//use database to find closest seq
vector<int> closest = database->findClosestSequences(seq, num);
+
+ if (m->control_pressed) { return tax; }
vector<string> closestNames;
for (int i = 0; i < closest.size(); i++) {
//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);
}
}
int smallest = 100;
for (int i = 0; i < closest.size(); i++) {
+ if (m->control_pressed) { return "control"; }
string tax = taxonomy[closest[i]]; //we know its there since we checked in getTaxonomy
//start at the highest level all the closest seqs have
string common = "";
for (int i = (smallest-1); i >= 0; i--) {
+ if (m->control_pressed) { return "control"; }
string thistax = taxons[0][i];
int num = 0;
return common;
}
catch(exception& e) {
- errorOut(e, "Knn", "findCommonTaxonomy");
+ m->errorOut(e, "Knn", "findCommonTaxonomy");
exit(1);
}
}