X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.h;h=27adf7c5993289bc0edeeb9f56b8de5939b2bfb0;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=3b48642aeec3b1cb5e4fc9e1a24d152d09dccc94;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/systemcommand.h b/systemcommand.h
index 3b48642..27adf7c 100644
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,20 +18,25 @@ class SystemCommand : public Command {
 	public:
 	
 		SystemCommand(string);	
-		SystemCommand() {}
+		SystemCommand() { setParameters(); abort = true; calledHelp = true; }
 		~SystemCommand(){}
-		vector<string> getRequiredParameters();
-		vector<string> getValidParameters();
-		vector<string> getRequiredFiles();
-		map<string, vector<string> > getOutputFiles() { return outputTypes; }
-		int execute();
-		void help();	
-		
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "system";		}
+		string getCommandCategory()		{ return "General";		}
+        string getHelpString();	
+        string getOutputPattern(string){ return ""; }	
+		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;
-		map<string, vector<string> > outputTypes;
+		
 		
 };