working on pam

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 19094e9e76ee76981b9d5bd501df3876d401b387..9243df3873a9687d43da9da940b32da1ce9a5091 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -675,11 +675,11 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float
                        if (output == "lt") { outFile << endl; }
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
                delete distCalculator;
@@ -745,11 +745,11 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, string
                        outFile << endl; 
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
                delete distCalculator;
@@ -812,8 +812,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
                        }
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-                               cout << i << '\t' << (time(NULL) - startTime) << endl;
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                         
@@ -829,8 +828,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
                        
                }
                
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;        
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                delete distCalculator;
                return 1;
        }
@@ -907,9 +905,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 
                
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-                               cout << i << '\t' << (time(NULL) - startTime) << endl;
-                       }
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");                   }
                        
                        
                        //send results to parent
@@ -923,8 +919,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
                        delete buf;
                }
                
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+               
                MPI_File_close(&outMPI);
                delete distCalculator;
                
@@ -1002,8 +998,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 
                
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-                               cout << i << '\t' << (time(NULL) - startTime) << endl;
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                        
@@ -1018,8 +1013,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
                        delete buf;
                }
                
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+               
                MPI_File_close(&outMPI);
                delete distCalculator;
                return 1;