finished chimeraslayer method and added get.listcount command

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index da807bdd5103e5f8f8024217e12b15e4ba1b59ce..48c67ec4569ef65381b087c02323545302097bfe 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -276,26 +276,27 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                        if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
                                alignment->resize(candidateSeq->getUnaligned().length()+1);
                        }
-                       
+       
                        report.setCandidate(candidateSeq);
        
                        Sequence temp = templateDB->findClosestSequence(candidateSeq);
                        Sequence* templateSeq = &temp;
-                       
+       
                        report.setTemplate(templateSeq);
                        report.setSearchParameters(search, templateDB->getSearchScore());
-                       
+                               
                        Nast nast(alignment, candidateSeq, templateSeq);
 
                        report.setAlignmentParameters(align, alignment);
-
+       
                        report.setNastParameters(nast);
 
                        alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
-                       
+                               
                        report.print();
                        
-                       delete candidateSeq;            
+                       delete candidateSeq;
+       
                }
                
                alignmentFile.close();