fixed problem with chimera.slayer realigner

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 50d3b2440f3a2523257d20faabba51098b345cd4..9e26b11a7708590389f59b1c82e76ebca72f1bc1 100644 (file)
--- 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