started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstr...

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 7ae3ff6dbb96224197dff97db4b435880738d87b..e92e19f519fb31ec9833736e1223f3f76c9281f3 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -439,28 +439,9 @@ vector<Sequence*> Pintail::findPairs(int start, int end) {
                vector<Sequence*> seqsMatches;  
                
                for(int i = start; i < end; i++){
-               
-                       float smallest = 10000.0;
-                       Sequence query = *(querySeqs[i]);
-                       Sequence* match;
-                       
-                       for(int j = 0; j < templateSeqs.size(); j++){
-                               
-                               Sequence temp = *(templateSeqs[j]);
-                               
-                               distcalculator->calcDist(query, temp);
-                               float dist = distcalculator->getDist();
-                               
-                               if (dist < smallest) { 
-                                       match = templateSeqs[j];
-                                       smallest = dist;
-                               }
-                       }
-                       
-                       //make copy so trimSeqs doesn't overtrim
-                       Sequence* copy = new Sequence(match->getName(), match->getAligned());
                        
-                       seqsMatches.push_back(copy);
+                       vector<Sequence*> copy = decalc->findClosest(querySeqs[i], templateSeqs, 1);
+                       seqsMatches.push_back(copy[0]);
                }
                
                return seqsMatches;