- if(search == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); }
- else if(search == "suffix") { templateDB = new SuffixDB(templateFileName); }
- else if(search == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); }
- else {
- mothurOut(search + " is not a valid search option. I will run the command using kmer, ksize=8.");
- mothurOutEndLine();
- kmerSize = 8;
-
- templateDB = new KmerDB(templateFileName, kmerSize);
- }
-
+ templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);