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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef PIRFILEPARSER_H
#define PIRFILEPARSER_H
#include <string>
#include "FileParser.h"
namespace clustalw
{
class PIRFileParser : public FileParser
{
public:
/* Functions */
PIRFileParser(string filePath);
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 */
/* Attributes */
string fileName;
};
}
#endif
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