X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.cpp;h=bfd283db0d1b66db7df4606d980cc9d54dad58a7;hb=9489965363593bb2a3e94f801b4079a32ddf8732;hp=a07e43392a1d96727d4870154bccef452119755b;hpb=291eaab661778e1fd02c5c22bc388daa97bb1d54;p=mothur.git

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index a07e433..bfd283d 100644
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -49,15 +49,15 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 				
 				parentParts.push_back(parent);
 
-				if (q.length() > longest)	{ longest = q.length(); }
-				if (p.length() > longest)	{ longest = p.length();	}
+				if (queryFrag->getUnaligned().length() > longest)	{ longest = queryFrag->getUnaligned().length(); }
+				if (parent->getUnaligned().length() > longest)	{ longest = parent->getUnaligned().length();	}
 			}
 
 			//align each peice to correct parent from results
 			for (int i = 0; i < queryParts.size(); i++) {
 				if ((queryParts[i]->getUnaligned() == "") || (parentParts[i]->getUnaligned() == "")) {;}
 				else {
-					alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+					Alignment* alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, longest+1); //default gapopen, match, mismatch, longestbase
 				
 					Nast nast(alignment, queryParts[i], parentParts[i]);
 					delete alignment;
@@ -82,7 +82,6 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 			//make sure you don't cutoff end of query 
 			if (parents[parents.size()-1].nastRegionEnd < (qAligned.length()-1)) {  newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd+1);  }
 			
-			//set query to new aligned string
 			query->setAligned(newQuery);
 
 			//free memory