store motifs as sequences instead of strings

[mussa.git] / alg / mussa.hpp

diff --git a/alg/mussa.hpp b/alg/mussa.hpp
index 2d497f7c4bd0c9b9d7d31b232e6f7ae9c8719485..5713a6dd9f0523bc8a71968c6ba09c0596f6f14f 100644 (file)
--- a/alg/mussa.hpp
+++ b/alg/mussa.hpp
@@ -146,14 +146,14 @@ public:
 
     // manage motif lists 
     //! add a motif it wont be applied until update_sequences_motif is called
-    void add_motif(const std::string& motifs, const Color& colors);
+    void add_motif(const Sequence& motifs, const Color& colors);
     //! add vector of motifs and colors to our motif collection 
     /*! this will automatically call update_sequences_motif
      *  this depends on sets and color maps being unique
      *  (aka if you add the same item more than once it doesn't
      *  increase the size of the data structure)
      */
-    void set_motifs(const std::vector<std::string>& motifs, 
+    void set_motifs(const std::vector<Sequence>& motifs, 
                     const std::vector<Color>& colors);
     //! load motifs from an ifstream
     /*! The file should look something like
@@ -166,7 +166,7 @@ public:
     //! load a list of motifs from a file named filename
     void load_motifs(boost::filesystem::path filename);
     //! return our motifs;
-    const std::set<std::string>& motifs() const;
+    const std::set<Sequence>& motifs() const;
 
     //! return color mapper
     boost::shared_ptr<AnnotationColors> colorMapper();
@@ -200,7 +200,7 @@ public:
     NwayPaths the_paths;
 
     //! motif list
-    std::set<std::string> motif_sequences;
+    std::set<Sequence> motif_sequences;
     //! color manager
     boost::shared_ptr<AnnotationColors> color_mapper;