rna_ensemble.hh

#ifndef LOCARNA_RNA_ENSEMBLE_HH
#define LOCARNA_RNA_ENSEMBLE_HH
 
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
 
#include <memory>
#include <iosfwd>
 
#include "aux.hh"
 
namespace LocARNA {
 
    class MultipleAlignment;
 
    class RnaEnsembleImpl; // forward to implementation class
 
    class PFoldParams;
 
    class RnaEnsemble {
    public:
        RnaEnsemble(const MultipleAlignment &ma,
                    const PFoldParams &params,
                    bool inLoopProbs,
                    bool use_alifold = true);
 
        RnaEnsemble(const RnaEnsemble &rna_ensemble);
 
        ~RnaEnsemble();
 
        RnaEnsemble &
        operator=(const RnaEnsemble &rna_ensemble);
 
        bool
        has_base_pair_probs() const;
 
        bool
        has_stacking_probs() const;
 
        bool
        has_in_loop_probs() const;
 
        const MultipleAlignment &
        multiple_alignment() const;
 
        size_type
        length() const;
 
        double
        min_free_energy() const;
 
        std::string
        min_free_energy_structure() const;
 
        // ------------------------------------------------------------
        // methods for base pair probabilities
 
        double
        arc_prob(size_type i, size_type j) const;
 
        double
        arc_2_prob(size_type i, size_type j) const;
 
        double
        arc_stack_prob(size_type i, size_type j) const;
 
        // ------------------------------------------------------------
        // compute probabilities paired upstream, downstream, and unpaired
 
        double
        paired_upstream_prob(size_type i) const;
 
        double
        paired_downstream_prob(size_type i) const;
 
        double
        unpaired_prob(size_type i) const;
 
        // the following methods need linking to librna
 
        double
        unpaired_in_loop_prob(size_type k, size_type i, size_type j) const;
 
        double
        unpaired_external_prob(size_type k) const;
 
        double
        arc_in_loop_prob(size_type ip,
                         size_type jp,
                         size_type i,
                         size_type j) const;
 
        double
        arc_external_prob(size_type i, size_type j) const;
 
    private:
        std::unique_ptr<RnaEnsembleImpl> pimpl_;
    };
}
 
#endif // LOCARNA_RNA_ENSEMBLE_HH