-#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 "sharedutilities.h"
-#include "readtree.h"
-
-class DeuniqueTreeCommand : public Command {
-
-public:
- DeuniqueTreeCommand(string);
- DeuniqueTreeCommand();
- ~DeuniqueTreeCommand() {}
-
- vector<string> setParameters();
- string getCommandName() { return "deunique.tree"; }
- string getCommandCategory() { return "Hypothesis Testing"; }
- string getHelpString();
- 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 outputDir, treefile, namefile;
- vector<string> outputNames;
- map<string, string> nameMap;
- int readNamesFile();
-};
-
-#endif