Update mussa build scripts to work with Boost 1.40 and CMake 2.6

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index c2de433fca1b9602f4c39065054c06f732047016..f7d3c364c868a003ff7db3ceb3238e0ea2b1a90a 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -78,6 +78,8 @@ 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 +205,7 @@ 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 
    */
@@ -215,6 +217,7 @@ public:
   //! create an initialized annotation with the "standard" types.
   SeqSpanRef make_annotation(std::string name, std::string type, size_type start, size_type stop) const;
   const SeqSpanRefList& annotations() const;
+  
   const MotifList& motifs() const;
 
   //! add a motif to our list of motifs
@@ -227,9 +230,11 @@ public:
   //! annotate the current sequence with other sequences
   void find_sequences(std::list<Sequence>::iterator start, 
                      std::list<Sequence>::iterator end);
+  SeqSpanRef seqspan() { return seq; }
   
   void save(boost::filesystem::fstream &save_file);
-  void load_museq(boost::filesystem::path load_file_path, int seq_num);
+  //void load_museq(boost::filesystem::path load_file_path, int seq_num);
+  static SequenceRef load_museq(boost::filesystem::fstream& load_file);
   
 protected:  
   SeqSpanRef seq;
@@ -262,5 +267,7 @@ protected:
     ar & BOOST_SERIALIZATION_NVP(motif_list);
   }
 };
-BOOST_CLASS_EXPORT(Sequence);
+
+//BOOST_CLASS_EXPORT(Sequence);
+//BOOST_CLASS_EXPORT_GUID(Sequence, "Sequence")
 #endif