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#ifndef SUMMARYTAXCOMMAND_H
#define SUMMARYTAXCOMMAND_H
/*
* summarytaxcommand.h
* Mothur
*
* Created by westcott on 9/23/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
/**************************************************************************************************/
class SummaryTaxCommand : public Command {
public:
SummaryTaxCommand(string);
SummaryTaxCommand();
~SummaryTaxCommand(){}
vector<string> setParameters();
string getCommandName() { return "summary.tax"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
string getDescription() { return "summarize the taxonomies of a set of sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string taxfile, outputDir, namefile, groupfile, refTaxonomy;
vector<string> outputNames;
map<string, int> nameMap;
};
/**************************************************************************************************/
#endif
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