added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / systemcommand.h

diff --git a/systemcommand.h b/systemcommand.h
index 892ac96268baeb2557c51cc67dd0fc571ea4dbfa..6dc09ef75690b43eb0e5045788308c1a4d26d93b 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,14 +18,17 @@ class SystemCommand : public Command {
        public:
        
                SystemCommand(string);  
-               SystemCommand() { abort = true; calledHelp = true; }
+               SystemCommand() { setParameters(); abort = true; calledHelp = true; }
                ~SystemCommand(){}
        
-               vector<string> setParameters() { return outputNames; } //dummy does not do anything
+               vector<string> setParameters();
                string getCommandName()                 { return "system";              }
                string getCommandCategory()             { return "General";             }
-               string getHelpString(); 
-       
+        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()); }