fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / distancedb.cpp

diff --git a/distancedb.cpp b/distancedb.cpp
index ca6ffe8ba61217ac0b66b353e8f33461f4916e52..b5c22b35bf7a58addcff79651e6841b9506ec8e2 100644 (file)
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -47,7 +47,7 @@ vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
                vector<int> topMatches;
                bool templateSameLength = true;
                string sequence = query->getAligned();
-               vector<seqDist> dists;
+               vector<seqDist> dists; 
                
                searchScore = -1.0;
        
@@ -56,24 +56,46 @@ vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
                if (sequence.length() != templateSeqsLength) { templateSameLength = false; }
                
                if (templateSameLength && templateAligned) {
-                       //calc distance from this sequence to every sequence in the template
-                       for (int i = 0; i < data.size(); i++) {
-                               distCalculator->calcDist(*query, data[i]);
-                               float dist = distCalculator->getDist();
+                       if (numWanted != 1) {
                                
-                               //save distance to each template sequence
-                               seqDist temp(-1, i, dist);
-                               dists.push_back(temp);
-                       }
-                       
-                       sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
-                       
-                       //save distance of best match
-                       searchScore = dists[0].dist;
-                       
-                       //fill topmatches with numwanted closest sequences indexes
-                       for (int i = 0; i < numWanted; i++) {
-                               topMatches.push_back(dists[i].seq2);
+                               dists.resize(data.size());
+                               
+                               //calc distance from this sequence to every sequence in the template
+                               for (int i = 0; i < data.size(); i++) {
+                                       distCalculator->calcDist(*query, data[i]);
+                                       float dist = distCalculator->getDist();
+                                       
+                                       //save distance to each template sequence
+                                       dists[i].seq1 = -1;
+                                       dists[i].seq2 = i;
+                                       dists[i].dist = dist;
+                               }
+                               
+                               sort(dists.begin(), dists.end(), compareSequenceDistance);  //sorts by distance lowest to highest
+                               
+                               //save distance of best match
+                               searchScore = dists[0].dist;
+                               
+                               //fill topmatches with numwanted closest sequences indexes
+                               for (int i = 0; i < numWanted; i++) {
+                                       topMatches.push_back(dists[i].seq2);
+                               }
+                       }else {
+                               int bestIndex = 0;
+                               float smallDist = 100000;
+                               for (int i = 0; i < data.size(); i++) {
+                                       distCalculator->calcDist(*query, data[i]);
+                                       float dist = distCalculator->getDist();
+                                       
+                                       //are you smaller?
+                                       if (dist < smallDist) {
+                                               bestIndex = i;
+                                               smallDist = dist;
+                                       }
+                               }
+                               
+                               searchScore = smallDist;
+                               topMatches.push_back(bestIndex);
                        }
                
                }else{