1 #ifndef DEUNIQUETREECOMMAND_H
2 #define DEUNIQUETREECOMMAND_H
5 * deuniquetreecommand.h
8 * Created by westcott on 5/27/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "sharedutilities.h"
18 class DeuniqueTreeCommand : public Command {
21 DeuniqueTreeCommand(string);
22 DeuniqueTreeCommand();
23 ~DeuniqueTreeCommand() {}
25 vector<string> setParameters();
26 string getCommandName() { return "deunique.tree"; }
27 string getCommandCategory() { return "Hypothesis Testing"; }
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Deunique.tree"; }
30 string getDescription() { return "add the redundant sequence names back into a tree of unique sequences"; }
33 void help() { m->mothurOut(getHelpString()); }
40 string outputDir, treefile, namefile;
41 vector<string> outputNames;
42 map<string, string> nameMap;