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