+++ /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
-