Code cleanup, mostly commented code deleted

dbc.cpp

@@ -234,7 +234,7 @@ int main(int argc, char* argv[])
 	  exit(1);
 	}
 
-      ofstream outstream3;
+      /*      ofstream outstream3;
       string outfile3 = path+"/"+bfn+"/bin_corrections_unlikelies.txt"; 
       outstream3.open(outfile3.c_str(), ios::out | ios::app);
       if(outstream3.fail())
@@ -242,6 +242,7 @@ int main(int argc, char* argv[])
 	  cout<<"Failed to open outstream3 to "<<outfile3<<endl;
 	  exit(1);
 	}
+      */
 
       outstream<<num_bins<<endl<<endl;
 
@@ -330,8 +331,8 @@ int main(int argc, char* argv[])
 		    }
 
 		  outstream<<endl;
-		  outstream3<<i<<" to "<<j<<endl;
-		  outstream3<<uscore<<endl<<most_unlikely<<endl<<endl;
+		  //		  outstream3<<i<<" to "<<j<<endl;
+		  //		  outstream3<<uscore<<endl<<most_unlikely<<endl<<endl;
 		}		  
 	    }	  
 	}

org.h

@@ -26,7 +26,7 @@ class org
   int total_num_aa;                  //total number of amino acids in the proteome
   int total_num_proteins;          //total number of proteins in the proteome
   int tag_length;
-  bool conserved; //what the hell is this?
+  bool conserved; 
   int filtering_steps;
   
   vector<string> files;            //e.g. NC_021726.faa
@@ -93,14 +93,12 @@ class org
     
   void fill_fields(string dir_par);
   void generate_tags(bool do_scrambled, bool partial_run);
-  //  void generate_scrambled_tags();
   void clear_tags();
   void clear_scr_tags();
   void write_out_aa_array(ofstream& outstream);
   int mark_keepers(vector<string> keepers);
   void write_out_gene(int index);
   void clear_proteins();
-  //  void increment_ggs(int gene_id,int gnums_size,int vector_size);
   void increment_ggs(int gene_id,int gnums_size,int vector_size,double d);
   void write_out_new_proteome(int index);
   void add_file(string s);
@@ -115,14 +113,6 @@ class org
   void write_filtered_set(ofstream& outstream, int filt_option);
   
   //GETTERS AND SETTERS
-  //void add_file(string f);
-  
-  //void set_uid(string u);
-  //vector<string> get_files();
-  
-  //string get_uid();
-  //string get_path();
-  //string get_bfn();
   int get_ordinal();
 };
 
@@ -161,11 +151,6 @@ void org::generate_tags(bool do_scrambled, bool partial_run)
   p.generate_tags(ordinal,do_scrambled,partial_run);
 }
 
-/*void org::generate_scrambled_tags()
-{
-  p.generate_scrambled_tags(ordinal);
-}
-*/
 void org::set_ordinal(int i)
 {
   ordinal=i;  
@@ -173,7 +158,6 @@ void org::set_ordinal(int i)
 
 void org::setp_set_keeper(int index,int i)
 {
-  //  cout<<"In setp_set_keeper(int,int): "<<index<<" "<<i<<endl;
   p.set_keeper(index,i);
 }
 
@@ -202,12 +186,6 @@ void org::setp_size_real_tags(int i)
   p.set_size_real_tags(i);
 }
 
-/*void org::setp_set_pv_val(int index,int i1, int i2, int i3, int i4, int i5)
-{
-  p.set_pv_val(index,i1,i2,i3,i4,i5);
-}
-*/
-
 void org::setp_set_pvv_gnums_val(int index, vector<int> vals)
 {
   p.set_pvv_gnums_val(index,vals);
@@ -232,11 +210,6 @@ void org::setp_chosen_column(int i)
   p.set_chosen_column(i);
 }
 
-/*void org::setp_set_pv_size(int i)
-{
-  p.set_pv_size(i);
-  }*/
-    
 void org::setp_set_pvv_size(int i)
 {
   p.set_pvv_size(i);
@@ -339,11 +312,7 @@ int org::read_faa_file(int i,int& total_aa)
 	      instream>>eater;
 	    }
 	  //we now have both the info_line and the protein sequence.
-	  //cout<<"Adding a protein"<<endl;
-	  //cout<<info_line<<endl;
 	  p.add_protein(info_line,aaseq);
-	  //cout<<"info_line = "<<info_line<<endl;
-	  //cout<<"aaseq = "<<aaseq<<endl;
 	  add_aa_counts(aaseq);
 	  result+=aaseq.length();
 	  aaseq="";
@@ -376,19 +345,6 @@ int org::get_tags_size()
   return p.get_tags_size();
 }
 
-/*
-//GETTERS AND SETTERS
-void org::add_file(string f)
-{
-  files.push_back(f);
-}
-
-vector<string> org::get_files()
-{
-  return files;
-}
-*/
-
 string org::get_file(int i)
 {
   if(i>=0 && i<files.size())
@@ -421,18 +377,7 @@ string org::get_directory()
 {
   return directory;
 }
-/*
-void org::set_uid(string u)
-{
-  uid = u;
-}
-
-string org::get_uid()
-{
-  return uid;
-}
 
-*/
 void org::set_path(string p)
 {
   path = p;
@@ -448,15 +393,6 @@ void org::set_dir(string s)
   dir=s;
 }
 
-
-/*
-string org::get_path()
-{
-  return path;
-}
-
-*/
-
 void org::add_aa_counts(string s)
 {
   for(int i=0; i<s.length(); i++)
@@ -489,13 +425,6 @@ void org::write_out_aa_array(ofstream& outstream)
     }
 }
 
-/*
-string org::get_bfn()
-{
-  return bfn;
-}
-*/
-
 string org::get_dir()
 {
   return dir;
@@ -520,7 +449,7 @@ void org::mark_gene_internal_repeats(int index)
 
 void org::write_out_gene(int index)
 {
-  p.print_protein_info(index);
+  //  p.print_protein_info(index);
 }
 
 void org::clear_proteins()
@@ -528,11 +457,6 @@ void org::clear_proteins()
   p.clear_proteins();
 }
 
-/*void org::increment_ggs(int gene_id,int gnums_size,int vector_size)
-{
-  p.increment_ggs(gene_id,gnums_size,vector_size);
-  }*/
-
 void org::increment_ggs(int gene_id,int gnums_size,int vector_size,double d)
 {
   p.increment_ggs(gene_id,gnums_size,vector_size,d);
@@ -546,24 +470,14 @@ void org::write_out_new_proteome(int index)
   cout<<"dir = "<<dir<<endl;
   cout<<"directory = "<<directory<<endl;
 
-  /*
-  string outcommand = "rm -r "+path+"/FAA_new/"+directory;
-  int system_return = system(outcommand.c_str());
-  outcommand = "mkdir "+path+"/FAA_new/"+directory;
-  system_return = system(outcommand.c_str());
-  */
-
   stringstream ss;
   ss<<index;
   string col;
   ss>>col;
 
-  //string s = path+bfn+"/FAA_new_col"+col+"/"+directory;
-  //cout<<"s = "<<s<<endl;
   vector<pair<int,int> > mscv;
   populate_mscv(mscv);
   p.write_out_new_proteome_v2(path,directory,files,ordinal,mscv,index);
-  //instream.open( (path+"/"+dir+"/"+directory+"/"+files.at(i)).c_str() );
 }
 
 void org::add_file(string s)
@@ -636,7 +550,6 @@ void org::populate_mscv(vector<pair<int,int> >& mscv)
   instream.open(infile.c_str());
   if(instream.fail())
     {
-      //Just leave it alone. File doesn't exist. Leave mscv empty.
     }
   else
     {
@@ -654,7 +567,6 @@ void org::populate_mscv(vector<pair<int,int> >& mscv)
 	      foo.first=gene_id;
 	      foo.second=count;
 	      mscv.push_back(foo);
-	      //mscv[gene_id]=count;
 	      instream>>gnum>>gene_id>>count;
 	    }
 	}

protein.h

@@ -17,13 +17,10 @@ class protein
   int gene_ids;
   bool deleter;
   bool manually_include; //beats deleter.
-  //set<int> genome_hits;
 
  public:
   protein();
   void mark_keeper();
-  //void add_hit(int i);
-  //void write_genome_hits(ofstream& outstream);
   void add_gnums(int i);
   void add_gis(int i);
   void mark_for_deletion();
@@ -40,7 +37,6 @@ class protein
   //getters
   string get_sequence();
   string get_info_line();
-  //int get_genome_hits_size();
   int get_gnums();
   int get_geneids();
   bool get_deleter();
@@ -77,41 +73,16 @@ void protein::set_id(int i)
   id = i;
 }
 
-/*void protein::add_hit(int i)
-{
-  genome_hits.insert(i);
-}
-*/
-
 string protein::get_sequence()
 {
   return sequence;
 }
 
-
-/*void protein::write_genome_hits(ofstream& outstream)
-{
-  set<int>::iterator it;
-  for(it=genome_hits.begin(); it!=genome_hits.end(); ++it)
-    {
-      outstream<<*it<<" ";
-    }
-  outstream<<endl;
-}
-*/
-
 string protein::get_info_line()
 {
   return info_line;
 }
 
-/*
-int protein::get_genome_hits_size()
-{
-  return genome_hits.size();
-}
-*/
-
 void protein::add_gnums(int i)
 {
   gnums+=i;
@@ -151,12 +122,8 @@ void protein::reset_deleters()
 {
   if(deleter)
     {
-      cout<<"reset_deleters for: "<<endl;
       print_protein_info();
       gnums=0;
-      //int staller;
-      //cout<<"Stalling: ";
-      //cin>>staller;
     }
 }