public:
ParsimonyCommand(string);
+ ParsimonyCommand();
~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
bool abort;
string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
void printParsimonyFile();
- void printUSummaryFile();
+ int printUSummaryFile();
void getUserInput();
};