added logfile feature

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index cb6abf97b8840aa32bfc4e9bf95315e30e4dbf10..0645fb031f0d2a4e98b4caba5695f30ecd555474 100644 (file)
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -102,9 +102,9 @@ void BlastAlignment::setPairwiseSeqs(){     //      This method call assigns the blast ge
                        pairwiseLength = 0;
                        
 //                     string dummy;
-//                     while(dummy != "query:"){       cout << dummy << endl;blastFile >> dummy;       }
+//                     while(dummy != "query:"){       mothurOut(dummy, ""); mothurOutEndLine(); blastFile >> dummy;   }
 //                     blastFile >> seqBend;
-//                     cout << seqBend << endl;
+//                     mothurOut(toString(seqBend), ""); mothurOutEndLine();
 //                     for(int i=0;i<seqBend;i++){
 //                             seqAaln += 'Z';
 //                             seqBaln += 'X';