groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else if (groups == "all") {
- if (groupfile != "") { Groups = groupMap->namesOfGroups; }
+ if (groupfile != "") { Groups = groupMap->getNamesOfGroups(); }
else { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; }
}else {
m->splitAtDash(groups, Groups);
accnos = m->isTrue(temp);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
if (cutoff == 0) { m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
if (namefile != "") { readNamesFile(); }
else { createNameMap(list); }
- if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
list = input->getListVector(); //get new list vector to process
}
- if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
- if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//run last label if you need to
if (needToRun == true) {
delete input;
- 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; }
}else { //you are using the namefile to determine abundance
if (outputDir == "") { outputDir = m->hasPath(namefile); }