X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.h;fp=systemcommand.h;h=6a4b884cba8ee21629219593cf43eae7b4c02447;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/systemcommand.h b/systemcommand.h
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+#ifndef SYSTEMCOMMAND_H
+#define SYSTEMCOMMAND_H
+
+/*
+ *  systemcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+
+class SystemCommand : public Command {
+	
+	public:
+	
+		SystemCommand(string);	
+		SystemCommand() { setParameters(); abort = true; calledHelp = true; }
+		~SystemCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "system";		}
+		string getCommandCategory()		{ return "General";		}
+		string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/System"; }
+		string getDescription()		{ return "execute system commands from within mothur"; }
+
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	private:
+		string command;
+		bool abort;
+		vector<string> outputNames;
+		
+		
+};
+
+#endif
+