1 /**
2  * Author: Mark Larkin
3  *
4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
5  */
6 #ifndef MSFFILEPARSER_H
7 #define MSFFILEPARSER_H
8 
9 #include <string>
10 #include "FileParser.h"
11 
12 namespace clustalw
13 {
14 
15 class MSFFileParser : public FileParser
16 {
17     public:
18         /* Functions */
19         MSFFileParser(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);
26 
27         /* Attributes */
28 
29     private:
30         /* Functions */
31 
32         /* Attributes */
33         string fileName;
34 };
35 
36 }
37 #endif
38 
39 
40