species.h

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#ifndef  PSPM_PSPM_SPECIES_H_
#define  PSPM_PSPM_SPECIES_H_

#include <vector>
#include <list>
#include <string>

//#include "iterator_set.h"
#include "cohort.h"

// forward declaration of Solver so Species can befriend it
class Solver;


class Species_Base{
    // Solver should be able to access Species' privates
    friend class Solver;

    protected: // private members
    int J;  
    int n_extra_statevars = 0;

    std::list<double> birth_flux_out_history;                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
    
    // These are only used by FMU solver. 
    // Others derive them from the state. 
    // Kept private so users dont accidently access them for other solvers
    std::vector <double> X; 
    std::vector <double> x;
    std::vector <double> h;
    std::vector <double> schedule; // used only by CM/EBT

    public:
    double birth_flux_in;
    
    //debug only
    bool bfin_is_u0in = false;
    

    public: // public members
    double xb; 
    bool is_resident;
    
    
    public: // public functions

    virtual ~Species_Base() = 0;
    
    int xsize();
    int size();

    void set_inputBirthFlux(double b);
    void set_bfin_is_u0in(bool flag);

    public:
    virtual void resize(int _J) = 0;
    virtual double get_maxSize() = 0;
    virtual void print() = 0;

    virtual void set_xb(double _xb) = 0;
    virtual void set_ub(double _ub) = 0;
    virtual void set_birthTime(int i, double t0) = 0;
    virtual void setX(int i, double _x) = 0;
    virtual void setU(int i, double _u) = 0;

    virtual double getX(int i) = 0;
    virtual double getU(int i) = 0;

    virtual double init_density(int i, double x, void * env) = 0;
    virtual void initAndCopyExtraState(double t, void * env, std::vector<double>::iterator &it) = 0;
    virtual void initBoundaryCohort(double t, void * env) = 0;

    virtual void copyExtraStateToCohorts(std::vector<double>::iterator &it) = 0;
    virtual void copyCohortsExtraToState(std::vector<double>::iterator &it) = 0;
    
    virtual double establishmentProbability(double t, void * env) = 0;
    virtual double calc_boundary_u(double gb, double pe) = 0;
    virtual double get_boundary_u() = 0;

    virtual void triggerPreCompute() = 0;

    // TODO: argument x can probably be removed from these functions
    virtual double growthRate(int i, double x, double t, void * env) = 0;
    virtual double growthRateOffset(int i, double x, double t, void * env) = 0;
    virtual std::vector<double> growthRateGradient(int i, double x, double t, void * env, double grad_dx) = 0;
    virtual std::vector<double> growthRateGradientCentered(int i, double xplus, double xminus, double t, void * env) = 0;
    virtual double mortalityRate(int i, double x, double t, void * env) = 0;
    virtual std::vector<double> mortalityRateGradient(int i, double x, double t, void * env, double grad_dx) = 0;
    virtual double birthRate(int i, double x, double t, void * env) = 0;
    virtual void getExtraRates(std::vector<double>::iterator &it) = 0;

    virtual void addCohort() = 0;
    template<class T> void addCohort(T bc);

    virtual void removeDensestCohort() = 0;
    virtual void removeDenseCohorts(double dxcut) = 0;
    virtual void removeDeadCohorts(double ucut) = 0;

//  virtual void backupCohort(int j) = 0;
//  virtual void restoreCohort(int j) = 0;
//  virtual void copyBoundaryCohortTo(int j) = 0;
};



template <class Model>
class Species : public Species_Base{
    protected:
    std::vector<Cohort<Model>> cohorts;
    Cohort<Model> boundaryCohort;
    
    Cohort<Model> savedCohort; // a cohort to save a backup of any other cohort

    public:
    // TODO: make these virtual? - not needed. They are virtual by default.
    Species(std::vector<double> breaks = std::vector<double>());
    Species(Model M);
    
    void resize(int _J);
    double get_maxSize();
    
    void print();
    
    void set_xb(double _xb);
    void set_ub(double _ub);
    void set_birthTime(int i, double t0);
    void setX(int i, double _x);
    void setU(int i, double _u);
    
    double getX(int i);
    double getU(int i);
    
    double init_density(int i, double x, void * env);
    void initAndCopyExtraState(double t, void * env, std::vector<double>::iterator &it);
    void initBoundaryCohort(double t, void * env);

    void copyExtraStateToCohorts(std::vector<double>::iterator &it);
    void copyCohortsExtraToState(std::vector<double>::iterator &it);

    double establishmentProbability(double t, void * env);
    double calc_boundary_u(double gb, double pe);
    double get_boundary_u();
    
    void triggerPreCompute();
    double growthRate(int i, double x, double t, void * env);
    double growthRateOffset(int i, double x, double t, void * env);
    std::vector<double> growthRateGradient(int i, double x, double t, void * env, double grad_dx);
    std::vector<double> growthRateGradientCentered(int i, double xplus, double xminus, double t, void * env);
    double mortalityRate(int i, double x, double t, void * env);
    std::vector<double> mortalityRateGradient(int i, double x, double t, void * env, double grad_dx);
    double birthRate(int i, double x, double t, void * env);
    void getExtraRates(std::vector<double>::iterator &it);

    void addCohort();
    void addCohort(Cohort<Model> bc);

    void removeDensestCohort();
    void removeDenseCohorts(double dxcut);
    void removeDeadCohorts(double ucut);
    
//  void backupCohort(int j);
//  void restoreCohort(int j);
//  void copyBoundaryCohortTo(int j);

    public:
    Cohort<Model>& getCohort(int i);
};


#include "../src/species.tpp"

#endif