AccessibilityVrna.h

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#ifndef INTARNA_ACCESSIBILITYVIENNA_H_
#define INTARNA_ACCESSIBILITYVIENNA_H_
 
#include "IntaRNA/Accessibility.h"
#include "IntaRNA/VrnaHandler.h"
 
#include "IntaRNA/Matrix.h"
 
#include <iostream>
 
 
extern "C" {
    #include <ViennaRNA/fold_vars.h>
    #include <ViennaRNA/params.h>
}
 
 
namespace IntaRNA {
 
class AccessibilityVrna : public Accessibility {
 
public:
 
 
    AccessibilityVrna( const RnaSequence& sequence
            , const size_t maxLength
            , const AccessibilityConstraint * const accConstraint
            , const VrnaHandler & vrnaHandler
            , const size_t plFoldW = 0
            , const double pfScale = VrnaHandler::getPfScaleDefault()
            );
 
    virtual ~AccessibilityVrna() override;
 
    virtual
    E_type
    getED( const size_t from, const size_t to ) const override;
 
 
    static
    void
    addConstraints( vrna_fold_compound_t & fold_compound
                , const Accessibility & acc );
 
 
    void writeBinary( std::ostream & out ) const override;
 
protected:
 
    typedef UpperBandedMatrix<E_type> EdMatrix;
 
    EdMatrix edValues;
 
 
    void
    fillByRNAplfold( const VrnaHandler &vrnaHandler
                        , const size_t plFoldW
                        , const size_t plFoldL
                        , const double pfScale);
 
    static
    void
    callbackForStorage( FLT_OR_DBL    *pr,
                        int           pr_size,
                        int           j,
                        int           max,
                        unsigned int  type,
                        void          *storageRT);
 
};
 
 
 
inline
void
AccessibilityVrna::writeBinary( std::ostream & out ) const
{
    Accessibility::writeBinary(out, &edValues);
}
 
inline
E_type
AccessibilityVrna::
getED( const size_t from, const size_t to ) const
{
    // input range check
    checkIndices(from,to);
 
    if ((to-from+1) <= getMaxLength() +1 ) { // "getMaxLength()+1" to allow for dangling-end probability computation
        // check for constrained end positions
        if (!getAccConstraint().isAccessible(from) || !getAccConstraint().isAccessible(to)) {
            // end position blocked --> omit accessibility
            return ED_UPPER_BOUND;
        }
        // return according ED value from the precomputed matrix
        return edValues (from,to);
    } else {
        // region length exceeds maximally allowed length -> no value
        return ED_UPPER_BOUND;
    }
}
 
 
} // namespace
 
#endif /* ACCESSIBILITYVIENNA_H_ */