test motif editor

[mussa.git] / alg / mussa.cpp

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index 58558ff6e14b498c3679c7bcc4dfea41fc5223dc..4b96d1b4d115a6f12915d1b3fd5a1d082d43212e 100644 (file)
--- 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;
@@ -635,8 +641,8 @@ Mussa::load(fs::path ana_file)
 
   analysis_path = ana_file;
   analysis_name = ana_path.leaf();
-  file_path_base =  ana_path.branch_path() / analysis_name;
-  a_file_path = file_path_base / (analysis_name + ".muway");
+  fs::path muway(analysis_name+".muway", fs::native);
+  a_file_path = analysis_path / muway;
   the_paths.load(a_file_path);
   // perhaps this could be more elegent, but at least this'll let
   // us know what our threshold and window sizes were when we load a muway
@@ -646,7 +652,8 @@ Mussa::load(fs::path ana_file)
 
   int seq_num = the_paths.sequence_count();
 
-  a_file_path = file_path_base / (analysis_name + ".museq");
+  fs::path museq(analysis_name + ".museq", fs::native);
+  a_file_path = analysis_path / museq;
 
   // this is a bit of a hack due to C++ not acting like it should with files
   for (i = 1; i <= seq_num; i++)
@@ -656,7 +663,8 @@ Mussa::load(fs::path ana_file)
     the_seqs.push_back(tmp_seq);
   }
   
-  fs::path motif_file = file_path_base / (analysis_name + ".mtl");
+  fs::path mtl(analysis_name + ".mtl", fs::native);
+  fs::path motif_file = analysis_path / mtl;
   if (fs::exists(motif_file)) {
     load_motifs(motif_file);
   }
@@ -675,15 +683,13 @@ Mussa::load(fs::path ana_file)
       append_info.str("");
       append_info << analysis_name <<  "_sp_" << i << "v" << i2 << ".flp";
       //clog << append_info.str() << endl;
-      a_file_path = file_path_base / append_info.str();
-      //clog << "path " << a_file_path.string() << endl;
+      fs::path flp(append_info.str(), fs::native);
+      a_file_path = analysis_path / flp;
       all_comps[i][i2].load(a_file_path);
-      //clog << "real size = " << all_comps[i][i2].size() << endl;
     }
   }
 }
 
-
 void
 Mussa::save_old()
 {
@@ -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