modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 4848eb20be0b5cfdb43715b5ba1589d253ba4571..6a4ae3db2f679ee4ccadf2b0ff3270f5da4f15aa 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -32,7 +32,6 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
                errorOut(e, "Nast", "Nast");
                exit(1);
        }
-
 }
 
 /**************************************************************************************************/
@@ -42,10 +41,10 @@ void Nast::pairwiseAlignSeqs(){     //      Here we call one of the pairwise alignment me
        try {
 
                alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
-               
+       
                string candAln = alignment->getSeqAAln();
                string tempAln = alignment->getSeqBAln();
-               
+       
                if(candAln == ""){
 
                        candidateSeq->setPairwise("");
@@ -78,7 +77,6 @@ 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) {
                errorOut(e, "Nast", "pairwiseAlignSeqs");