From: westcott <westcott>
Date: Fri, 18 Jun 2010 11:37:36 +0000 (+0000)
Subject: fixed problem with chimera.slayer realigner
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=291eaab661778e1fd02c5c22bc388daa97bb1d54

fixed problem with chimera.slayer realigner
---

diff --git a/chimerarealigner.cpp b/chimerarealigner.cpp
index 9a25162..a07e433 100644
--- a/chimerarealigner.cpp
+++ b/chimerarealigner.cpp
@@ -34,9 +34,9 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 
 			//take query and break apart into pieces using breakpoints given by results of parents
 			for (int i = 0; i < parents.size(); i++) {
-			
 				int length = parents[i].nastRegionEnd - parents[i].nastRegionStart+1;
 				string q = qAligned.substr(parents[i].nastRegionStart, length);
+	
 				Sequence* queryFrag = new Sequence(query->getName(), q);
 
 				queryParts.push_back(queryFrag);
@@ -55,10 +55,13 @@ void ChimeraReAligner::reAlign(Sequence* query, vector<results> parents) {
 
 			//align each peice to correct parent from results
 			for (int i = 0; i < queryParts.size(); i++) {
-				alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
+				if ((queryParts[i]->getUnaligned() == "") || (parentParts[i]->getUnaligned() == "")) {;}
+				else {
+					alignment = new NeedlemanOverlap(-2.0, match, misMatch, longest+1); //default gapopen, match, mismatch, longestbase
 				
-				Nast nast(alignment, queryParts[i], parentParts[i]);
-				delete alignment;
+					Nast nast(alignment, queryParts[i], parentParts[i]);
+					delete alignment;
+				}
 			}
 
 			//recombine pieces to form new query sequence
@@ -78,7 +81,7 @@ 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);
 
diff --git a/makefile b/makefile
index ef5cfe7..3e83112 100644
--- a/makefile
+++ b/makefile
@@ -463,7 +463,7 @@ mothur : \
 		./logsd.o\
 		./geom.o\
 		./setlogfilecommand.o\
-		-o mothur
+		-o ../Release/mothur
 
 clean : 
 		rm \
diff --git a/nast.cpp b/nast.cpp
index 50d3b24..9e26b11 100644
--- a/nast.cpp
+++ b/nast.cpp
@@ -38,13 +38,12 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
 
 void Nast::pairwiseAlignSeqs(){	//	Here we call one of the pairwise alignment methods to align our unaligned candidate
 								//	and template sequences
-	try {
-
+	try {	
 		alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
 
 		string candAln = alignment->getSeqAAln();
 		string tempAln = alignment->getSeqBAln();
-	
+
 		if(candAln == ""){
 
 			candidateSeq->setPairwise("");
@@ -91,6 +90,11 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 //	here we do steps C-F of Fig. 2 from DeSantis et al.
 	try {
 	
+		//cout << candAln << endl;
+		//cout << tempAln << endl;
+		//cout << newTemplateAlign << endl;
+		//cout << endl;
+		
 		int longAlignmentLength = newTemplateAlign.length();	
 	
 		for(int i=0; i<longAlignmentLength; i++){				//	use the long alignment as the standard