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src/ell/rna/RNAFreeEnergy.hh

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00001 #ifndef RNAFREEENERGY_HH_
00002 #define RNAFREEENERGY_HH_
00003 
00004 
00005 #include <biu/RNAStructure.hh>
00006 
00007 namespace ell
00008 {
00009 
00018     class RNAFreeEnergy : public biu::RNAStructure
00019     {
00020     protected:
00024         static const biu::AllowedBasePairs      COMMON_BPAIRS;
00025 
00029         static const biu::Alphabet              COMMON_ALPHABET;
00030         
00032         static const double ENERGY_INF; 
00033         
00035         mutable double energy;
00036 
00037     public:
00041         typedef std::pair<size_t, size_t> SingleMove;
00042 
00043         RNAFreeEnergy(  const std::string& rnaSeqStr,
00044                         const std::string& rnaStructBracketDotStr);
00045 
00046         RNAFreeEnergy(  biu::Sequence* rnaSeq,
00047                         const biu::Structure* const rnaStructBracketDot,
00048                         const bool seqIsShared = false);
00049 
00050         RNAFreeEnergy(const RNAFreeEnergy& rnaFreeEnerg);
00051         virtual ~RNAFreeEnergy();
00052         
00058         void applySingleMoveInPlace(const SingleMove& move);
00059         
00065         bool isValidSingleMove(const SingleMove& move) const;
00066         
00074         size_t nextCompatibleSingleMovePos(const size_t pos) const;
00075 
00076         static const biu::Alphabet* getSequenceAlphabet() {
00077             return &COMMON_ALPHABET;
00078         }
00079 
00080     // abstract functions (BioMolecule)
00081         
00085         virtual double  getEnergy() const;
00086 
00087         RNAFreeEnergy&  operator= (const RNAFreeEnergy& rnaStruct2);
00088 
00092     virtual void setStructure(const biu::Structure& str);
00093 
00094     protected:
00095         
00098         virtual void moleculeChanged();
00099     };
00100 
00101 } // namespace biu
00102 
00103 #endif /*RNAFREEENERGY_HH_*/