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

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 30815a077c19ff7663d498223c49e73ddc268809..e970bab34f9276a680bce6e29faa9cf829684e12 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -858,7 +858,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
                                }
                        }
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
+                               m->mothurOutJustToScreen(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
                        }
                }
                
@@ -867,7 +867,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
                
                if (m->control_pressed) { return fDistFileName; }
                
-               m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
+               m->mothurOutJustToScreen(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 
                ofstream distFile(fDistFileName.c_str());
                distFile << outStream.str();            
@@ -2236,6 +2236,8 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
             double begClock = clock();
             unsigned long long begTime;
             
+            string fileNameForOutput = filenames[i];
+            
             for (int g = 0; g < theseFlowFileNames.size(); g++) {
                 
                 string flowFileName = theseFlowFileNames[g];
@@ -2269,7 +2271,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                 begTime = time(NULL);
                
                 
-                flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI);        
+                flowDistParentFork(numFlowCells, distFileName, numUniques, mapUniqueToSeq, mapSeqToUnique, lengths, flowDataPrI, flowDataIntI);
                 
                 m->mothurOutEndLine();
                 m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
@@ -2434,7 +2436,7 @@ int ShhherCommand::driver(vector<string> filenames, string thisCompositeFASTAFil
                        }
             
             numCompleted++;
-                       m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
+                       m->mothurOut("Total time to process " + fileNameForOutput + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
                }
                
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
@@ -2543,9 +2545,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int
                                }
                        }
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime));
-                               m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
-                               m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - begTime));
+                               m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n");
                        }
                }
                
@@ -2555,9 +2556,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int
                
                if (m->control_pressed) {}
                else {
-                       m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
-                       m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
-                       m->mothurOutEndLine();
+                       m->mothurOutJustToScreen(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
+                       m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n");
                }
         
         return 0;