core/fasta.cpp: defines and computes int* Sequence.seq

algo/core/fasta.cpp

@@ -142,6 +142,7 @@ void OnlineFasta::next() {
   current.label.erase();
   current.sequence.erase();
   current.quality.erase();
+  current.seq = NULL;
 
   if  (hasNext()) {
     switch(line[0]) {
@@ -189,6 +190,22 @@ void OnlineFasta::next() {
 
     // Sequence in uppercase
     transform(current.sequence.begin(), current.sequence.end(), current.sequence.begin(), (int (*)(int))toupper);
+
+    // Compute seq
+    current.seq = new int[current.sequence.length()];
+    for (int i=0; i< current.sequence.length(); i++)
+      {
+	int B ;
+	switch(current.sequence[i]) {
+	case 'A': B = 0; break;
+	case 'C': B = 1; break;
+	case 'G': B = 2; break;
+	case 'T': B = 3; break;
+	  B = 4; break;
+	}
+	current.seq[i] = B ;
+      }
+
   } else
     unexpectedEOF();
 }

algo/core/fasta.h

@@ -12,8 +12,9 @@ typedef struct read_t
 {
   string label_full;
   string label;
-  string sequence;
+  string sequence; // Sequence: original string representation
   string quality;
+  int*   seq;      // Sequence: seq representation
 } Sequence;
 
 typedef enum {

algo/core/tools.cpp

@@ -97,6 +97,7 @@ Sequence create_sequence(string label_full, string label, string sequence, strin
   seq.label = label;
   seq.sequence = sequence;
   seq.quality = quality;
+  // ! TODO: seq.seq, factorize with fasta.cpp
   return seq;
 }