else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
}
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
- convert(itersString, iters);
+ m->mothurConvert(itersString, iters);
string temp = validParameter.validFile(parameters, "distance", false);
if (temp == "not found") { phylip = false; outputForm = ""; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
if (!random) { iters = 0; } //turn off random calcs
m->splitAtDash(groups, Groups);
m->setGroups(Groups);
}
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
}
}