if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "jclass-thetayc"; }
lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
}
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//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(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
//set phylip file as new current phylipfile
string current = "";