tie breaker fix to chimera.slayer

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 9894adbda2aab2f4ddac2b786c69bffc8778335f..f0b1ecc4fb1d31cbb79837579604cffaf84863e9 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -780,7 +780,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                //sort by smallest distance
                sort(distsRight.begin(), distsRight.end(), compareSeqDist);
                sort(distsLeft.begin(), distsLeft.end(), compareSeqDist);
-               
+                               
                //merge results         
                map<string, string> seen;
                map<string, string>::iterator it;
@@ -825,12 +825,17 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                        i++;
                }
 
-               if (numWanted > dists.size()) { m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine(); numWanted = dists.size(); }
+               if (numWanted > dists.size()) { 
+                       //m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine(); 
+                       numWanted = dists.size();
+               }
 
 //cout << numWanted << endl;
                for (int i = 0; i < numWanted; i++) {
 //cout << dists[i].seq->getName() << '\t' << dists[i].dist << endl;
+
                        Sequence* temp = new Sequence(db[dists[i].index]->getName(), db[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
+                       
                        seqsMatches.push_back(temp);
                        indexes.push_back(dists[i].index);
                }
@@ -952,7 +957,6 @@ map<int, int> DeCalculator::trimSeqs(Sequence* query, vector<Sequence*> topMatch
                map<int, int> trimmedPos;
                //check to make sure that is not whole seq
                if ((rearPos - frontPos - 1) <= 0) {  
-                       //m->mothurOut("[ERROR]: when I trim " + query->getName() + ", the entire sequence is trimmed. Skipping."); m->mothurOutEndLine();  
                        query->setAligned("");
                        //trim topMatches
                        for (int i = 0; i < topMatches.size(); i++) {