switch to using boost::filesystem

[mussa.git] / alg / mussa.hpp

diff --git a/alg/mussa.hpp b/alg/mussa.hpp
index b4a6e26d4638d5cbed7dc1f25c29ffc7d9a3ad41..675658d4a65ad55a2b2f71076a48f363afe87cdb 100644 (file)
--- a/alg/mussa.hpp
+++ b/alg/mussa.hpp
@@ -13,6 +13,7 @@
 //                        ----------------------------------------
 //                          ---------- mussa_class.hh -----------
 //                        ----------------------------------------
+#include <boost/filesystem/path.hpp>
 
 #include <list>
 #include <string>
@@ -37,15 +38,16 @@ class Mussa
     Mussa(const Mussa &);
 
     void save();
-    void save_muway(std::string save_path);
+    //! save the nway comparison
+    void save_muway(boost::filesystem::path save_path);
     //! load a saved analysis directory
-    void load(std::string ana_path);
+    void load(boost::filesystem::path ana_path);
 
     //! clear parameters and initialize data lists
     void clear();
 
-    // set parameters from a file - 'mupa' ~ mussa parameters
-    void load_mupa_file(std::string para_file_path);
+    //! set parameters from a file - 'mupa' ~ mussa parameters
+    void load_mupa_file(boost::filesystem::path para_file_path);
 
     // set parameters individually (eg from user input into gui classes)
     //! set analysis name
@@ -105,7 +107,8 @@ class Mussa
      *  \param[in] sub_seq_end ending slice index to select a subsequence
      *             use 0 to go to the end.
      */
-    void load_sequence(std::string seq_file, std::string annot_file, 
+    void load_sequence(boost::filesystem::path seq_file, 
+                       boost::filesystem::path annot_file, 
                        int fasta_index, int sub_seq_start=0, int sub_seq_end=0);
     //! allow examining the sequences we have loaded
     const std::vector<Sequence>& sequences() const;
@@ -132,7 +135,7 @@ class Mussa
      */
     void load_motifs(std::istream &);
     //! load a list of motifs from a file named filename
-    void load_motifs(std::string filename);
+    void load_motifs(boost::filesystem::path filename);
     //! return our motifs;
     const std::set<std::string>& motifs() const;