- if (makeCount) {
- for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
- vector<string> groups = compositeCt.getNamesOfGroups();
- if (m->inUsersGroups(itGroup->second, groups)) {
- vector<int> tempGroupCounts; tempGroupCounts.resize(groups.size(), 0);
- compositeCt.push_back(itGroup->first, tempGroupCounts);
- compositeCt.setAbund(itGroup->first, itGroup->second, 1);
- }else{
- compositeCt.addGroup(itGroup->second);
- vector<int> tempGroupCounts; tempGroupCounts.resize(groups.size()+1, 0);
- compositeCt.push_back(itGroup->first, tempGroupCounts);
- compositeCt.setAbund(itGroup->first, itGroup->second, 1);
- }
- }
- }else {
- if (l == 0) {
- ofstream outCGroup;
- m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
- outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
- }
- m->appendFiles(outputGroupFileName, compositeGroupFile);
- if (!allFiles) { m->mothurRemove(outputGroupFileName); }
- else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
+ if (l == 0) {
+ ofstream outCGroup;
+ m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
+ outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);