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[mothur.git] / 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
+