test annotating a sequence with fasta records in a stream

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index d476dfef2b9a3347a9706a57d295073c32c8f663..fc8a0cfe7b2eea9d2690f5adfdc9af5b0b175544 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -203,7 +203,7 @@ 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 
    */
@@ -228,9 +228,11 @@ 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;