+
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() == 0) {
+ numGroups = tmap->getNumGroups();
+ }else {
+ //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) {
+ numGroups = tmap->getNumGroups();
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ }else if (globaldata->Groups.size() == 1) {
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ numGroups = tmap->getNumGroups();
+ globaldata->Groups.clear();
+ }else { numGroups = globaldata->Groups.size(); }
+ }