working on pam

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 16fcbf56247bb73bc979f50d4b06ee4ec20e1e7c..9243df3873a9687d43da9da940b32da1ce9a5091 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -594,6 +594,9 @@ void DistanceCommand::createProcesses(string filename) {
                
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != (pDataArray[i]->endLine-pDataArray[i]->startLine)) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->endLine-pDataArray[i]->startLine) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
@@ -672,11 +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;
@@ -742,11 +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;
@@ -809,8 +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"); 
                        }
                        
                         
@@ -826,8 +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;
        }
@@ -904,9 +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
@@ -920,8 +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;
                
@@ -999,8 +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"); 
                        }
                        
                        
@@ -1015,8 +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;