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