- Command() { m = MothurOut::getInstance(); }
- virtual vector<string> getValidParameters() = 0;
- virtual vector<string> getRequiredParameters() = 0; //adding "or" as the last element indicates one of the previous is needed
- virtual vector<string> getRequiredFiles() = 0; //adding "or" as the last element indicates one of the previous is needed
- virtual map<string, vector<string> > getOutputFiles() = 0; //file type to names
+ Command() { m = MothurOut::getInstance(); }
+
+ //needed by gui
+ virtual string getCommandName() = 0;
+ virtual string getCommandCategory() = 0;
+ virtual string getHelpString() = 0;
+ virtual string getCitation() = 0;
+ virtual string getDescription() = 0;
+
+ virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ virtual vector<string> setParameters() = 0; //to fill parameters
+ virtual vector<CommandParameter> getParameters() { return parameters; }
+