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[mothur.git] / deuniquetreecommand.h

diff --git a/deuniquetreecommand.h b/deuniquetreecommand.h
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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 "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