src/LocARNA/fitonoff.hh

#ifndef LOCARNA_FIT_ON_OFF_HH
#define LOCARNA_FIT_ON_OFF_HH

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

#include <string>
#include <vector>

#include <cmath>

namespace LocARNA {

    typedef std::vector<double> numseq_t;
    typedef std::vector<double>::size_type size_type;

    typedef long double pf_t;

    class FitOnOff {
        double delta_01;
        double delta_10;
        numseq_t x;

        double beta;

        pf_t exp_delta_01; 
        pf_t exp_delta_10; 

        std::vector<std::vector<pf_t> > v; 

        std::vector<std::vector<bool> > t; 

        std::vector<bool> trace;

    public:
        FitOnOff(numseq_t &x_, double delta_01_, double delta_10_, double beta_)
            : delta_01(delta_01_), delta_10(delta_10_), x(x_), beta(beta_) {
            v.resize(2);
            v[0].resize(x.size() + 1);
            v[1].resize(x.size() + 1);

            t.resize(2);
            t[0].resize(x.size() + 1);
            t[1].resize(x.size() + 1);
            trace.resize(x.size() + 1);

            exp_delta_01 = exp(-beta * delta_01);
            exp_delta_10 = exp(-beta * delta_10);
        }

        double
        viterbi(double c0, double c1, bool traceback);

        double
        best_once_on(double c0, double c1);

        pf_t
        forward(double c0, double c1);

        std::pair<double, double>
        optimize(double c0, double c1);

        void
        write_viterbi_path_compact(std::ostream &out, double c0, double c1);

        void
        write_viterbi_path(std::ostream &out, double c0, double c1) const;

        // DEBUGGING

        void
        print_table(const std::string &name, const std::vector<bool> &v) const;

        void
        print_table(const std::string &name, const std::vector<pf_t> &v) const;

        void
        print_tables() const;
    };

} // END namespace LocARNA

#endif // LOCARNA_FIT_ON_OFF_HH