core/segment.{h,cpp}: AlignBox, ostream &operator<<

algo/core/segment.cpp

@@ -46,6 +46,18 @@ string AlignBox::getSequence(string sequence) {
 }
 
 
+ostream &operator<<(ostream &out, const AlignBox &box)
+{
+  out << "[/" << box.del_left << " " ;
+  out << "@" << box.start << " " ;
+  out << box.ref_label << "(" << box.ref_nb << ") " ;
+  out << "@" << box.end << " " ;
+  out << box.del_right << "/]" ;
+
+  return out ;
+}
+
+
 
 Segmenter::~Segmenter() {}
 
@@ -621,14 +633,9 @@ bool comp_pair (pair<int,int> i,pair<int,int> j)
  * @param reverse_ref:  if true, reverse the reference sequences (VkVk)
  * @param reverse_both: if true, reverse both the read and the reference sequences (J segment)
  * @param local:        if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions and onlyBottomTriangle (V and J segments)
+ * @param box:          the AligBox to fill
  * @param segment_cost: the cost used by the dynamic programing
- * @return score:       the maximized score, together with the following values:
- * @return tag:           - the name of the sequence
- * @return del:           - the number of deletions at the end of the reference sequence (or at the start if 'reverse_both')
- * @return del2:          - the number of deletions at the start of the reference sequence (used with 'local')
- * @return begin:         - the start position of the aligned segment in the read
- * @return length:        - the length of the alignmed segment in the read
- * @return best_best_i: ?
+ * @post  box is filled
  */
 
 int align_against_collection(string &read, Fasta &rep, bool reverse_ref, bool reverse_both, bool local,

algo/core/segment.h

@@ -68,6 +68,10 @@ const char* const segmented_mesg[] = { "?",
 
 
 
+/**
+ * An alignment box (AlignBox) gather all parameters for a recombined gene segment (V, D, J, other D...)
+ **/
+
 class AlignBox
 {
  public:
@@ -76,16 +80,19 @@ class AlignBox
   int end;
   int del_right;
 
+  AlignBox();
+  string getSequence(string sequence);
+
+  /* Identifier, label and sequence of the reference sequence (the best one) */
   int ref_nb;
   string ref_label;
   string ref;
-  vector<pair<int, int> > score;
-
-  string getSequence(string sequence);
 
-  AlignBox();
+  /* Identifiers and scores of other possible reference sequence */
+  vector<pair<int, int> > score;
 };
 
+ostream &operator<<(ostream &out, const AlignBox &box);
 
 /**
  * Check whether there is an overlap between two boxes,