X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniquetreecommand.h;fp=deuniquetreecommand.h;h=5131c114986e67c70c43019c44f67830c5ce1e4b;hb=0cc0c01eb5127ef2b09b894e1f224ccc1d70bef0;hp=0000000000000000000000000000000000000000;hpb=43835751a12097ea9d46a4ce68e2671ba7aff9d4;p=mothur.git

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 "treemap.h"
+#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"; }
+	
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }
+	
+	
+private:
+	TreeMap* tmap;
+	int numUniquesInName;
+	
+	bool abort;
+	string outputDir, treefile, namefile;
+	vector<string> outputNames;
+	map<string, string> nameMap;
+	int readNamesFile();
+};
+
+#endif