go_fish.cuh

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/*
 *      go_fish.cuh
 *
 *      Author: David Lawrie
 *      GO Fish Simulation API
 */

#ifndef GO_FISH_API_H_
#define GO_FISH_API_H_
#include <cuda_runtime.h>
#include "../3P/_outside_libraries/helper_math.h"
#include "../3P/go_fish_data_struct.h"

namespace Sim_Model{

/* ----- mutation, dominance, & inbreeding models ----- */
struct selection_constant
{
    float s;  
    inline selection_constant();  
    inline selection_constant(float s);  
    template <typename Functor_demography, typename Functor_inbreeding>
    inline selection_constant(float gamma, Functor_demography demography, Functor_inbreeding F, int forward_generation_shift = 0); 
    __device__ __forceinline__ float operator()(const int population, const int generation, const float freq) const;  
};

struct selection_linear_frequency_dependent
{
    float slope;  
    float intercept;  
    inline selection_linear_frequency_dependent();  
    inline selection_linear_frequency_dependent(float slope, float intercept);  
    template <typename Functor_demography, typename Functor_inbreeding>
    inline selection_linear_frequency_dependent(float gamma_slope, float gamma_intercept, Functor_demography demography, Functor_inbreeding F, int forward_generation_shift = 0); 
    __device__ __forceinline__ float operator()(const int population, const int generation, const float freq) const; 
};
 
struct selection_sine_wave
{
    float A;  
    float pi;  
    float rho;  
    float D;  
    int generation_shift;  
    inline selection_sine_wave();  
    inline selection_sine_wave(float A, float pi, float D, float rho = 0, int generation_shift = 0); 
    template <typename Functor_demography, typename Functor_inbreeding>
    inline selection_sine_wave(float gamma_A, float pi, float gamma_D, Functor_demography demography, Functor_inbreeding F, float rho = 0, int generation_shift = 0, int forward_generation_shift = 0); 
    __device__ __forceinline__ float operator()(const int population, const int generation, const float freq) const; 
};

template <typename Functor_sel, typename Functor_sel_pop>
struct selection_population_specific
{
    int pop;  
    int generation_shift; 
    Functor_sel s;  
    Functor_sel_pop s_pop;  
    inline selection_population_specific(); 
    inline selection_population_specific(Functor_sel s_in, Functor_sel_pop s_pop_in, int pop, int generation_shift = 0);  
    __device__ __forceinline__ float operator()(const int population, const int generation, const float freq) const; 
};

template <typename Functor_sel1, typename Functor_sel2>
struct selection_piecewise
{
    int inflection_point;  
    int generation_shift; 
    Functor_sel1 s1;  
    Functor_sel2 s2;  
    inline selection_piecewise(); 
    inline selection_piecewise(Functor_sel1 s1_in, Functor_sel2 s2_in, int inflection_point, int generation_shift = 0);  
    __device__ __forceinline__ float operator()(const int population, const int generation, const float freq) const; 
};
/* ----- end selection models ----- */
/* ----- inbreeding, mutation, & dominance models ----- */
struct F_mu_h_constant
{
    float p;  
    inline F_mu_h_constant();  
    inline F_mu_h_constant(float p);  
    __host__ __forceinline__ float operator()(const int population, const int generation) const;  
};
 
struct F_mu_h_sine_wave
{
    float A; 
    float pi; 
    float rho; 
    float D; 
    int generation_shift; 

    inline F_mu_h_sine_wave(); 
    inline F_mu_h_sine_wave(float A, float pi, float D, float rho = 0, int generation_shift = 0); 
    __host__ __forceinline__ float operator()(const int population, const int generation) const; 
};

template <typename Functor_p, typename Functor_p_pop>
struct F_mu_h_population_specific
{
    int pop;  
    int generation_shift; 
    Functor_p p;  
    Functor_p_pop p_pop;  
    inline F_mu_h_population_specific(); 
    inline F_mu_h_population_specific(Functor_p p_in, Functor_p_pop p_pop_in, int pop, int generation_shift = 0);   
    __host__ __forceinline__ float operator()(const int population, const int generation) const; 
};

template <typename Functor_p1, typename Functor_p2>
struct F_mu_h_piecewise
{
    int inflection_point;  
    int generation_shift; 
    Functor_p1 p1;  
    Functor_p2 p2;  
    inline F_mu_h_piecewise(); 
    inline F_mu_h_piecewise(Functor_p1 p1_in, Functor_p2 p2_in, int inflection_point, int generation_shift = 0); 
    __host__ __forceinline__ float operator()(const int population, const int generation) const; 
};
/* ----- end of inbreeding, mutation, & dominance models ----- */ 
/* ----- demography models ----- */
struct demography_constant
{
    int N;  
    inline demography_constant();  
    inline demography_constant(int p);  
    __host__ __device__  __forceinline__ int operator()(const int population, const int generation) const;  
};
 
struct demography_sine_wave
{
    float A; 
    float pi; 
    float rho; 
    float D; 
    int generation_shift; 

    inline demography_sine_wave(); 
    inline demography_sine_wave(float A, float pi, int D, float rho = 0, int generation_shift = 0); 
    __host__ __device__  __forceinline__ int operator()(const int population, const int generation) const; 
};

struct demography_exponential_growth
{
    float rate;  
    int initial_population_size;  
    int generation_shift; 

    inline demography_exponential_growth(); 
    inline demography_exponential_growth(float rate, int initial_population_size, int generation_shift = 0); 
    __host__ __device__ __forceinline__ int operator()(const int population, const int generation) const; 
};

struct demography_logistic_growth
{
    float rate;  
    int initial_population_size;  
    int carrying_capacity;  
    int generation_shift; 

    inline demography_logistic_growth(); 
    inline demography_logistic_growth(float rate, int initial_population_size, int carrying_capacity, int generation_shift = 0); 
    __host__ __device__ __forceinline__ int operator()(const int population, const int generation) const; 
};

template <typename Functor_d, typename Functor_d_pop>
struct demography_population_specific
{
    int pop;  
    int generation_shift; 
    Functor_d d;  
    Functor_d_pop d_pop;  
    inline demography_population_specific(); 
    inline demography_population_specific(Functor_d d_in, Functor_d_pop d_pop_in, int pop, int generation_shift = 0);  
    __host__ __device__ __forceinline__ int operator()(const int population, const int generation) const;
};

template <typename Functor_d1, typename Functor_d2>
struct demography_piecewise
{
    int inflection_point;  
    int generation_shift; 
    Functor_d1 d1;  
    Functor_d2 d2;  
    inline demography_piecewise(); 
    inline demography_piecewise(Functor_d1 d1_in, Functor_d2 d2_in, int inflection_point, int generation_shift = 0);  
    __host__ __device__ __forceinline__ int operator()(const int population, const int generation) const; 
};
/* ----- end of demography models ----- */
/* ----- migration models ----- */
struct migration_constant_equal
{
    float m;  
    int num_pop;  
    inline migration_constant_equal();  
    inline migration_constant_equal(float m, int num_pop);  
    __host__ __device__ __forceinline__ float operator()(const int pop_FROM, const int pop_TO, const int generation) const; 
};

template <typename Functor_m1>
struct migration_constant_directional
{
    float m;  
    int pop1;  
    int pop2;  
    Functor_m1 rest;  
    inline migration_constant_directional(); 
    inline migration_constant_directional(float m, int pop1, int pop2, Functor_m1 rest_in);  
    __host__ __device__ __forceinline__ float operator()(const int pop_FROM, const int pop_TO, const int generation) const; 
};

template <typename Functor_m1, typename Functor_m2>
struct migration_piecewise
{
    int inflection_point;  
    int generation_shift; 
    Functor_m1 m1;  
    Functor_m2 m2;   
    inline migration_piecewise(); 
    inline migration_piecewise(Functor_m1 m1_in, Functor_m2 m2_in, int inflection_point, int generation_shift = 0); 
    __host__ __device__ __forceinline__ float operator()(const int pop_FROM, const int pop_TO, const int generation) const; 
};
/* ----- end of migration models ----- */
/* ----- preserving & sampling functions ----- */
struct bool_off{
    __host__ __forceinline__ bool operator()(const int generation) const; 
};

struct bool_on{
    __host__ __forceinline__ bool operator()(const int generation) const; 
};

/* will switch to variadic templates/initializer lists when switching to C++11
struct bool_pulse_array{
    bool * array;
    int num_generations;
    int generation_start;
    inline bool_pulse_array();
    inline bool_pulse_array(const bool default_return, const int generation_start, const int num_generations, int generation_pulse...);
    __host__ __forceinline__ bool operator()(const int generation) const;
    ~bool_pulse_array();

private:
    inline bool_pulse_array(int generation_pulse...);
    inline bool_pulse_array(int generation_pulse);
}; */

template <typename Functor_default, typename Functor_action>
struct bool_pulse{
    int pulse;  
    int generation_shift; 
    Functor_default f_default;  
    Functor_action f_action;  
    bool_pulse(); 
    bool_pulse(int pulse, int generation_shift = 0); 
    bool_pulse(Functor_default f_default_in, Functor_action f_action, int pulse, int generation_shift = 0);  
    __host__ __forceinline__ bool operator()(const int generation) const; 
};

template <typename Functor_first, typename Functor_second>
struct bool_piecewise{
    int inflection_point;  
    int generation_shift; 
    Functor_first f1;  
    Functor_second f2;  
    inline bool_piecewise(); 
    inline bool_piecewise(int inflection_point, int generation_shift = 0); 
    inline bool_piecewise(Functor_first f1_in, Functor_second f2_in, int inflection_point, int generation_shift = 0);  
    __host__ __forceinline__ bool operator()(const int generation) const; 
};
/* ----- end of preserving & sampling functions ----- */
} /* ----- end namespace Sim_Model ----- */

namespace GO_Fish{

/* ----- go_fish_impl  ----- */
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>
__host__ 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);
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>
__host__ 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);
/* ----- end go_fish_impl ----- */

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

/* ----- importing functor implementations ----- */
#include "../3P/_internal/template_inline_simulation_functors.cuh"
/* ----- end importing functor implementations ----- */

/* ----- importing go_fish_impl  ----- */
#include "../3P/_internal/go_fish_impl.cuh"
/* ----- end importing go_fish_impl ----- */


#endif /* GO_FISH_API_H_ */