added mothurOutJustToScreen function and changed all counter outputs to use it.

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 033fbcad422abb62cd2470866bd4666db9e907bd..d2fbe935356a2f0752efa683a893a5892e1b2eb2 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -294,7 +294,8 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
             
             summaryfile = validParameter.validFile(parameters, "summary", true);
                        if (summaryfile == "not open") { summaryfile = ""; abort = true; }
-                       else if (summaryfile == "not found") { summaryfile = "";  }     
+                       else if (summaryfile == "not found") { summaryfile = "";  }
+            else { m->setSummaryFile(summaryfile); }
             
             if ((namefile != "") && (countfile != "")) {
                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
@@ -2408,10 +2409,10 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");       }
                
                        
                goodFile.close();
@@ -2503,7 +2504,7 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
                        }
                        
                        //report progress
-                       if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
+                       if((i) % 100 == 0){     m->mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n");           }
                }
                                
                return 1;