4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
6 #ifndef PIRFILEPARSER_H
7 #define PIRFILEPARSER_H
10 #include "FileParser.h"
15 class PIRFileParser : public FileParser
19 PIRFileParser(string filePath);
20 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
22 virtual int countSeqs();
23 virtual void getSecStructure(vector<char>& gapPenaltyMask,
24 vector<char>& secStructMask, string& secStructName,
25 int &structPenalties, int length);