//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> allGroups = groupMap->getNamesOfGroups();
+ util->setGroups(Groups, allGroups);
delete util;
if (m->control_pressed) { delete groupMap; return 0; }
//read through the list file keeping any otus that contain any sequence from the groups selected
readListGroup();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str());return 0; }
+ if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; }
if(labels.count(list->getLabel()) == 1){
processList(list, groupMap, out, outGroup, wroteSomething);
}
- if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str()); return 0; }
+ if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;