ext_rna_data_impl.hh

#ifndef LOCARNA_EXT_RNA_DATA_IMPL_HH
#define LOCARNA_EXT_RNA_DATA_IMPL_HH

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

#include <iosfwd>
#include "ext_rna_data.hh"
#include "sequence.hh"
#include "sparse_vector.hh"

namespace LocARNA {

    // class Sequence;
    // class RnaEnsemble;
    // class PFoldParams;

    class ExtRnaDataImpl {
    public:
        // ----------------------------------------
        // TYPES
        
        typedef SparseVector<double> arc_prob_vector_t;
        
        typedef RnaDataImpl::arc_prob_matrix_t arc_prob_matrix_t;
        
        typedef SparseMatrix<arc_prob_vector_t> arc_prob_vector_matrix_t;

        typedef SparseMatrix<arc_prob_matrix_t> arc_prob_matrix_matrix_t;
        
        
        // ----------------------------------------
        // ATTRIBUTES

        ExtRnaData *self_; 
        
        double p_bpilcut_;
        
        double p_uilcut_;
        
        arc_prob_matrix_matrix_t arc_in_loop_probs_;

        arc_prob_vector_matrix_t unpaired_in_loop_probs_;

        bool has_in_loop_probs_;
        
        // ----------------------------------------
        // CONSTRUCTORS
        

        ExtRnaDataImpl(ExtRnaData *self,
                       double p_bpilcut,
                       double p_uilcut);
        
        // ----------------------------------------
        // METHODS

    private:
        void
        init_fixed_unpaired_in_loop(size_t i,
                                    size_t j,
                                    const RnaStructure &structure);
        void
        init_fixed_basepairs_in_loop(size_t i,
                                     size_t j,
                                     const RnaStructure &structure);
    public:

        
        void
        init_from_fixed_structure(const SequenceAnnotation &structure);

        void
        init_from_ext_rna_ensemble(const RnaEnsemble &rna_ensemble);    

        std::istream &
        read_pp_in_loop_probabilities(std::istream &in);

        
        void
        read_pp_in_loop_probabilities_kwline(const std::string &line);

        void
        read_pp_in_loop_probabilities_line(const std::string &line);
        
        std::ostream &
        write_pp_in_loop_probabilities(std::ostream &out,
                                       double p_outbpcut,
                                       double p_outbpilcut,
                                       double p_outuilcut
                                       ) const;

        std::ostream &
        write_pp_in_loop_probability_line(std::ostream &out,
                                          size_t i, size_t j,
                                          double p_bpcut,
                                          double p_ucut) const;
        std::ostream &
        write_pp_basepair_in_loop_probabilities(std::ostream &out,
                                                const arc_prob_matrix_t &probs,
                                                double p_cut) const;
        
        std::ostream &
        write_pp_unpaired_in_loop_probabilities(std::ostream &out,
                                                const arc_prob_vector_t &probs,
                                                double p_cut) const;

        void
        drop_worst_bps(size_t keep);

        void
        drop_worst_uil(size_t keep);

        void
        drop_worst_bpil(size_t keep);



        void
        drop_worst_bpil_precise(double ratio);

    }; // end ExtRnaDataImpl


} //end namespace LocARNA


#endif // LOCARNA_EXT_RNA_DATA_IMPL_HH