//create database
if(method == "kmer") { database = new KmerDB(tempFile, kmerSize); }
else if(method == "suffix") { database = new SuffixDB(numSeqs); }
- else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, ""); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid); }
else if(method == "distance") { database = new DistanceDB(); }
else {
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
}
}
/**************************************************************************************************/
-Classify::Classify() { m = MothurOut::getInstance(); database = NULL; }
+Classify::Classify() { m = MothurOut::getInstance(); database = NULL; flipped=false; }
/**************************************************************************************************/
int Classify::readTaxonomy(string file) {