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; 
        using base_alphabet_type = Alphabet<char,4>;
 
        explicit Ribofit(std::array<char, 4> alphabet) : alphabet_(alphabet) {}
 
        virtual ~Ribofit(){};
 
        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 base_alphabet_type &
        alphabet() const {
            return alphabet_;
        }
 
        const matrix_t &
        get_basematch_scores(double identity, matrix_t &basematch_scores) const;
 
 
    protected:
        base_alphabet_type alphabet_;
 
    };
 
    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