4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
7 * This file is for parsing pearson format files.
10 #ifndef PEARSONFILEPARSER_H
11 #define PEARSONFILEPARSER_H
14 #include "FileParser.h"
20 class PearsonFileParser : public FileParser
24 PearsonFileParser(string filePath);
25 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
26 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
27 virtual int countSeqs();
28 virtual void getSecStructure(vector<char>& gapPenaltyMask,
29 vector<char>& secStructMask, string& secStructName,
30 int &structPenalties, int length);