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#ifndef SPLITGROUPSCOMMAND_H
#define SPLITGROUPSCOMMAND_H
/*
* splitgroupscommand.h
* Mothur
*
* Created by westcott on 9/20/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
/* split.groups - given a group file, split sequences and names files in to separate files *.group1.fasta and .group1.names. */
#include "command.hpp"
#include "groupmap.h"
#include "sequence.hpp"
/***************************************************************************************/
class SplitGroupCommand : public Command {
public:
SplitGroupCommand(string);
SplitGroupCommand();
~SplitGroupCommand() {}
vector<string> setParameters();
string getCommandName() { return "split.groups"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
string getDescription() { return "split a name or fasta file by group"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
string outputDir, namefile, groupfile, countfile, groups, fastafile;
vector<string> Groups;
bool abort;
int runNameGroup();
int runCount();
};
/***************************************************************************************/
#endif
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