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src/biu/AllowedBasePairs.hh

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#ifndef ALLOWEDBASEPAIRS_HH_
#define ALLOWEDBASEPAIRS_HH_

#include <set>

#include "biu/Alphabet.hh"
#include "biu/Matrix.hh"

namespace biu
{
    class AllowedBasePairs {
    private:
        typedef std::pair<Alphabet::AlphElem, Alphabet::AlphElem> BPair;
        
        const Alphabet* alph;
        
        biu::Matrix< bool > allowedPairs ;
        
    public:
        AllowedBasePairs(   const Alphabet* alphabet
                            , const std::string& bps
                            , const bool symmetric = true );
        
        ~AllowedBasePairs();

        bool operator== (const AllowedBasePairs& abp2) const;
        bool operator!= (const AllowedBasePairs& abp2) const;
        
        bool allowedBasePair(   const Alphabet::AlphElem& first,
                                const Alphabet::AlphElem& second) const;
                                
        const Alphabet* getAlphabet() const;
        
        
    };  


} // namespace biu

#include "biu/AllowedBasePairs.icc"

#endif /*ALLOWEDBASEPAIRS_HH_*/