algo/core: reindent

algo/core/affectanalyser.cpp

@@ -289,7 +289,7 @@ string KmerAffectAnalyser::toString() const{
 }
 
 string KmerAffectAnalyser::toStringValues() const{
-    string kmer;
+  string kmer;
   for (size_t i = 0; i < affectations.size(); i++) {
     kmer += affectations[i].toStringValues();
   }

algo/core/cluster-junctions.cpp

@@ -88,8 +88,8 @@ void comp_matrix::load(string file){
   for(unsigned int i=0; i<sort_clones.size();i++){
     in_comp.read(tampon, sort_clones.size()*sizeof(char));
     for(unsigned int j=0;j<sort_clones.size(); j++){
-	m[i][j]=tampon[j];
-      }
+      m[i][j]=tampon[j];
+    }
   }
   free(tampon);
 
@@ -157,25 +157,25 @@ list<list<junction> >  comp_matrix::cluster(string forced_edges, int w, ostream
       
       size_t j = 0; 
       for (list <pair<junction,size_t> >::const_iterator it1 = sort_clones.begin();
-        (it1 != sort_clones.end()) & (j<matrix_size); ++it1) 
-      {
-        j++;
-        j2=it1->first;
-        int distance = (int)m[c2][c1];
+	   (it1 != sort_clones.end()) & (j<matrix_size); ++it1) 
+	{
+	  j++;
+	  j2=it1->first;
+	  int distance = (int)m[c2][c1];
             
-        if (distance <= epsilon){
+	  if (distance <= epsilon){
             neighbor[j1].push_back(j2);
-        }
-        c1++;
-        c++;
+	  }
+	  c1++;
+	  c++;
         }//fin it1
-        c2++;
-        c1=0;
-      }//fin it0
+      c2++;
+      c1=0;
+    }//fin it0
     
-/////////////////////////
-//Forced - edges
-    if (forced_edges.size())
+  /////////////////////////
+  //Forced - edges
+  if (forced_edges.size())
     {
       ifstream fe(forced_edges.c_str());
   
@@ -243,7 +243,7 @@ list<list<junction> >  comp_matrix::cluster(string forced_edges, int w, ostream
 	nVoisins=0;
 	
 	for (list<string>::iterator it1 = voisins1.begin();
-	it1 != voisins1.end(); ++it1 ) nVoisins+=count[*it1];
+	     it1 != voisins1.end(); ++it1 ) nVoisins+=count[*it1];
 	
 	if (nVoisins<minPts){
 	  //noise
@@ -268,7 +268,7 @@ list<list<junction> >  comp_matrix::cluster(string forced_edges, int w, ostream
 	      
 	      nVoisins=0;
 	      for (list<string>::iterator it1 = voisins2.begin();it1 != voisins2.end();
-	      ++it1 )nVoisins+=count[*it1];
+		   ++it1 )nVoisins+=count[*it1];
 	      //si la junction possede assez de voisins
 	      if (nVoisins>=minPts){
 		//on ajoute ses voisins a la liste des voisins du cluster
@@ -308,9 +308,9 @@ list<list<junction> >  comp_matrix::cluster(string forced_edges, int w, ostream
 	  list< string > c2;
 	  
 	  for (list< pair<int,string> >::iterator c_it = c.begin(); c_it != c.end();
-	      ++c_it ){
+	       ++c_it ){
 	    pair<int,string> pair=*c_it;
-	  c2.push_back(pair.second);
+	    c2.push_back(pair.second);
 	  }
 	  c2.reverse();
 	  cluster.push_back(c2);

algo/core/compare-all.cpp

@@ -38,7 +38,7 @@ SimilarityMatrix compare_all(list <Sequence> sequences,
 
   for (list <Sequence>::const_iterator it1 = sequences.begin();
        it1 != sequences.end(); ++it1 )
-  num = 0 ;
+    num = 0 ;
 
   list<string>::const_iterator itLabel = sequence_names.begin();
   for (list <Sequence>::const_iterator it1 = sequences.begin();

algo/core/representative.cpp

@@ -294,26 +294,26 @@ bool KmerRepresentativeComputer::tryToExtendRepresentative(const vector<Kmer> co
     else
       pos_of_interest = i - 1;
     if (pos_of_interest < (int) counts[current_seed].size() && pos_of_interest >= 0) {
-    if (isSufficienlyExpressed(counts[current_seed][pos_of_interest].count, sequences.size())) {
-      i += direction;
-
-      if (nb_seeds > 1) {
-        size_t seed_length = seeds[current_seed].size();
-        for (size_t pos = 0; pos < seed_length; pos++) {
-          bool previous_cover = cover[pos_of_interest+pos];
-          cover[pos_of_interest+pos] |= (seeds[current_seed][pos] == '#');
-          if (! previous_cover && cover[pos_of_interest+pos])
-            length_cover++;
-        }
-      } else {
-        int pos_modif = (direction == -1) ? pos_of_interest : i;
-        if (!cover[pos_modif])
-          length_cover++;
-        cover[pos_modif] = true;
+      if (isSufficienlyExpressed(counts[current_seed][pos_of_interest].count, sequences.size())) {
+	i += direction;
+
+	if (nb_seeds > 1) {
+	  size_t seed_length = seeds[current_seed].size();
+	  for (size_t pos = 0; pos < seed_length; pos++) {
+	    bool previous_cover = cover[pos_of_interest+pos];
+	    cover[pos_of_interest+pos] |= (seeds[current_seed][pos] == '#');
+	    if (! previous_cover && cover[pos_of_interest+pos])
+	      length_cover++;
+	  }
+	} else {
+	  int pos_modif = (direction == -1) ? pos_of_interest : i;
+	  if (!cover[pos_modif])
+	    length_cover++;
+	  cover[pos_modif] = true;
+	}
+
+	was_extended = true;
       }
-
-      was_extended = true;
-    }
     }
   }
   return was_extended;

algo/core/segment.cpp

@@ -1085,8 +1085,8 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
   box_J->end = sequence.length()-1;
 
   // Why could this happen ?
-      if (box_J->start>=(int) sequence.length())
-	  box_J->start=sequence.length()-1;
+  if (box_J->start>=(int) sequence.length())
+    box_J->start=sequence.length()-1;
 
   // seg_N will be recomputed in finishSegmentation()