VrnaHandler.h

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#ifndef VIENNAHANDLER_H_
#define VIENNAHANDLER_H_
 
#include "IntaRNA/general.h"
#include <string>
 
extern "C" {
    #include <ViennaRNA/model.h>
    #include <ViennaRNA/params.h>
}
 
namespace IntaRNA {
 
class VrnaHandler {
 
public:
 
    static constexpr const char* Turner99 = "Turner99";
    static constexpr const char* Turner04 = "Turner04";
    static constexpr const char* Andronescu07 = "Andronescu07";
 
protected:
 
    vrna_md_t model;
 
    Z_type RT;
 
public:
 
    VrnaHandler(
            Z_type temperature = 37.0
            , const std::string & vrnaParamFile = std::string(Turner04)
            , const bool noGUclosure = false
            , const bool noLP = false );
 
    virtual ~VrnaHandler();
 
    vrna_md_t
    getModel(
            const int max_bp_span = -1,
            const int window_size = -1,
            const double pfScale = getPfScaleDefault() ) const;
 
    Z_type
    getRT() const;
 
    static
    Z_type
    getRT( const Z_type temperature );
 
 
    static
    double
    getPfScaleDefault();
 
 
 
};
 
 
inline
Z_type
VrnaHandler::
getRT() const
{
    return RT;
}
 
 
} // namespace
 
#endif /* VIENNAHANDLER_H_ */