int num_mutations_time_sample(int sample_index);
 
    inline int final_generation();
 
    inline int sampled_generation(int sample_index);
 
    inline bool extinct(int sample_index, int population_index);
 
    inline int effective_number_of_chromosomes(int sample_index, int population_index);
 
    inline float frequency(int sample_index, int population_index, int mutation_index);
 
    inline mutID mutation_ID(int mutation_index);
 
    inline void delete_time_sample(int sample_index);

    inline void reset();
 
    inline ~allele_trajectories();

    friend void swap(allele_trajectories & a, allele_trajectories & b);

    friend std::ostream & operator<<(std::ostream & stream, allele_trajectories & A);

    template <typename Functor_mutation, typename Functor_demography, typename Functor_migration, typename Functor_selection, typename Functor_inbreeding, typename Functor_dominance, typename Functor_preserve, typename Functor_timesample>
    friend void run_sim(allele_trajectories & all_results, const Functor_mutation mu_rate, const Functor_demography demography, const Functor_migration mig_prop, const Functor_selection sel_coeff, const Functor_inbreeding FI, const Functor_dominance dominance, const Functor_preserve preserve_mutations, const Functor_timesample take_sample, const allele_trajectories & prev_sim);

    friend class Spectrum_details::transfer_allele_trajectories;
private:

    struct time_sample{
        float * mutations_freq; //allele frequency of mutations in final generation
        bool * extinct; //extinct[pop] == true, flag if population is extinct by time sample
        int * Nchrom_e; //effective number of chromosomes in each population
        int num_mutations; //number of mutations in frequency array (columns array length for freq)
        int sampled_generation; //number of generations in the simulation at point of sampling

        time_sample();
        ~time_sample();
    };

    inline void initialize_run_constants();

    inline void initialize_sim_result_vector(int new_length);

    sim_constants sim_run_constants; //stores constants of the simulation run currently held by time_samples
    time_sample ** time_samples; //the actual allele trajectories output from the simulation
    int num_samples; //number of time samples taken from the simulation
    mutID * mutations_ID; //unique ID for each mutation in simulation
    int all_mutations; //number of mutations in mutation ID array - maximal set of mutations stored in allele_trajectories
}; 
inline std::ostream & operator<<(std::ostream & stream, const mutID & id);

inline std::ostream & operator<<(std::ostream & stream, allele_trajectories & A);
 
inline void swap(allele_trajectories & a, allele_trajectories & b);

/* ----- end sim result output ----- */

} /* ----- end namespace GO_Fish ----- */

/* ----- import inline function definitions ----- */
#include "../3P/_internal/inline_go_fish_data_struct.hpp"
/* ----- end ----- */

#endif /* GO_FISH_DATA_H_ */