final fixes for 1.7

[mothur.git] / knn.cpp

diff --git a/knn.cpp b/knn.cpp
index 0a62e743b0dd8d4f5435d504127a70724f9f27a8..706d2435117513d4a7149e0cc2a670e0e18dc7bb 100644 (file)
--- a/knn.cpp
+++ b/knn.cpp
@@ -10,7 +10,7 @@
 #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) {
@@ -18,8 +18,9 @@ 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
@@ -39,6 +40,7 @@ string Knn::getTaxonomy(Sequence* seq) {
                        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) {