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, size_t N>
    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, 4> &alphabet_;
        double struct_weight_;
        double indel_opening_;
        double indel_;
 
    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, 4> &alphabet,
                   double pf_struct_weight,
                   double indel_opening,
                   double indel);
 
        double
        sigma(size_type i, size_type j) const;
 
        double
        indel_opening() const {
            return indel_opening_;
        }
 
        double
        indel() const {
            return indel_;
        }
 
        void
        reverse();
    };
}
 
#endif // LOCARNA_STRAL_SCORE_HH