- //is this a taxonomy that needs to be extended?
- if (seqLevels[name] < highestLevel) {
- extendTaxonomy(name, tax, highestLevel);
- }else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
- truncateTaxonomy(name, tax, highestLevel);
+ ofstream out;
+ equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
+ m->openOutputFile(equalizedFile, out);
+
+
+ string name, tax;
+ while (in) {
+
+ if (m->control_pressed) { break; }
+
+ in >> name >> tax; m->gobble(in);
+
+ if (containsConfidence) { m->removeConfidences(tax); }
+
+ //is this a taxonomy that needs to be extended?
+ if (seqLevels[name] < highestLevel) {
+ extendTaxonomy(name, tax, highestLevel);
+ }else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
+ truncateTaxonomy(name, tax, highestLevel);
+ }
+
+ out << name << '\t' << tax << endl;