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src/ell/rna/DW_RNA.hh

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#ifndef DW_RNA_HH_
#define DW_RNA_HH_

#include "ell/DirectWalk.hh"

#include <string>
#include <vector>
    
namespace ell {

    class DW_RNA_MorganHiggs : public DirectWalk {
        
    protected:
        
        const size_t iterations; 
        
    public:
        
        DW_RNA_MorganHiggs( const size_t iterations );
        
        virtual ~DW_RNA_MorganHiggs();
            
        virtual 
        StateCollector*
        walk(   const State* const begin
                , const State* const end
                , StateCollector* const scWalk
            ) const;
        
        size_t
        getIterations(void) const;
        
    protected:
        
        static
        double 
        addBond(    std::string& sequence
                    , std::vector<size_t>& v_struct
                    , size_t start
                    , size_t end
                    , StateCollector* sc );
        
        static
        double 
        deleteBond( std::string& sequence
                    , std::vector<size_t>& v_struct
                    , size_t start
                    , StateCollector* sc );

        
    };
    
} // namespace ell



#endif /*DW_RNA_HH_*/