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#ifndef MERGEFILECOMMAND_H
#define MERGEFILECOMMAND_H
/*
* mergefilecommand.h
* Mothur
*
* Created by Pat Schloss on 6/14/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
#include "counttable.h"
class MergeFileCommand : public Command {
public:
MergeFileCommand(string);
~MergeFileCommand(){}
vector<string> setParameters();
string getCommandName() { return "merge.files"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Merge.files"; }
string getDescription() { return "appends files creating one file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> fileNames, outputNames;
string outputFileName, fastafile, namefile, countfile, taxfile;
int numInputFiles;
bool abort;
bool appendMode;
string mergeFileData();
};
#endif
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