working on pam

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index e5e9601781fdff5e35125b49de6ba452e180f9a2..4e1b8d39f81dc067c60575d1938a21fd1de8dee0 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -245,11 +245,11 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
                        delete candidateSeq;
                        
                        //report progress
-                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");         }
                        
                }
                //report progress
-               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");         }
                
                delete alignment;
                delete templateDB;