random chagnes from pat

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 28cc659e9c5a6090bcd6cb5edecdc7cf9d6c9ec0..bf65fa2b46ea319bf54ab74a9696bb9e7b22fafe 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -45,7 +45,7 @@ void Nast::pairwiseAlignSeqs(){       //      Here we call one of the pairwise alignment me
 
                string candAln = alignment->getSeqAAln();
                string tempAln = alignment->getSeqBAln();
-
+       
                if(candAln == ""){
 
                        candidateSeq->setPairwise("");
@@ -78,6 +78,7 @@ void Nast::pairwiseAlignSeqs(){       //      Here we call one of the pairwise alignment me
 
                candidateSeq->setPairwise(candAln);                                     //      set the pairwise sequences in the Sequence objects for
                templateSeq->setPairwise(tempAln);                                      //      the candidate and template sequences
+
        }
        catch(exception& e) {
                m->errorOut(e, "Nast", "pairwiseAlignSeqs");
@@ -91,11 +92,6 @@ 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();