core/fasta.{h,cpp}: Fasta objects can have names

These names are the names of the underlying file(s).
Moreover, we define some constants.

algo/core/fasta.cpp

@@ -44,6 +44,13 @@ void Fasta::init(int extract_field, string extract_separator)
   this -> extract_field = extract_field ;
   this -> extract_separator = extract_separator ; 
   total_size = 0;
+  name = "";
+}
+
+Fasta::Fasta(bool virtualfasta, string name)
+{
+  init(0, "");
+  this -> name = name;
 }
 
 Fasta::Fasta(int extract_field, string extract_separator)
@@ -77,6 +84,8 @@ void Fasta::add(const string &filename, bool verbose) {
       throw invalid_argument(" !! Error in opening file: "+ filename);
     }
 
+  name += filename + " ";
+
   if (verbose)
   cout << " <== " << filename ;
   add(is, verbose);

algo/core/fasta.h

@@ -51,7 +51,10 @@ public:
 	Fasta(const string &input, 
 	      int extract_field=0, string extract_separator="|",
               bool verbose=true);
-	
+
+        Fasta(bool virtualfasta, const string name); // virtualfasta unused
+
+        string name;
 	int size() const;
         int totalSize() const;
 
@@ -190,6 +193,9 @@ istream& operator>>(istream& in, Fasta& fasta);
 ostream& operator<<(ostream& out, Fasta& fasta);
 ostream &operator<<(ostream &out, const Sequence &seq);
 
+const Fasta FASTA_UNKNOWN = Fasta(true, "_");
+const Fasta FASTA_AMBIGUOUS = Fasta(true, "?");
+
 /**
  * Count the number of sequences in a Fasta file
  * @return the number of sequences