4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
6 #ifndef CLUSTALFILEPARSER_H
7 #define CLUSTALFILEPARSER_H
10 #include "FileParser.h"
15 class ClustalFileParser : public FileParser
19 ClustalFileParser(string filePath);
21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
22 virtual vector<Sequence> getSeqRange(int firstSeq, int num, 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);
32 bool clustalBlankline(char* line); // Only used in this class!