#include "knn.h"
/**************************************************************************************************/
-Knn::Knn(string tfile, string tempFile, string method, int kmerSize, int gapOpen, int gapExtend, int match, int misMatch, int n)
+Knn::Knn(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int n)
: Classify(tfile, tempFile, method, kmerSize, gapOpen, gapExtend, match, misMatch), num(n) {}
/**************************************************************************************************/
string Knn::getTaxonomy(Sequence* seq) {
string tax;
//use database to find closest seq
+
vector<int> closest = database->findClosestSequences(seq, num);
-
+
vector<string> closestNames;
for (int i = 0; i < closest.size(); i++) {
//find that sequences taxonomy in map
if (tax == "") { mothurOut("There are no common levels for sequence " + seq->getName() + ". " + seq->getName() + " will be disregarded."); mothurOutEndLine(); tax = "bad seq"; }
}
+ simpleTax = tax;
return tax;
}
catch(exception& e) {