#include "kmerdb.hpp"
#include "suffixdb.hpp"
#include "blastdb.hpp"
+#include "distancedb.hpp"
/**************************************************************************************************/
-
-Classify::Classify(string tfile, string tempFile, string method, int kmerSize, int gapOpen, int gapExtend, int match, int misMatch) : taxFile(tfile), templateFile(tempFile) {
- try {
+Classify::Classify(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch) : taxFile(tfile), templateFile(tempFile) {
+ try {
+
readTaxonomy(taxFile);
int start = time(NULL);
}
else if(method == "suffix") { database = new SuffixDB(numSeqs); }
else if(method == "blast") { database = new BlastDB(gapOpen, gapExtend, match, misMatch); }
+ else if(method == "distance") { database = new DistanceDB(); }
else {
mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
mothurOutEndLine();
taxonomy[name] = taxInfo;
- //itTax = taxList.find(taxInfo);
- //if (itTax == taxList.end()) { //this is new taxonomy
- //taxList[taxInfo] = 1;
- //}else { taxList[taxInfo]++; }
phyloTree->addSeqToTree(name, taxInfo);
gobble(inTax);