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#ifndef DEUNIQUETREECOMMAND_H
#define DEUNIQUETREECOMMAND_H
/*
* deuniquetreecommand.h
* Mothur
*
* Created by westcott on 5/27/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "readtree.h"
class DeuniqueTreeCommand : public Command {
public:
DeuniqueTreeCommand(string);
~DeuniqueTreeCommand() = default;
vector<string> setParameters();
string getCommandName() { return "deunique.tree"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Deunique.tree"; }
string getDescription() { return "add the redundant sequence names back into a tree of unique sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
int numUniquesInName;
bool abort;
string treefile, namefile;
vector<string> outputNames;
map<string, string> nameMap;
int readNamesFile();
};
#endif
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