vector<string> setParameters();
string getCommandName() { return "set.dir"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
+
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
string getDescription() { return "set input, output and default directories"; }
private:
CommandFactory* commandFactory;
string output, input, tempdefault;
- bool abort, debugOnly;
+ bool abort, debugOnly, modifyNames;
vector<string> outputNames;