added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index beea1bf915fccffa6b1f92e212e8125db6010af9..65edcf75366d4096b1256266b05296146c30167b 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -179,11 +179,11 @@ DistanceCommand::DistanceCommand(string option) {
                        convert(temp, countends); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "compress", false);         if(temp == "not found"){  temp = "F"; }
                        convert(temp, compress);
@@ -289,11 +289,11 @@ int DistanceCommand::execute(){
                                
                                driverMPI(start, end, outMPI, cutoff); 
                                
-                               if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);   return 0; }
                        
                                //wait on chidren
                                for(int i = 1; i < processors; i++) { 
-                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);    return 0; }
                                        
                                        char buf[5];
                                        MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
@@ -302,7 +302,7 @@ int DistanceCommand::execute(){
                                //do your part
                                driverMPI(start, end, outMPI, cutoff); 
                                
-                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
                        
                                char buf[5];
                                strcpy(buf, "done"); 
@@ -322,7 +322,7 @@ int DistanceCommand::execute(){
                                if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
                                else { driverMPI(start, end, outputFile, mySize, output); }
        
-                               if (m->control_pressed) {  outputTypes.clear();  delete distCalculator;  return 0; }
+                               if (m->control_pressed) {  outputTypes.clear();   return 0; }
                                
                                int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
                                MPI_File outMPI;
@@ -341,7 +341,7 @@ int DistanceCommand::execute(){
                                for(int b = 1; b < processors; b++) { 
                                        unsigned long long fileSize;
                                        
-                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   return 0; }
                                        
                                        MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); 
                                        
@@ -371,7 +371,7 @@ int DistanceCommand::execute(){
                                if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
                                else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
                                
-                               if (m->control_pressed) { delete distCalculator;  return 0; }
+                               if (m->control_pressed) {  return 0; }
                        
                                //tell parent you are done.
                                MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);