store motifs as sequences instead of strings

[mussa.git] / alg / mussa.cpp

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index af704e8e696d64250b7b12fe9a954dda4596b089..44f9adb47b0726fd10874febad5a9fc6b1fef65e 100644 (file)
--- a/alg/mussa.cpp
+++ b/alg/mussa.cpp
@@ -714,13 +714,13 @@ Mussa::load_old(char * load_file_path, int s_num)
   //the_paths.save("tmp.save");
 }
 
-void Mussa::add_motif(const string& motif, const Color& color)
+void Mussa::add_motif(const Sequence& motif, const Color& color)
 {
   motif_sequences.insert(motif);
   color_mapper->appendInstanceColor("motif", motif, color);
 }
 
-void Mussa::set_motifs(const vector<string>& motifs, 
+void Mussa::set_motifs(const vector<Sequence>& motifs, 
                        const vector<Color>& colors)
 {
   if (motifs.size() != colors.size()) {
@@ -804,7 +804,7 @@ void Mussa::update_sequences_motifs()
     // clear out old motifs
     (*seq_i)->clear_motifs();
     // for all the motifs in our set, attach them to the current sequence
-    for(set<string>::iterator motif_i = motif_sequences.begin();
+    for(set<Sequence>::iterator motif_i = motif_sequences.begin();
         motif_i != motif_sequences.end();
         ++motif_i)
     {
@@ -813,7 +813,7 @@ void Mussa::update_sequences_motifs()
   }
 }
 
-const set<string>& Mussa::motifs() const
+const set<Sequence>& Mussa::motifs() const
 {
   return motif_sequences;
 }