implement alphabet for sequence

[mussa.git] / alg / mussa.cpp

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index 47a6b0fe464e72670a0e55b2726d8001ece47de6..50991c1e1d1411a574f9663b6f43ffbacfa8a0ef 100644 (file)
--- a/alg/mussa.cpp
+++ b/alg/mussa.cpp
@@ -792,7 +792,7 @@ struct push_back_motif {
   void operator()(std::string::const_iterator, 
                   std::string::const_iterator) const 
   {
-    Sequence seq(seq_string);
+    Sequence seq(seq_string, Sequence::nucleic_alphabet);
     // shouldn't we have a better field than "fasta header" and speices?
     seq.set_fasta_header(name);
     // we need to clear the name in case the next motif doesn't have one.
@@ -809,7 +809,7 @@ struct push_back_motif {
 void Mussa::load_motifs(std::istream &in)
 {
   std::string data;
-  const char *alphabet = Sequence::nucleic_iupac_alphabet.c_str();
+  const char *alphabet = Alphabet::nucleic_alphabet.c_str();
   string seq;
   string name;
   float red = 1.0;