alg/seq.hpp

   1 #ifndef SEQ_HPP_
   2 #define SEQ_HPP_
   3
   4 #include <string>
   5
   6 #include <boost/serialization/base_object.hpp>
   7 #include <boost/serialization/export.hpp>
   8 #include <boost/serialization/list.hpp>
   9 #include <boost/serialization/nvp.hpp>
  10 #include <boost/serialization/string.hpp>
  11 #include <boost/serialization/shared_ptr.hpp>
  12 #include <boost/serialization/utility.hpp>
  13 #include <boost/serialization/version.hpp>
  14 #include <boost/serialization/vector.hpp>
  15
  16 #include <boost/shared_ptr.hpp>
  17
  18 #include "alphabet.hpp"
  19 //! These classes provide for the internal implementation for the Sequence class
  20
  21 /** the only purpose of this class is that the shared_ptr template
  22  * functions need the serialization support to be in-class.
  23  */
  24
  25 class SeqString : public std::string
  26 {
  27 public:
  28   typedef std::string::difference_type difference_type;
  29   typedef std::string::iterator iterator;
  30   typedef std::string::reverse_iterator reverse_iterator;
  31   typedef std::string::const_iterator const_iterator;
  32   typedef std::string::const_reverse_iterator const_reverse_iterator;
  33   typedef std::string::reference reference;
  34   typedef std::string::const_reference const_reference;
  35   typedef std::string::size_type size_type;
  36   typedef std::string::value_type value_type;
  37   static const size_type npos = std::string::npos;
  38
  39   SeqString(AlphabetRef a=reduced_nucleic_alphabet) :
  40     std::string(),
  41     alphabet(a),
  42     rc_map(Alphabet::get_alphabet(a).get_complement_map())
  43   {}
  44   SeqString(const std::string &s, AlphabetRef a=reduced_nucleic_alphabet) :
  45     std::string(s),
  46     alphabet(a),
  47     rc_map(Alphabet::get_alphabet(a).get_complement_map())
  48   {}
  49
  50   AlphabetRef get_alphabet_ref() { return alphabet; }
  51   const Alphabet& get_alphabet() const;
  52
  53   std::string create_reverse_complement_map() const;
  54
  55 private:
  56   AlphabetRef alphabet;
  57 public:
  58   const std::string rc_map;
  59 private:
  60   friend class boost::serialization::access;
  61   template<class Archive>
  62   void serialize(Archive& ar, const unsigned int /*version*/) {
  63     //ar & BOOST_SERIALIZATION_BASE_OBJECT_NVP(std::string);
  64     ar & boost::serialization::make_nvp("bases",
  65       boost::serialization::base_object<std::string>(*this)
  66     );
  67     ar & BOOST_SERIALIZATION_NVP(alphabet);
  68   }
  69 };
  70 typedef boost::shared_ptr<SeqString> SeqStringRef;
  71
  72 #endif /*SEQ_HPP_*/