src/LocARNA/ribofit.hh

#ifndef LOCARNA_RIBOFIT_HH
#define LOCARNA_RIBOFIT_HH

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

#include <cstdlib>
#include <string>
#include <fstream>
#include <math.h>

#include "sequence.hh"
#include "alphabet.hh"
#include "matrix.hh"

namespace LocARNA {

    class Ribofit {
    public:
        typedef Matrix<double> matrix_t; 

    protected:
        Alphabet<char> alphabet_;

    public:
        explicit Ribofit(const char *alphabet) : alphabet_(alphabet, 4) {}

        virtual ~Ribofit(){};

    public:
        virtual double
        basematch_score(char i, char j, double identity) const = 0;

        virtual double
        arcmatch_score(char i, char j, char k, char l, double identity)
            const = 0;

        const Alphabet<char> &
        alphabet() const {
            return alphabet_;
        }

        const matrix_t &
        get_basematch_scores(double identity, matrix_t &basematch_scores) const;
    };

    class Ribofit_will2014 : public Ribofit {
#include "ribofit_will2014.ihh"

    public:
        Ribofit_will2014() : Ribofit(will2014_nucleotides) {}

        ~Ribofit_will2014(){};

    protected:
        double
        basematch_score(char i, char j, double identity) const {
            return will2014_bmscore(alphabet_.idx(i), alphabet_.idx(j),
                                    identity);
        }

        double
        arcmatch_score(char i, char j, char k, char l, double identity) const {
            return will2014_amscore(alphabet_.idx(i), alphabet_.idx(j),
                                    alphabet_.idx(k), alphabet_.idx(l),
                                    identity);
        }
    };

} // end namespace LocARNA

#endif // LOCARNA_RIBOFIT_HH