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 "rna_data_impl.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 RnaStructure &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