switch to using boost::filesystem

[mussa.git] / alg / sequence.hpp

diff --git a/alg/sequence.hpp b/alg/sequence.hpp
index 85fd692fa02475d9c369cd1dcb836500ad3d1966..06dd3fad5125560a37cd5d26c5c6bc08ad98118d 100644 (file)
--- a/alg/sequence.hpp
+++ b/alg/sequence.hpp
@@ -14,8 +14,8 @@
 //                           ---------- sequence.hh -----------
 //                        ----------------------------------------
 
-
-#include <fstream>
+#include <boost/filesystem/path.hpp>
+#include <boost/filesystem/fstream.hpp>
 #include <list>
 #include <string>
 #include <vector>
@@ -83,12 +83,12 @@ class Sequence
     //! load sequence AGCT from fasta file
     /*! \throws mussa_load_error 
      */
-    void load_fasta(const std::string file_path, int seq_num=1, 
+    void load_fasta(const boost::filesystem::path file_path, int seq_num=1, 
                     int start_index=0, int end_index=0);
     //! load sequence annotations
     /*! \throws mussa_load_error 
      */
-    void load_annot(const std::string file_path, int start_index, int end_index);
+    void load_annot(const boost::filesystem::path file_path, int start_index, int end_index);
     const std::list<annot>& annotations() const;
     const std::list<motif>& motifs() const;
     const std::string& get_species() const;
@@ -127,7 +127,7 @@ class Sequence
     /*! \throws motif_normalize_error if there is an invalid symbol
      */
     static std::string motif_normalize(std::string a_motif);
-    void save(std::fstream &save_file);
-    void load_museq(std::string load_file_path, int seq_num); 
+    void save(boost::filesystem::fstream &save_file);
+    void load_museq(boost::filesystem::path load_file_path, int seq_num); 
 };
 #endif