//get maxLevel from phylotree so you know how many 'unclassified's to add
int maxLevel = taxaSum.getMaxLevel();
-
+
//read taxfile - this reading and rewriting is done to preserve the confidence scores.
string name, taxon;
while (!inTax.eof()) {
bool done = false;
int count = 0;
-
+
while (!done) {
if (m->control_pressed) { return 0; }
Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
if (candidateSeq->getName() != "") {
+
taxonomy = classify->getTaxonomy(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 0; }
}
//report progress
if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
-
+
inFASTA.close();
outTax.close();
outTaxSimple.close();