1 /**
2  * Author: Mark Larkin
3  *
4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
5  */
6 /**
7  * This file is for parsing pearson format files.
8  * CHANGE:
9  */
10 #ifndef PEARSONFILEPARSER_H
11 #define PEARSONFILEPARSER_H
12 
13 #include <string>
14 #include "FileParser.h"
15 
16 namespace clustalw
17 {
18 using namespace std;
19 
20 class PearsonFileParser : public FileParser
21 {
22     public:
23         /* Functions */
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);
31 
32         /* Attributes */
33 
34     private:
35         /* Functions */
36 
37         /* Attributes */
38         string fileName;
39 };
40 
41 }
42 #endif
43 
44