X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.cpp;h=f0b1ecc4fb1d31cbb79837579604cffaf84863e9;hb=d8ed98e71c2da5b39b8a778e2c694a4ddff677eb;hp=9894adbda2aab2f4ddac2b786c69bffc8778335f;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/decalc.cpp b/decalc.cpp
index 9894adb..f0b1ecc 100644
--- 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++) {