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+#ifndef GETGROUPSCOMMAND_H
+#define GETGROUPSCOMMAND_H
+
+/*
+ *  getgroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/10/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+
+class GetGroupsCommand : public Command {
+	
+public:
+	
+	GetGroupsCommand(string);	
+	GetGroupsCommand();
+	~GetGroupsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.groups";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
+	string getDescription()		{ return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
+private:
+	set<string> names;
+	map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+										   //then the other files need to change the unique name in their file to match.
+										   //only add the names that need to be changed to keep the map search quick
+	string accnosfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
+	bool abort;
+	vector<string> outputNames, Groups;
+	GroupMap* groupMap;
+	
+	int readFasta();
+	int readName();
+	int readGroup();
+	void readAccnos();
+	int readList();
+	int readTax();
+	int fillNames();
+	int readShared();
+    int readDesign();
+	
+};
+
+#endif
+
+
+