pat's edits prior to v.1.5

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index d672fc3df2a405a1057781dacd84c4a9f2b50d6f..958f29b39213c3fda29e810af8832fef4afa83e1 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -171,6 +171,8 @@ int AlignCommand::execute(){
                        mothurOutEndLine();
                        alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
                }
+               mothurOut("Aligning sequences...");
+               mothurOutEndLine();
                
                string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
                string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
@@ -283,7 +285,7 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                        report.setAlignmentParameters(align, alignment);
 
                        report.setNastParameters(nast);
-                       
+
                        alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
                        
                        report.print();