core/fasta.{h,cpp}: Fasta parser, remember a marked position from the gapped sequence

The gapped sequences should be all aligned. One may want to remember a specific position.

algo/core/fasta.cpp

@@ -168,19 +168,26 @@ OnlineFasta::~OnlineFasta() {
 }
 
 void OnlineFasta::init() {
+  mark_pos = 0;
   nb_sequences_parsed = 0;
   nb_sequences_returned = 0;
   char_nb = 0;
   line_nb = 0;
-  line = getInterestingLine();
   current.seq = NULL;
+  current.marked_pos = 0;
   current_gaps = 0;
+
+  line = getInterestingLine();
 }
 
 unsigned long long OnlineFasta::getPos() {
   return char_nb;
 }
 
+void OnlineFasta::setMarkPos(int mark_pos) {
+  this -> mark_pos = mark_pos;
+}
+
 size_t OnlineFasta::getLineNb() {
   return line_nb;
 }
@@ -225,6 +232,11 @@ void OnlineFasta::addLineToCurrentSequence(string line)
       }
 
       current.sequence += c;
+
+      if (mark_pos) {
+        if (current.sequence.length() + current_gaps == mark_pos)
+          current.marked_pos = current.sequence.length();
+      }
     }
 }
 
@@ -239,6 +251,7 @@ void OnlineFasta::next() {
   if (current.seq) {
     delete [] current.seq;
     current.seq = NULL;
+    current.marked_pos = 0;
     current_gaps = 0;
   }
 

algo/core/fasta.h

@@ -17,6 +17,7 @@ typedef struct read_t
   string sequence; // Sequence: original string representation
   string quality;
   int*   seq;      // Sequence: seq representation
+  int    marked_pos; // Some marked position in the sequence
 } Sequence;
 
 typedef enum {
@@ -35,6 +36,7 @@ class Fasta
 
         int total_size;
         int extract_field;
+        int mark_pos;
 	string extract_separator;
 	
 	vector<Sequence> reads;
@@ -103,6 +105,7 @@ class OnlineFasta {
   size_t line_nb;
   unsigned long long char_nb;
 
+  int mark_pos;
   void addLineToCurrentSequence(string line);
 
   int nb_sequences_parsed;
@@ -135,6 +138,11 @@ class OnlineFasta {
 
   ~OnlineFasta();
 
+  /**
+   * sets a position to be followed in gapped sequences
+   */
+  void setMarkPos(int mark_pos);
+
   /**
    * @return the position in the file
    */