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#ifndef OPTIONPARSER_H
#define OPTIONPARSER_H
/*
* optionparser.h
* Mothur
*
* Created by Sarah Westcott on 6/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "mothur.h"
#include "mothurout.h"
#include "command.hpp"
#include "utils.hpp"
#include "currentfile.h"
/***********************************************************************/
class OptionParser {
public:
OptionParser(string, vector<string>);
OptionParser(string, map<string, string>&);
~OptionParser() = default;
map<string, string> getParameters(); //adds inputdir to parameters if indicated
private:
map<string, string> parameters;
MothurOut* m;
CurrentFile* current;
Utils util;
set<string> fileTypes;
void fillFileTypes(set<string>&);
};
/***********************************************************************/
#endif
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