else {
pickedGroups = true;
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; }
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
delete input;
out.close();