-void Tree::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 (globaldata->gTreemap->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 < globaldata->gTreemap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gTreemap->namesOfGroups[i]);
- }
- }
-
- }else {
- for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gTreemap->namesOfGroups[i]);
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }