X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nast.cpp;fp=nast.cpp;h=9e26b11a7708590389f59b1c82e76ebca72f1bc1;hb=291eaab661778e1fd02c5c22bc388daa97bb1d54;hp=50d3b2440f3a2523257d20faabba51098b345cd4;hpb=2f17ce987b15dca9a309116d9df5131a1d3a35ee;p=mothur.git

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