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src/ell/rna/RNAFreeEnergy.hh

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#ifndef RNAFREEENERGY_HH_
#define RNAFREEENERGY_HH_


#include <biu/RNAStructure.hh>

namespace ell
{

    class RNAFreeEnergy : public biu::RNAStructure
    {
    protected:
        static const biu::AllowedBasePairs      COMMON_BPAIRS;

        static const biu::Alphabet              COMMON_ALPHABET;
        
        static const double ENERGY_INF; 
        
        mutable double energy;

    public:
        typedef std::pair<size_t, size_t> SingleMove;

        RNAFreeEnergy(  const std::string& rnaSeqStr,
                        const std::string& rnaStructBracketDotStr);

        RNAFreeEnergy(  biu::Sequence* rnaSeq,
                        const biu::Structure* const rnaStructBracketDot,
                        const bool seqIsShared = false);

        RNAFreeEnergy(const RNAFreeEnergy& rnaFreeEnerg);
        virtual ~RNAFreeEnergy();
        
        void applySingleMoveInPlace(const SingleMove& move);
        
        bool isValidSingleMove(const SingleMove& move) const;
        
        size_t nextCompatibleSingleMovePos(const size_t pos) const;

        static const biu::Alphabet* getSequenceAlphabet() {
            return &COMMON_ALPHABET;
        }

    // abstract functions (BioMolecule)
        
        virtual double  getEnergy() const;

        RNAFreeEnergy&  operator= (const RNAFreeEnergy& rnaStruct2);

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

    protected:
        
        virtual void moleculeChanged();
    };

} // namespace biu

#endif /*RNAFREEENERGY_HH_*/