if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
calc = validParameter.validFile(parameters, "calc", false);
string temp;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
if (abort == false) {
globaldata->gTreemap = tmap;
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; }
if(allLines == 1 || labels.count(order->getLabel()) == 1){
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
int error = process(order);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
order = input->getSharedOrderVector(lastLabel);
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
int error = process(order);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; }
//run last line if you need to
if (needToRun == true) {
order = input->getSharedOrderVector(lastLabel);
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
int error = process(order);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; }
delete order;
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear();delete input; delete util; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear();delete input; delete util; return 0; }
//reset groups parameter
globaldata->Groups.clear();