+void ParsimonyCommand::setGroups() {
+ try {
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() != 0) {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
+ cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ // erase the invalid group from globaldata->Groups
+ globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ }
+ }
+
+ //if the user only entered invalid groups
+ if (globaldata->Groups.size() == 0) {
+ cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+
+ }else {
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/*****************************************************************/
+
+