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+#ifndef MGCLUSTERCOMMAND_H
+#define MGCLUSTERCOMMAND_H
+
+/*
+ *  mgclustercommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 12/11/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "readblast.h"
+#include "sparsematrix.hpp"
+#include "nameassignment.hpp"
+#include "cluster.hpp"
+#include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+
+/**********************************************************************/
+
+class MGClusterCommand : public Command {
+
+public:
+	MGClusterCommand(string);
+	MGClusterCommand();
+	~MGClusterCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "mgcluster";	}
+	string getCommandCategory()		{ return "Clustering";	}
+	string getHelpString();	
+	string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
+	string getDescription()		{ return "cluster your sequences into OTUs using a blast file"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
+private:
+	ReadBlast* read;
+	NameAssignment* nameMap;
+	Cluster* cluster;
+	HCluster* hcluster;
+	ListVector* list;
+	ListVector oldList;
+	vector<seqDist> overlapMatrix;
+	vector<string> outputNames;
+	
+	string blastfile, method, namefile, overlapFile, distFile, outputDir;
+	ofstream sabundFile, rabundFile, listFile;
+	double cutoff;
+	float penalty;
+	int precision, length, precisionLength;
+	bool abort, minWanted, hclusterWanted, merge, hard;
+	
+	void printData(ListVector*);
+	ListVector* mergeOPFs(map<string, int>, float);
+	void sortHclusterFiles(string, string);
+	vector<seqDist> getSeqs(ifstream&);
+
+};
+
+/**********************************************************************/
+
+#endif
+
+
+