removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / systemcommand.h

diff --git a/systemcommand.h b/systemcommand.h
index 55b772b71ddaa62767746d7543f61ae09a5b5e39..892ac96268baeb2557c51cc67dd0fc571ea4dbfa 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -20,18 +20,20 @@ class SystemCommand : public Command {
                SystemCommand(string);  
                SystemCommand() { 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() { return outputNames; } //dummy does not do anything
+               string getCommandName()                 { return "system";              }
+               string getCommandCategory()             { return "General";             }
+               string getHelpString(); 
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
        private:
                string command;
                bool abort;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
+               
                
 };