created mothurOut class to handle logfiles

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index 624210f5f977ac505a32119e574561ec7e92dcc2..04c7716de2958ec69353a53c0d737f8ae9cfe9dd 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:"){       mothurOut(dummy, ""); mothurOutEndLine(); blastFile >> dummy;   }
+//                     while(dummy != "query:"){       m->mothurOut(dummy, ""); m->mothurOutEndLine(); blastFile >> dummy;     }
 //                     blastFile >> seqBend;
-//                     mothurOut(toString(seqBend), ""); mothurOutEndLine();
+//                     m->mothurOut(toString(seqBend), ""); m->mothurOutEndLine();
 //                     for(int i=0;i<seqBend;i++){
 //                             seqAaln += 'Z';
 //                             seqBaln += 'X';