finish implementing annotation by sequence

[mussa.git] / alg / sequence.cpp

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index f3f68a80431bfa7dabfa7139994b361d9fcdd6c8..d7b4acd9c9f78c9f4c90e96fc3f145d3a2f2c396 100644 (file)
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -275,7 +275,7 @@ struct push_back_annot {
   void operator()(std::string::const_iterator, 
                   std::string::const_iterator) const 
   {
-    std::cout << "adding annot: " << begin << " " << end << " " << name << " " << type << std::endl;
+    //std::cout << "adding annot: " << begin << " " << end << " " << name << " " << type << std::endl;
     annot_list.push_back(annot(begin, end, name, type));
   };
 };
@@ -305,7 +305,7 @@ struct push_back_seq {
     {
       if (*seq_i != '\n') new_seq += *seq_i;
     }
-    std::cout << "adding seq: " << name << " " << new_seq << std::endl;
+    //std::cout << "adding seq: " << name << " " << new_seq << std::endl;
     
     Sequence s(new_seq);
     s.set_header(name);
@@ -360,6 +360,9 @@ Sequence::parse_annot(std::string data, int start_index, int end_index)
                 //end grammar
                 ) /*,
                 spirit::space_p*/).full;
+                
+  // go seearch for query sequences 
+  find_sequences(query_seqs.begin(), query_seqs.end());
 }
 
 /*
@@ -937,6 +940,8 @@ void Sequence::add_string_annotation(std::string a_seq,
                                      std::string name)
 {
   std::vector<int> seq_starts = find_motif(a_seq);
+  
+  //std::cout << "searching for " << a_seq << " found " << seq_starts.size() << std::endl;
 
   for(std::vector<int>::iterator seq_start_i = seq_starts.begin();
       seq_start_i != seq_starts.end();