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src/ell/rna/RNAFreeEnergy_TB.hh

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#ifndef RNAFREEENERGY_TB_HH_
#define RNAFREEENERGY_TB_HH_


#include <biu/RNAStructure_TB.hh>

namespace ell
{

    class RNAFreeEnergy_TB : public biu::RNAStructure_TB
    {
    protected:
        static const biu::AllowedBasePairs      COMMON_BPAIRS;

        static const biu::Alphabet              COMMON_ALPHABET;
        
        static const double ENERGY_INF; 
        
        mutable double energy;
        
        short* seqVienna;
        short* pairTable;

    public:
        
        static bool calculateEnergyChanges;
        
        typedef std::pair<size_t, size_t> SingleMove;

        RNAFreeEnergy_TB(   const std::string& rnaSeqStr
                            , const std::string& rnaStructBracketDotStr
                            , const double energy = ENERGY_INF );

        RNAFreeEnergy_TB(   biu::Sequence* rnaSeq
                            , const biu::Structure* const rnaStructBracketDot
                            , const bool seqIsShared = false
                            , const double energy = ENERGY_INF );

        RNAFreeEnergy_TB(const RNAFreeEnergy_TB& rnaFreeEnerg);
        
        virtual ~RNAFreeEnergy_TB();
        
        void applySingleMoveInPlace(const SingleMove& move);
        
        bool isValidSingleMove(const SingleMove& move) const;
        
        static const biu::Alphabet* getSequenceAlphabet() {
            return &COMMON_ALPHABET;
        }

    // abstract functions (BioMolecule)
        
        virtual double  getEnergy( void ) const;
        
    virtual void setEnergy( const double energy );

        RNAFreeEnergy_TB&   operator= (const RNAFreeEnergy_TB& rnaStruct2);

    virtual void setStructure(const biu::Structure& str);

    protected:
        
        virtual void moleculeChanged();
        
        virtual void updateSeqVienna();
        
    protected:
        
        static bool ViennaFoldParamsSet;
        
        static void setViennaFoldParams(void);
        
    };

} // namespace biu

  // include definitions
#include "ell/rna/RNAFreeEnergy_TB.icc"

#endif /*RNAFREEENERGY_TB_HH_*/