//is this sequence in the taxonomy file
if (it == taxonomy.end()) { //error not in file
- mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file. It will be eliminated as a match to sequence " + seq->getName() + "."); mothurOutEndLine();
+ m->mothurOut("Error: sequence " + names[closest[i]] + " is not in the taxonomy file. It will be eliminated as a match to sequence " + seq->getName() + "."); m->mothurOutEndLine();
}else{ closestNames.push_back(it->first); }
}
if (closestNames.size() == 0) {
- mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); mothurOutEndLine();
+ m->mothurOut("Error: All the matches for sequence " + seq->getName() + " have been eliminated. " + seq->getName() + " will be disregarded."); m->mothurOutEndLine();
tax = "bad seq";
}else{
tax = findCommonTaxonomy(closestNames);
- if (tax == "") { mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); mothurOutEndLine(); tax = "bad seq"; }
+ if (tax == "") { m->mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); m->mothurOutEndLine(); tax = "bad seq"; }
}
simpleTax = tax;
return tax;
}
catch(exception& e) {
- errorOut(e, "Knn", "getTaxonomy");
+ m->errorOut(e, "Knn", "getTaxonomy");
exit(1);
}
}
return common;
}
catch(exception& e) {
- errorOut(e, "Knn", "findCommonTaxonomy");
+ m->errorOut(e, "Knn", "findCommonTaxonomy");
exit(1);
}
}