src/LocARNA/pfold_params.hh

#ifndef LOCARNA_PFOLD_PARAMS_HH
#define LOCARNA_PFOLD_PARAMS_HH

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

extern "C" {
#include <ViennaRNA/data_structures.h>
}

#include <limits>
#include "aux.hh"

namespace LocARNA {

    class PFoldParams {
        vrna_md_t md_; 
        int stacking_; 
    public:
        PFoldParams(bool noLP, bool stacking, int max_bp_span, int dangling);

        const vrna_md_t &
        model_details() const {
            return md_;
        }

        /* provide read access for selected model details */

        bool
        noLP() const {
            return md_.noLP == 1;
        }

        bool
        stacking() const {
            return stacking_;
        }

        size_t
        max_bp_span() const {
            return md_.max_bp_span >= 0 ? md_.max_bp_span
                                        : std::numeric_limits<size_t>::max();
        }

        int
        dangling() const {
            return md_.dangles;
        }
    };
}

#endif // LOCARNA_PFOLD_PARAMS_HH