sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / distancedb.cpp

diff --git a/distancedb.cpp b/distancedb.cpp
index 8d0c6298578c4311a59407610ae28a87f48ee493..27e278574493c89d0197d99cbe71c0c3dd03d0d9 100644 (file)
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -13,8 +13,9 @@
 #include "distancedb.hpp"
 #include "onegapignore.h"
 
+
 /**************************************************************************************************/
-DistanceDB::DistanceDB() { 
+DistanceDB::DistanceDB() : Database() { 
        try {
                templateAligned = true;  
                templateSeqsLength = 0; 
@@ -49,6 +50,7 @@ void DistanceDB::addSequence(Sequence seq) {
 vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
        try {
                vector<int> topMatches;
+               Scores.clear();
                bool templateSameLength = true;
                string sequence = query->getAligned();
                vector<seqDist> dists; 
@@ -87,6 +89,7 @@ vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
                                //fill topmatches with numwanted closest sequences indexes
                                for (int i = 0; i < numWanted; i++) {
                                        topMatches.push_back(dists[i].seq2);
+                                       Scores.push_back(dists[i].dist);
                                }
                        }else {
                                int bestIndex = 0;
@@ -103,6 +106,7 @@ vector<int> DistanceDB::findClosestSequences(Sequence* query, int numWanted){
                                }
                                searchScore = smallDist;
                                topMatches.push_back(bestIndex);
+                               Scores.push_back(smallDist);
                        }
                
                }else{