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src/biu/RNAStructure.hh

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#ifndef RNASTRUCTURE_HH_
#define RNASTRUCTURE_HH_


#include "BioMolecule.hh"
#include "AllowedBasePairs.hh"

namespace biu
{
    class RNAStructure : public BioMolecule
    {
    protected:
        
        Sequence*       rnaSeq;
        
        const bool      seqShared;
        
        static const size_t MIN_LOOP_LENGTH;

        static const Alphabet           STRUCT_ALPH;

        Structure*      rnaStructBracketDot;
        
        std::vector<size_t> rnaBonds;
        
        const AllowedBasePairs*     bPair;
        
    public:
    
        static const Alphabet::AlphElem STRUCT_BND_OPEN;
        static const Alphabet::AlphElem STRUCT_BND_CLOSE;
        static const Alphabet::AlphElem STRUCT_UNBOUND;
        
        static const size_t INVALID_INDEX;

        RNAStructure(   const std::string& rnaSeqStr, 
                        const std::string& rnaStructBracketDotStr, 
                        const AllowedBasePairs* const bPair);
                 
        RNAStructure(   Sequence* rnaSeq, 
                        const Structure* const rnaStructBracketDot, 
                        const AllowedBasePairs* const bPair,
                        const bool seqIsShared);
                 
        RNAStructure(const RNAStructure& rnaStruct);
        
        virtual ~RNAStructure();
        
        RNAStructure&   operator= (const RNAStructure& rnaStruct2);
        bool            operator== (const RNAStructure& rnaStruct2) const;
        bool            operator!= (const RNAStructure& rnaStruct2) const;

        bool            hasValidStructure() const;
        
        bool            hasValidBasePairs() const;
        
        bool            hasMinLoopLength() const;
        
        bool isAllowedBasePair(size_t first, size_t second) const;

        size_t getClosingBond(size_t openingBond) const { 
            return rnaBonds[openingBond]; 
        }
        
        size_t getMinLoopLength() const {
            return MIN_LOOP_LENGTH; 
        }

        std::string getSequenceString() const {
            return bPair->getAlphabet()->getString(*rnaSeq);
        }

        std::string getStructureString() const {
            return STRUCT_ALPH.getString(*rnaStructBracketDot);
        }

        static const Alphabet* getStructureAlphabet() {
            return &STRUCT_ALPH;
        }
        
    // abstract functions (BioMolecule)
    
        Sequence getSequence() const {
            assertbiu(rnaSeq != NULL, "no sequence available");
            return *rnaSeq;
        }

        size_t  getLength() const {
            assertbiu(rnaSeq != NULL, "no sequence available");
            return rnaSeq->size();
        }
    
        Structure getStructure() const {
            assertbiu(rnaStructBracketDot != NULL, "no structure available");
            return *rnaStructBracketDot;
        }
        
        virtual void setStructure(const Structure& str) {
            assertbiu(rnaSeq->size() == str.size(), "structure has wrong length");
            delete rnaStructBracketDot;
            rnaStructBracketDot = new Structure(str);
        }
        
        const Structure & getStructureRef() const {
            assertbiu(rnaStructBracketDot != NULL, "no structure available");
            return *rnaStructBracketDot;
        }
        
        
        virtual bool        isValid() const;
        
        virtual std::string getStringRepresentation() const;
        
    protected:
        
        void initBonds();
        
    };
    
} // namespace biu

#endif /*RNASTRUCTURE_HH_*/