common_subsequence.hpp

Go to the documentation of this file.

#ifndef COMMON_SUBSEQUENCE_HPP_
#define COMMON_SUBSEQUENCE_HPP_
//#include "boost/container/flat_set.hpp"
#include "boost/assert.hpp"
#include "vdj_pipe/detail/vector_set.hpp"
#include "vdj_pipe/sequence_position.hpp"

namespace vdj_pipe{ namespace gdst{

struct Common_subseq {
   explicit Common_subseq(const unsigned start = 0, const unsigned len = 0)
   : start_(start), len_(len)
   {}

   unsigned start_; 
   unsigned len_; 

//   boost::container::flat_set<super_seq> seq_;
   detail::Vector_set<super_seq> seq_;
};

inline bool mismatching_end(
         const unsigned start1,
         const unsigned len1,
         const unsigned start2,
         const unsigned len2,
         const unsigned match_len
) {
   BOOST_ASSERT(start1 + match_len <= len1);
   BOOST_ASSERT(start2 + match_len <= len2);
   return
            (start1 && start2) ||
            ( start1 + match_len != len1 && start2 + match_len != len2 )
            ;
}

}//namespace gdst
}//namespace vdj_pipe
#endif /* COMMON_SUBSEQUENCE_HPP_ */