X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=alg%2Fmussa.cpp;h=4b96d1b4d115a6f12915d1b3fd5a1d082d43212e;hb=f88eea68b95773eb5683dcca6cf3fa59b9f00036;hp=f205fe4d0ab01b98019ea110f4f94a808e3d5a02;hpb=1c6bc3823f973cee4880ee2ef87d0598567da73f;p=mussa.git

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index f205fe4..4b96d1b 100644
--- a/alg/mussa.cpp
+++ b/alg/mussa.cpp
@@ -32,8 +32,8 @@ Mussa::Mussa()
   : color_mapper(new AnnotationColors)
 {
   clear();
-  connect(&the_paths, SIGNAL(progress(const std::string&, int, int)), 
-          this, SIGNAL(progress(const std::string&, int, int)));
+  connect(&the_paths, SIGNAL(progress(const QString&, int, int)), 
+          this, SIGNAL(progress(const QString&, int, int)));
 }
 
 Mussa::Mussa(const Mussa& m)
@@ -49,8 +49,14 @@ Mussa::Mussa(const Mussa& m)
     analysis_path(m.analysis_path),
     dirty(m.dirty)
 {
-  connect(&the_paths, SIGNAL(progress(const std::string&, int, int)), 
-          this, SIGNAL(progress(const std::string&, int, int)));
+  connect(&the_paths, SIGNAL(progress(const QString&, int, int)), 
+          this, SIGNAL(progress(const QString&, int, int)));
+}
+
+MussaRef Mussa::init() 
+{
+  boost::shared_ptr<Mussa> m(new Mussa());
+  return m;
 }
 
 boost::filesystem::path Mussa::get_analysis_path() const
@@ -322,7 +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;
@@ -788,7 +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