Remove prototype boost serialiation code.

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 1a4c9eb7a1e6d93079d6a98179efa24469fe6450..706f499f29a48596a0471245448a61568ff0535f 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -17,16 +17,6 @@
 #include <boost/filesystem/path.hpp>
 #include <boost/filesystem/fstream.hpp>
 
-#include <boost/serialization/base_object.hpp>
-#include <boost/serialization/export.hpp>
-#include <boost/serialization/list.hpp>
-#include <boost/serialization/nvp.hpp>
-#include <boost/serialization/string.hpp>
-#include <boost/serialization/shared_ptr.hpp>
-#include <boost/serialization/utility.hpp>
-#include <boost/serialization/version.hpp>
-#include <boost/serialization/vector.hpp>
-
 #include <boost/shared_ptr.hpp>
 #include <boost/enable_shared_from_this.hpp>
 
@@ -69,7 +59,6 @@ private:
     ar & BOOST_SERIALIZATION_NVP(sequence);
   }
 };
-BOOST_CLASS_EXPORT(motif);
 
 class Sequence;
 typedef boost::shared_ptr<Sequence> SequenceRef;
@@ -78,6 +67,8 @@ typedef boost::shared_ptr<Sequence> SequenceRef;
 class Sequence 
 {
 public:
+
+
   typedef SeqString::value_type value_type;
   typedef SeqString::difference_type difference_type;
   typedef SeqString::iterator iterator;
@@ -203,7 +194,7 @@ public:
   void load_annot(const boost::filesystem::path file_path, int start_index, int end_index);
   //! load sequence annotations
   //! \throws mussa_load_error 
-  void load_annot(std::fstream& data_stream, int start_index, int end_index);
+  void load_annot(std::istream& data_stream, int start_index, int end_index);
   //! parse annotation file
   /*! \throws annotation_load_error 
    */
@@ -254,16 +245,6 @@ protected:
   //! look for a string sequence type and and it to an annotation list
   void add_string_annotation(std::string a_seq, std::string name);
   
-  // boost::serialization support
-  friend class boost::serialization::access;
-  template<class Archive>
-  void serialize(Archive& ar, const unsigned int /*version*/) {
-    ar & BOOST_SERIALIZATION_NVP(seq);
-    ar & BOOST_SERIALIZATION_NVP(header);
-    ar & BOOST_SERIALIZATION_NVP(species);
-    ar & BOOST_SERIALIZATION_NVP(annotation_list);
-    ar & BOOST_SERIALIZATION_NVP(motif_list);
-  }
 };
-BOOST_CLASS_EXPORT(Sequence);
+
 #endif