core/fasta.{h,cpp}: default constructor also takes extract_field and...

core/fasta.{h,cpp}: default constructor also takes extract_field and extract_separator, factorize constructors

Even if we start from an empty Fasta, we should remember these values.

algo/core/fasta.cpp

@@ -25,21 +25,28 @@
 #include <stdexcept>
 #include "fasta.h"
 
-Fasta::Fasta(){
+
+void Fasta::init(int extract_field, string extract_separator)
+{
+  this -> extract_field = extract_field ;
+  this -> extract_separator = extract_separator ; 
+  total_size = 0;
+}
+
+Fasta::Fasta(int extract_field, string extract_separator)
+{
+  init(extract_field, extract_separator);
 }
 
 Fasta::Fasta(const string &input, 
 	     int extract_field, string extract_separator,
 	     ostream &out) 
 {
+  init(extract_field, extract_separator);
+
   if (!input.size()) // Do not open empty files (D germline if not segmentD)
     return ;
 
-  // oout = out;
-  this -> extract_field = extract_field ;
-  this -> extract_separator = extract_separator ;
-  total_size = 0;
-
   add(input);  
 
   out << "  <== " << input

algo/core/fasta.h

@@ -29,6 +29,8 @@ typedef enum {
 
 class Fasta
 {
+        void init(int extract_field, string extract_separator);
+
         int total_size;
         int extract_field;
 	string extract_separator;
@@ -37,7 +39,7 @@ class Fasta
 	// ostream *oout ;
 
 public:
-	Fasta();
+        Fasta(int extract_field=0, string extract_separator="|");
         /**
          * Read all the sequences in the input filename and record them in the object.
          *