1.18.1

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 9c84429fe3cc00df92fff4e2ae358ae8553692a4..2e577d2275edbd3212dfc064307d7c144c9ab469 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -688,6 +688,7 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                indexes.clear();
                
                vector<Sequence*> seqsMatches;  
+               
                vector<SeqDist> distsLeft;
                vector<SeqDist> distsRight;
                
@@ -759,14 +760,14 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                        float distRight = distcalculator->getDist();
                        
                        SeqDist subjectLeft;
-                       subjectLeft.seq = db[j];
+                       subjectLeft.seq = NULL;
                        subjectLeft.dist = distLeft;
                        subjectLeft.index = j;
                        
                        distsLeft.push_back(subjectLeft);
                        
                        SeqDist subjectRight;
-                       subjectRight.seq = db[j];
+                       subjectRight.seq = NULL;
                        subjectRight.dist = distRight;
                        subjectRight.index = j;
                        
@@ -790,18 +791,18 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
                int lasti = 0;
                for (int i = 0; i < distsLeft.size(); i++) {
                        //add left if you havent already
-                       it = seen.find(distsLeft[i].seq->getName());
+                       it = seen.find(db[distsLeft[i].index]->getName());
                        if (it == seen.end()) {  
                                dists.push_back(distsLeft[i]);
-                               seen[distsLeft[i].seq->getName()] = distsLeft[i].seq->getName();
+                               seen[db[distsLeft[i].index]->getName()] = db[distsLeft[i].index]->getName();
                                lastLeft =  distsLeft[i].dist;
                        }
 
                        //add right if you havent already
-                       it = seen.find(distsRight[i].seq->getName());
+                       it = seen.find(db[distsRight[i].index]->getName());
                        if (it == seen.end()) {  
                                dists.push_back(distsRight[i]);
-                               seen[distsRight[i].seq->getName()] = distsRight[i].seq->getName();
+                               seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
                                lastRight =  distsRight[i].dist;
                        }
                        
@@ -824,12 +825,14 @@ 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(dists[i].seq->getName(), dists[i].seq->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
+                       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);
                }
@@ -951,7 +954,6 @@ 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 your sequences, the entire sequence is trimmed."); m->mothurOutEndLine();  
                        query->setAligned("");
                        //trim topMatches
                        for (int i = 0; i < topMatches.size(); i++) {