core/germline.{h,cpp}: factorize the three Germline constructors with Germline::init()

algo/core/germline.cpp

 
 #include "germline.h"
 
-Germline::Germline(string _code, char _shortcut,
-		   string f_rep_5, string f_rep_4, string f_rep_3,
-		   int _delta_min, int _delta_max)
+void Germline::init(string _code, char _shortcut,
+                    int _delta_min, int _delta_max)
 {
   code = _code ;
   shortcut = _shortcut ;
   index = 0 ;
 
+  affect_5 = "V" ;
+  affect_4 = "" ;
+  affect_3 = "J" ;
+  
+  delta_min = _delta_min ;
+  delta_max = _delta_max ;
+
+  stats.setLabel(code);
+}
+
+Germline::Germline(string _code, char _shortcut,
+		   string f_rep_5, string f_rep_4, string f_rep_3,
+		   int _delta_min, int _delta_max)
+{
+  init(_code, _shortcut, _delta_min, _delta_max);
+
   f_reps_5.push_back(f_rep_5);
   f_reps_4.push_back(f_rep_4);
   f_reps_3.push_back(f_rep_3);
 
-  affect_5 = "V" ;
-  affect_4 = "";
-  affect_3 = "J" ;
-
   rep_5 = Fasta(f_rep_5, 2, "|", cout);
   rep_4 = Fasta(f_rep_4, 2, "|", cout);
   rep_3 = Fasta(f_rep_3, 2, "|", cout);
-
-  delta_min = _delta_min ;
-  delta_max = _delta_max ;
-
-  stats.setLabel(code);
 }
 
 
@@ -32,18 +38,12 @@ Germline::Germline(string _code, char _shortcut,
 		   list <string> _f_reps_5, list <string> _f_reps_4, list <string> _f_reps_3,
 		   int _delta_min, int _delta_max)
 {
-  code = _code ;
-  shortcut = _shortcut ;
-  index = 0 ;
+  init(_code, _shortcut, _delta_min, _delta_max);
 
   f_reps_5 = _f_reps_5 ;
   f_reps_4 = _f_reps_4 ;
   f_reps_3 = _f_reps_3 ;
 
-  affect_5 = "V" ;
-  affect_4 = "";
-  affect_3 = "J" ;
-
   for (list<string>::const_iterator it = f_reps_5.begin(); it != f_reps_5.end(); ++it)
     rep_5 = Fasta(*it, 2, "|", cout); // TODO: something like 'rep_5 += ...'
   
@@ -52,11 +52,6 @@ Germline::Germline(string _code, char _shortcut,
 
   for (list<string>::const_iterator it = f_reps_3.begin(); it != f_reps_3.end(); ++it)
     rep_3 = Fasta(*it, 2, "|", cout);
-
-  delta_min = _delta_min ;
-  delta_max = _delta_max ;
-
-  stats.setLabel(code);
 }
 
 
@@ -64,24 +59,11 @@ Germline::Germline(string _code, char _shortcut,
            Fasta _rep_5, Fasta _rep_4, Fasta _rep_3,
 		   int _delta_min, int _delta_max)
 {
-  code = _code ;
-  shortcut = _shortcut ;
-  index = 0 ;
-
-  // affect_5 = KmerAffect("", "V", 0) ;
-  // affect_3 = KmerAffect("", "J", 0) ;
-  affect_5 = "V" ;
-  affect_4 = "" ;
-  affect_3 = "J" ;
+  init(_code, _shortcut, _delta_min, _delta_max);
 
   rep_5 = _rep_5 ;
   rep_4 = _rep_4 ;
   rep_3 = _rep_3 ;
-
-  delta_min = _delta_min ;
-  delta_max = _delta_max ;
-
-  stats.setLabel(code);
 }
 
 void Germline::new_index(string seed)

algo/core/germline.h

@@ -12,6 +12,9 @@ using namespace std;
 
 class Germline {
  private:
+  void init(string _code, char _shortcut,
+            int _delta_min, int _delta_max);
+
   void update_index();
 
  public: