working on mgcluster count file change

[mothur.git] / systemcommand.h

diff --git a/systemcommand.h b/systemcommand.h
index 410a12e7657a1c0625281429e261a519dccf45ef..6dc09ef75690b43eb0e5045788308c1a4d26d93b 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,13 +18,25 @@ class SystemCommand : public Command {
        public:
        
                SystemCommand(string);  
-               ~SystemCommand(){};
-               int execute();
-               void help();    
-               
+               SystemCommand() { setParameters(); abort = true; calledHelp = true; }
+               ~SystemCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "system";              }
+               string getCommandCategory()             { return "General";             }
+        string getOutputFileNameTag(string, string) { return ""; }
+        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;
+               
                
 };