fix many mussa_class.cxx warnings

Got rid of a bunch of signed vs unsigned warning messages by using size_type,
and also put the bodies of a few if or for statements in { }

diff --git a/alg/mussa_class.cxx b/alg/mussa_class.cxx
index 8992446af61b8f8aa2359efbeb0a924d351ff7fe..64286aa04d07a02496ead24361257de6358928a1 100644 (file)
--- a/alg/mussa_class.cxx
+++ b/alg/mussa_class.cxx
@@ -169,7 +169,6 @@ Mussa::load_mupa_file(string para_file_path)
   int sub_seq_start, sub_seq_end;
   bool seq_params, did_seq;
   string err_msg;
-  int bogo;
   bool parsing_path;
   int new_index, dir_index;
 
@@ -298,7 +297,7 @@ void
 Mussa::analyze(int w, int t, enum Mussa::analysis_modes the_ana_mode, double new_ent_thres)
 {
   time_t t1, t2, begin, end;
-  double setuptime, seqloadtime, seqcomptime, nwaytime, savetime, totaltime;
+  double seqloadtime, seqcomptime, nwaytime, savetime, totaltime;
 
   begin = time(NULL);
 
@@ -406,24 +405,23 @@ Mussa::load_sequence_data()
 void
 Mussa::seqcomp()
 {
-  int i, i2;     // loop vars over sequences to analyze
   vector<int> seq_lens;
   vector<FLPs> empty_FLP_vector;
   FLPs dummy_comp;
   string save_file_string;
 
   empty_FLP_vector.clear();
-  for(i = 0; i < the_seqs.size(); i++)
+  for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
   {
     all_comps.push_back(empty_FLP_vector); 
-    for(i2 = 0; i2 < the_seqs.size(); i2++)
+    for(vector<Sequence>::size_type i2 = 0; i2 < the_seqs.size(); i2++)
       all_comps[i].push_back(dummy_comp);
   }
-  for(i = 0; i < the_seqs.size(); i++)
+  for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
     seq_lens.push_back(the_seqs[i].size());
 
-  for(i = 0; i < the_seqs.size(); i++)
-    for(i2 = i+1; i2 < the_seqs.size(); i2++)
+  for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+    for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
     {
       cout << "seqcomping: " << i << " v. " << i2 << endl;
       all_comps[i][i2].setup(window, threshold);
@@ -436,22 +434,23 @@ void
 Mussa::nway()
 {
   vector<string> some_Seqs;
-  int i;
 
   the_paths.set_soft_thres(soft_thres);
 
-  if (ana_mode == TransitiveNway)
+  if (ana_mode == TransitiveNway) {
     the_paths.trans_path_search(all_comps);
-
-  else if (ana_mode == RadialNway)
+  }
+  else if (ana_mode == RadialNway) {
     the_paths.radiate_path_search(all_comps);
-
+  }
   else if (ana_mode == EntropyNway)
   {
     //unlike other methods, entropy needs to look at the sequence at this stage
     some_Seqs.clear();
-    for(i = 0; i < the_seqs.size(); i++)
+    for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+    {
       some_Seqs.push_back(the_seqs[i].get_seq());
+    }
 
     the_paths.setup_ent(ent_thres, some_Seqs); // ent analysis extra setup
     the_paths.entropy_path_search(all_comps);
@@ -470,7 +469,7 @@ Mussa::save()
   string save_name, save_path, create_dir_cmd, flp_filepath;
   fstream save_file;
   ostringstream append_info;
-  int i, i2, dir_create_status;
+  int dir_create_status;
 
 
   // not sure why, but gotta close file each time since can't pass file streams
@@ -512,8 +511,10 @@ Mussa::save()
   save_file << "<Mussa_Sequence>" << endl;
   //save_file.close();
 
-  for(i = 0; i < the_seqs.size(); i++)
+  for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+  {
     the_seqs[i].save(save_file);
+  }
 
   //save_file.open(save_path.c_str(), ios::app);
   save_file << "</Mussa_Sequence>" << endl;
@@ -526,8 +527,8 @@ Mussa::save()
   //save_path = file_path_base + save_name + "/" + save_name + ".muway"; //os X
   the_paths.save(save_path);
 
-  for(i = 0; i < the_seqs.size(); i++)
-    for(i2 = i+1; i2 < the_seqs.size(); i2++)
+  for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
+    for(vector<Sequence>::size_type i2 = i+1; i2 < the_seqs.size(); i2++)
     {
       append_info.str("");
       append_info <<  "_sp_" << i << "v" << i2;
@@ -634,11 +635,10 @@ void
 Mussa::save_old()
 {
   fstream save_file;
-  int i;
 
   save_file.open(analysis_name.c_str(), ios::out);
 
-  for(i = 0; i < the_seqs.size(); i++)
+  for(vector<Sequence>::size_type i = 0; i < the_seqs.size(); i++)
     save_file << the_seqs[i].get_seq() << endl;
 
   save_file << window << endl;