--- /dev/null
+/**
+ * Author: Mark Larkin
+ *
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
+ */
+/**
+ * This file is for parsing pearson format files.
+ * CHANGE:
+ */
+#ifndef PEARSONFILEPARSER_H
+#define PEARSONFILEPARSER_H
+
+#include <string>
+#include "FileParser.h"
+
+namespace clustalw
+{
+using namespace std;
+
+class PearsonFileParser : public FileParser
+{
+ public:
+ /* Functions */
+ PearsonFileParser(string filePath);
+ virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
+ virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
+ virtual int countSeqs();
+ virtual void getSecStructure(vector<char>& gapPenaltyMask,
+ vector<char>& secStructMask, string& secStructName,
+ int &structPenalties, int length);
+
+ /* Attributes */
+
+ private:
+ /* Functions */
+
+ /* Attributes */
+ string fileName;
+};
+
+}
+#endif
+