X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniquetreecommand.h;fp=deuniquetreecommand.h;h=18a6e5e95491603f051b847467db80512d3ad517;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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