added parse.list command

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index f247037cc915fd1d54d9d1e050abde8f73711fba..c91c9fab537172b3e02808b700af881affffc368 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -26,13 +26,11 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
                maxInsertLength = 0;
                pairwiseAlignSeqs();    //      This is part A in Fig. 2 of DeSantis et al.
                regapSequences();               //      This is parts B-F in Fig. 2 of DeSantis et al.
-
        }
        catch(exception& e) {
                errorOut(e, "Nast", "Nast");
                exit(1);
        }
-
 }
 
 /**************************************************************************************************/
@@ -40,12 +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 {
-               
+
                alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
-       
+
                string candAln = alignment->getSeqAAln();
                string tempAln = alignment->getSeqBAln();
-
+       
                if(candAln == ""){
 
                        candidateSeq->setPairwise("");
@@ -78,7 +76,6 @@ 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");