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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/** The aim of this class is to return one sequence at a time.
* Note that the file must be open when it is passed to the FileParser.
* The parser does not know the name of the file to open. Only the filereader knows.
*
* Changes:
*
* Mark 24-1-2007. I added the function findDelimiter to determine if '\r' or '\n'
* will be used as the line delimiter when parsing the file.
*
* 10-02-07,Nigel Brown(EMBL): Removed delimiter and findDelimiter()
* members, as functionality now handled by the stream class.
*/
#ifndef FILEPARSER_H
#define FILEPARSER_H
#include <ctype.h>
#include "../alignment/Sequence.h"
#include "../general/userparams.h"
#include <iostream>
#include "InFileStream.h"
namespace clustalw
{
class FileParser
{
public:
/* Functions */
FileParser();
virtual ~FileParser();
virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq) = 0;
virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL) = 0;
virtual int countSeqs() = 0; // VIRTUAL
virtual void getSecStructure(vector<char>& gapPenaltyMask,
vector<char>& secStructMask,
string& secStructName, int &structPenalties, int length) = 0;
void fillCharTab(void);
char getDelimiter(string filename);
/* Attributes */
char chartab[128];
int getParseExitCode() { return parseExitCode; };
protected:
void freeFileResources(InFileStream* filePtr);
InFileStream* _fileIn;
int parseExitCode; // reason for returning empty sequence
// vector; same as used in FileReader
private:
/* Functions */
/* Attributes */
};
}
#endif
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