X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=65edcf75366d4096b1256266b05296146c30167b;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=f7dff2e3cb3fb5e81cc8d17af0bcd8d303a5ab6a;hpb=fc1ed1ae1b022719176910ab71993bd6535810ad;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index f7dff2e..65edcf7 100644
--- 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"); 
@@ -317,12 +317,12 @@ int DistanceCommand::execute(){
 			
 				//do your part
 				string outputMyPart;
-				unsigned long int mySize;
+				unsigned long long mySize;
 				
 				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;
@@ -339,9 +339,9 @@ int DistanceCommand::execute(){
 
 				//wait on chidren
 				for(int b = 1; b < processors; b++) { 
-					unsigned long int fileSize;
+					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); 
 					
@@ -367,11 +367,11 @@ int DistanceCommand::execute(){
 				MPI_File_close(&outMPI);
 			}else { //you are a child process
 				//do your part
-				unsigned long int size;
+				unsigned long long size;
 				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);
@@ -387,7 +387,7 @@ int DistanceCommand::execute(){
 			else { driver(0, numSeqs, outputFile, "square");  }
 		}else{ //you have multiple processors
 			
-			unsigned long int numDists = 0;
+			unsigned long long numDists = 0;
 			
 			if (output == "square") {
 				 numDists = numSeqs * numSeqs;
@@ -817,7 +817,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
 	try {
 		ValidCalculators validCalculator;
 		Dist* distCalculator;
@@ -913,7 +913,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
 	try {
 		ValidCalculators validCalculator;
 		Dist* distCalculator;