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#ifndef COUNTGROUPSCOMMAND_H
#define COUNTGROUPSCOMMAND_H
/*
* countgroupscommand.h
* Mothur
*
* Created by westcott on 8/9/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
class CountGroupsCommand : public Command {
public:
CountGroupsCommand(string);
~CountGroupsCommand(){}
vector<string> setParameters();
string getCommandName() { return "count.groups"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
string getDescription() { return "counts the number of sequences in each group"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string sharedfile, groupfile, countfile, groups, accnosfile;
bool abort;
vector<string> Groups;
vector<string> outputNames;
};
#endif
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