ext_rna_data.hh

#ifndef LOCARNA_EXT_RNA_DATA_HH
#define LOCARNA_EXT_RNA_DATA_HH
 
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
 
#include <memory>
#include <iosfwd>
#include "aux.hh"
#include "sparse_matrix.hh"
#include "rna_data.hh"
 
namespace LocARNA {
 
    class RnaEnsemble;
    class ExtRnaDataImpl;
    class PFoldParams;
    class RnaStructure;
 
    class ExtRnaData : public RnaData {
        friend class ExtRnaDataImpl;
    public:
        ExtRnaData(const RnaEnsemble &rna_ensemble,
                   double p_bpcut,
                   double p_bpilcut,
                   double p_uilcut,
                   double max_bps_length_ratio,
                   double max_uil_length_ratio,
                   double max_bpil_length_ratio,
                   const PFoldParams &pfoldparams);
 
        ExtRnaData(const std::string &filename,
                   double p_bpcut,
                   double p_bpilcut,
                   double p_uilcut,
                   double max_bps_length_ratio,
                   double max_uil_length_ratio,
                   double max_bpil_length_ratio,
                   const PFoldParams &pfoldparams);
        ~ExtRnaData();
 
        double
        arc_in_loop_cutoff_prob() const;
 
        double
        arc_in_loop_prob(pos_type i, pos_type j, pos_type p, pos_type q) const;
 
        double
        arc_external_prob(pos_type i, pos_type j) const;
 
        double
        unpaired_in_loop_cutoff_prob() const;
 
        double
        unpaired_in_loop_prob(pos_type k, pos_type p, pos_type q) const;
 
        double
        unpaired_external_prob(pos_type k) const;
 
        std::ostream &
        write_size_info(std::ostream &out) const;
 
        std::ostream &
        write_pp(std::ostream &out,
                 double p_outbpcut = 0,
                 double p_outbpilcut = 0,
                 double p_outuilcut = 0) const;
 
    protected:
        virtual std::istream &
        read_pp(std::istream &in);
 
        virtual void
        init_from_fixed_structure(const RnaStructure &structure,
                                  const PFoldParams &pfoldparams);
 
        virtual void
        init_from_rna_ensemble(const RnaEnsemble &rna_ensemble,
                               const PFoldParams &pfoldparams);
 
        virtual bool
        inloopprobs_ok() const;
 
    private:
        std::unique_ptr<ExtRnaDataImpl> ext_pimpl_;
 
        ExtRnaData(const ExtRnaData &);
 
        ExtRnaData &
        operator=(const ExtRnaData &);
 
 
    }; // end class ExtRnaData
}
 
#endif // LOCARNA_EXT_RNA_DATA_HH