src/LocARNA/rna_ensemble_impl.hh

#ifndef LOCARNA_RNA_ENSEMBLE_IMPL_HH
#define LOCARNA_RNA_ENSEMBLE_IMPL_HH

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

#include "rna_ensemble.hh"
#include "multiple_alignment.hh"
#include "sparse_matrix.hh"

#include "mcc_matrices.hh"

namespace LocARNA {

    class RnaEnsembleImpl {
    public:
        // RnaEnsemble *self_; //!<- pointer to corresponding RnaEnsemble object

        MultipleAlignment sequence_; 

        bool pair_probs_available_;

        bool stacking_probs_available_;

        bool in_loop_probs_available_;

        // std::vector<FLT_OR_DBL> qm1; // store qm1 for debugging
        std::vector<FLT_OR_DBL>
            qm2_; 
        std::vector<FLT_OR_DBL>
            expMLbase_; 

        McC_matrices_base *McCmat_; 


        bool used_alifold_;

        double min_free_energy_; 
        std::string min_free_energy_structure_; 


        RnaEnsembleImpl(const MultipleAlignment &sequence,
                        const PFoldParams &pfparams,
                        bool inLoopProbs,
                        bool use_alifold);

        ~RnaEnsembleImpl();


        int
        ptype_of_admissible_basepair(size_type i, size_type j) const;

        void
        compute_ensemble_probs(const PFoldParams &params,
                               bool inLoopProbs,
                               bool use_alifold);

        double
        arc_2_prob_noali(size_type i, size_type j) const;

        double
        arc_2_prob_ali(size_type i, size_type j) const;

        double
        unpaired_in_loop_prob_ali(size_type k, size_type i, size_type j) const;

        double
        unpaired_in_loop_prob_noali(size_type k,
                                    size_type i,
                                    size_type j) const;

        double
        arc_in_loop_prob_ali(size_type ip,
                             size_type jp,
                             size_type i,
                             size_type j) const;

        double
        arc_in_loop_prob_noali(size_type ip,
                               size_type jp,
                               size_type i,
                               size_type j) const;

        void
        compute_Qm2();

        void
        compute_Qm2_ali();

        void
        compute_McCaskill_matrices(const PFoldParams &params, bool inLoopProbs);

        void
        compute_McCaskill_alifold_matrices(const PFoldParams &params,
                                           bool inLoopProbs);
    };

} // end namespace LocARNA

#endif // LOCARNA_RNA_ENSEMBLE_IMPL_HH