refactor glsequence to be more testable

[mussa.git] / alg / nway_paths.cxx

diff --git a/alg/nway_paths.cxx b/alg/nway_paths.cxx
index 2dd22598555f6a8608680b031040825484e6ff09..9471d7237968001cafdd45a13745216bba674fd0 100644 (file)
--- a/alg/nway_paths.cxx
+++ b/alg/nway_paths.cxx
@@ -34,8 +34,8 @@ NwayPaths::setup(int w, int t)
   win_size = w;
   pathz.clear();
 
-  cout << "nway: thres = " << threshold
-       << ", soft threo = " << soft_thres << endl;
+  //cout << "nway: thres = " << threshold
+  //     << ", soft threo = " << soft_thres << endl;
 }
 
 void
@@ -59,7 +59,7 @@ NwayPaths::simple_refine()
 
   refined_pathz.clear();
 
-  cout << "path number is: " << pathz.size() << endl;
+  //cout << "path number is: " << pathz.size() << endl;
   pathz_i = pathz.begin();
 
   // only try to extend when pathz isn't empty.
@@ -88,7 +88,6 @@ NwayPaths::simple_refine()
   
       if (extending)
       {
-        //cout << "Raaaawwwrrr!  I am extending\n";
         win_ext_len++;
       }
       else
@@ -104,7 +103,7 @@ NwayPaths::simple_refine()
       }
     }
   }
-  cout << "r_path number is: " << refined_pathz.size() << endl;
+  //cout << "r_path number is: " << refined_pathz.size() << endl;
 }
 
 
@@ -217,8 +216,8 @@ NwayPaths::load(string load_file_path)
     threshold = atoi (data.c_str());
     file_data_line = file_data_line.substr(space_split_i+1);
     
-    cout << "seq_num=" << species_num << " win=" << win_size;
-    cout << " thres=" << threshold << endl;
+    //cout << "seq_num=" << species_num << " win=" << win_size;
+    //cout << " thres=" << threshold << endl;
     
     // clear out the current data
     refined_pathz.clear();
@@ -301,8 +300,6 @@ NwayPaths::path_search(vector<vector<FLPs> > all_comparisons, ConservedPath path
     ++new_nodes_i;
   }
 }
-//          cout << "    ****I have the power...\n";
-
 /* use this if I ever get the friggin seqcomp match lists to sort...
       if (binary_search(trans_check_nodes.begin(), trans_check_nodes.end(), 
                         *new_nodes_i))
@@ -318,7 +315,6 @@ NwayPaths::find_paths_r(vector<vector<FLPs> > all_comparisons)
 
   pathz.clear();
   window_num = all_comparisons[0][1].size();
-  cout << window_num << endl;
   // loop thru all windows in first species
   for (win_i = 0; win_i < window_num; win_i++)
   {
@@ -329,7 +325,6 @@ NwayPaths::find_paths_r(vector<vector<FLPs> > all_comparisons)
     new_nodes_end = new_nodes.end();
     //if (new_nodes_i != new_nodes_end)
     //cout << "* species 0 node: " << win_i << endl;
-    //  cout << "foookin hell\n";
     path.push_back(0);
     while(new_nodes_i != new_nodes_end)
     {