fix problems with motif changes not showing up in sequencebrowser

[mussa.git] / alg / mussa.cpp

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index 295fd49be50b76ea04411d551cb4ffbbb602cf30..f75290c58705c68ea8e7ccb152da253fde976cbb 100644 (file)
--- a/alg/mussa.cpp
+++ b/alg/mussa.cpp
@@ -328,7 +328,7 @@ void Mussa::append_sequence(boost::shared_ptr<Sequence> a_seq)
 }
 
 
-const vector<boost::shared_ptr<Sequence> >& 
+const vector<SequenceRef>& 
 Mussa::sequences() const
 {
   return the_seqs;
@@ -794,7 +794,7 @@ void Mussa::load_motifs(fs::path filename)
 void Mussa::load_motifs(std::istream &in)
 {
   std::string data;
-  const char *alphabet = Alphabet::nucleic_cstr;
+  const char *alphabet = Alphabet::dna_cstr;
   motif_parser::ParsedMotifs parsed_motifs(motif_sequences, color_mapper);
 
   // slurp our data into a string
@@ -835,7 +835,7 @@ void Mussa::update_sequences_motifs()
 {
   // once we've loaded all the motifs from the file, 
   // lets attach them to the sequences
-  for(vector<boost::shared_ptr<Sequence> >::iterator seq_i = the_seqs.begin();
+  for(vector<SequenceRef >::iterator seq_i = the_seqs.begin();
       seq_i != the_seqs.end();
       ++seq_i)
   {