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>
#include "sequence.hh"
 
namespace LocARNA {
 
    class Alignment;
    class Sequence;
    class RnaData;
    class Scoring;
 
    class AlignmentImpl {
    public:
        const Sequence seqA_; 
        const Sequence seqB_; 
 
        Alignment::edges_t edges_;
 
        std::string strA_; 
        std::string strB_; 
 
        AlignmentImpl(const Sequence &seqA,
                      const Sequence &seqB)
            : seqA_(seqA),
              seqB_(seqB),
              edges_(),
              strA_(),
              strB_() {}
 
 
        bool
        empty() const { return edges_.empty(); }
 
    };
 
} // end namespace LocARNA
 
#endif // LOCARNA_ALIGNMENT_IMPL_HH