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