src/LocARNA/alignment_impl.hh

#ifndef LOCARNA_ALIGNMENT_IMPL_HH
#define LOCARNA_ALIGNMENT_IMPL_HH

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <iosfwd>
#include <vector>

namespace LocARNA {

    template <class T>
    class plusvector;
    class Alignment;
    class Sequence;
    class RnaData;
    class Scoring;

    class AlignmentImpl {
    public:
        Alignment *self_; 

        const Sequence &seqA_; 
        const Sequence &seqB_; 

        Alignment::edge_ends_t a_;

        Alignment::edge_ends_t b_;

        std::string strA_; 
        std::string strB_; 

        AlignmentImpl(Alignment *self,
                      const Sequence &seqA,
                      const Sequence &seqB)
            : self_(self),
              seqA_(seqA),
              seqB_(seqB),
              a_(),
              b_(),
              strA_(),
              strB_() {}

        void
        write_debug(std::ostream &out) const;

        static void
        write_debug(std::ostream &out, const Alignment::edge_ends_t &ends);

        static std::string
        dot_bracket_structure(const std::string &str,
                              const Alignment::edge_ends_t &x);
    };

} // end namespace LocARNA

#endif // LOCARNA_ALIGNMENT_IMPL_HH