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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef FILEREADER_H
#define FILEREADER_H
#include <vector>
#include <string>
#include <memory>
#include "../alignment/Alignment.h"
#include "../alignment/Sequence.h"
#include "../general/userparams.h"
#include "../general/utils.h"
#include "FileParser.h"
#include "ClustalFileParser.h"
#include "PearsonFileParser.h"
#include "PIRFileParser.h"
#include "GDEFileParser.h"
#include "MSFFileParser.h"
#include "RSFFileParser.h"
#include "EMBLFileParser.h"
namespace clustalw
{
class FileReader
{
public:
/* Functions */
FileReader();
~FileReader();
int seqInput(Alignment* alignPtr, bool append, string *offendingSeq);
int readSeqs(Alignment* alignPtr, int firstSeq, string *offendingSeq);
int profileInput(Alignment* alignPtr);
/* Attributes */
private:
/* Functions */
void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
/* Attributes */
string sequenceFileName;
bool noEmptySequence(vector<Sequence> seqRangeVector, string *offendingSeq);
InFileStream* fileIn;
int structPenalties;
string secStructName;
vector<char> secStructMask; // Will need to be cleared out before every reading!
vector<char> gapPenaltyMask;
vector<string> formatNames;
};
}
#endif
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