- //update total map with new random scores
- for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
- //does this score already exist in the total map
- it2 = totalrscoreFreq.find(it->first);
- //if yes then add them
- if (it2 != totalrscoreFreq.end()) {
- it2->second += it->second;
- }else{ //its a new score
- totalrscoreFreq[it->first] = 1;
+ string allGroups = "";
+ numGroups = 0;
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() != 0) {
+ if (globaldata->Groups[0] != "all") {
+ //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]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
+ allGroups = allGroups.substr(0, allGroups.length()-1);
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ allGroups += globaldata->Groups[i] + "-";
+ numGroups++;
+ }
+ allGroups = allGroups.substr(0, allGroups.length()-1);
+ }
+ }else{//user has enter "all" and wants the default groups
+ globaldata->Groups.clear();
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
+ allGroups = allGroups.substr(0, allGroups.length()-1);
+ globaldata->setGroups("");