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 <iosfwd>
#include "aux.hh"
#include "sparse_matrix.hh"
#include "rna_data.hh"

namespace LocARNA {

    class RnaEnsemble;
    class ExtRnaDataImpl;
    class PFoldParams;

    class ExtRnaData: public RnaData {
    private:
        friend class ExtRnaDataImpl;
        ExtRnaDataImpl *ext_pimpl_;  
    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);

    private:
        ExtRnaData(const ExtRnaData &);
    public:

        ~ExtRnaData();
        
    private:
        ExtRnaData &
        operator =(const ExtRnaData &);
    public:

        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;
        
        
        // IO
        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 SequenceAnnotation &structure,
                                  bool stacking);

        virtual
        void
        init_from_rna_ensemble(const RnaEnsemble &rna_ensemble,
                               const PFoldParams &pfoldparams);

        virtual
        bool
        inloopprobs_ok() const;
                
    }; // end class ExtRnaData
  
}

#endif // LOCARNA_EXT_RNA_DATA_HH