+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-#ifndef CLUSTALFILEPARSER_H
-#define CLUSTALFILEPARSER_H
-
-#include <string>
-#include "FileParser.h"
-
-namespace clustalw
-{
-
-class ClustalFileParser : public FileParser
-{
- public:
- /* Functions */
- ClustalFileParser(string filePath);
- ~ClustalFileParser();
- virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
- virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
- virtual int countSeqs();
- virtual void getSecStructure(vector<char>& gapPenaltyMask,
- vector<char>& secStructMask,
- string& secStructName, int &structPenalties, int length);
-
- /* Attributes */
-
- private:
- /* Functions */
- bool clustalBlankline(char* line); // Only used in this class!
- string fileName;
- /* Attributes */
-
-};
-
-}
-#endif