src/LocARNA/stral_score.hh

#ifndef LOCARNA_STRAL_SCORE_HH
#define LOCARNA_STRAL_SCORE_HH

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>

#include "aux.hh"
#include "sequence.hh"

namespace LocARNA {

    template <class T>
    class Matrix;
    template <class T>
    class Alphabet;
    class RnaData;

    class StralScore {
        typedef std::vector<double> p_vec_t;

        Sequence seqA;
        Sequence seqB;

        p_vec_t p_upA;   
        p_vec_t p_downA; 
        p_vec_t p_unA;   

        p_vec_t p_upB;   
        p_vec_t p_downB; 
        p_vec_t p_unB;   

        const Matrix<double> &sim_mat;
        const Alphabet<char> &alphabet;
        double pf_struct_weight;
        double gap_opening;
        double gap_extension;

    private:
        void
        init_prob_vecs(const RnaData &rna,
                       p_vec_t &p_up,
                       p_vec_t &p_down,
                       p_vec_t &p_un);

    public:
        StralScore(const RnaData &rnaA,
                   const RnaData &rnaB,
                   const Matrix<double> &sim_mat_,
                   const Alphabet<char> &alphabet_,
                   double pf_struct_weight_,
                   double gap_opening_,
                   double gap_extension_);

        double
        sigma(size_type i, size_type j) const;

        double
        alpha() const {
            return gap_opening;
        }

        double
        beta() const {
            return gap_extension;
        }

        void
        reverse();
    };
}

#endif // LOCARNA_STRAL_SCORE_HH