rna_ensemble.hh

#ifndef LOCARNA_RNA_ENSEMBLE_HH
#define LOCARNA_RNA_ENSEMBLE_HH

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

#include <iosfwd>

#include "aux.hh"

namespace LocARNA {

    class MultipleAlignment;

    class RnaEnsembleImpl; // forward to implementation class

    class PFoldParams;

    class RnaEnsemble {
    private:
        RnaEnsembleImpl *pimpl_;  
    public:
        
        RnaEnsemble(const MultipleAlignment &ma,
                    const PFoldParams &params,
                    bool inLoopProbs, 
                    bool use_alifold=true);
        
        RnaEnsemble(const RnaEnsemble &rna_ensemble);

        RnaEnsemble &operator =(const RnaEnsemble &rna_ensemble);
        
        virtual 
        ~RnaEnsemble();
        
        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;

    };

}

#endif // LOCARNA_RNA_ENSEMBLE_HH