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