added pipeline commands which involved change to command factory and command class...

[mothur.git] / systemcommand.h

diff --git a/systemcommand.h b/systemcommand.h
index 410a12e7657a1c0625281429e261a519dccf45ef..3b48642aeec3b1cb5e4fc9e1a24d152d09dccc94 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,13 +18,20 @@ class SystemCommand : public Command {
        public:
        
                SystemCommand(string);  
-               ~SystemCommand(){};
+               SystemCommand() {}
+               ~SystemCommand(){}
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
        private:
                string command;
                bool abort;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                
 };