X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=fc98e0fc45c3b576a3e2420ac415c016266b4c1c;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=fd80ec965b4040f78dce01579e1974760fbb2a89;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index fd80ec9..fc98e0f 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -223,13 +223,13 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
 			
 			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, "window", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "numwanted", false);		if (temp == "not found") { temp = "20"; }
-			convert(temp, numwanted);
+			m->mothurConvert(temp, numwanted);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -293,13 +293,13 @@ int ChimeraCcodeCommand::execute(){
 
 			string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
 			
-			if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear(); return 0;	}
+			if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear(); return 0;	}
 			
 		#ifdef USE_MPI
 		
 				int pid, numSeqsPerProcessor; 
 				int tag = 2001;
-				vector<unsigned long int> MPIPos;
+				vector<unsigned long long> MPIPos;
 								
 				MPI_Status status; 
 				MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -325,7 +325,7 @@ int ChimeraCcodeCommand::execute(){
 				MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 				MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 
-				if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear();  delete chimera; return 0;  }
+				if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();  delete chimera; return 0;  }
 			
 				if (pid == 0) { //you are the root process 
 					string outTemp = "For full window mapping info refer to " + mapInfo + "\n";
@@ -355,7 +355,7 @@ int ChimeraCcodeCommand::execute(){
 					//align your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 					
-					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear();  delete chimera; return 0;  }
+					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  m->mothurRemove(outputFileName);  m->mothurRemove(accnosFileName);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();  delete chimera; return 0;  }
 
 				}else{ //you are a child process
 					MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -371,7 +371,7 @@ int ChimeraCcodeCommand::execute(){
 					//align your part
 					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
 					
-					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  outputTypes.clear(); delete chimera; return 0;  }
+					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  outputTypes.clear(); delete chimera; return 0;  }
 				}
 				
 				//close files 
@@ -390,19 +390,21 @@ int ChimeraCcodeCommand::execute(){
 
 			outHeader.close();
 			
-			vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
-				
-			for (int i = 0; i < (positions.size()-1); i++) {
-				lines.push_back(new linePair(positions[i], positions[(i+1)]));
-			}	
+			
 			
 			//break up file
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
+			
+				for (int i = 0; i < (positions.size()-1); i++) {
+					lines.push_back(new linePair(positions[i], positions[(i+1)]));
+				}	
+			
 				if(processors == 1){
 										
 					numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 					
-					if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
+					if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 					
 				}else{
 					processIDS.resize(0);
@@ -415,19 +417,19 @@ int ChimeraCcodeCommand::execute(){
 					//append output files
 					for(int i=1;i<processors;i++){
 						m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
-						remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+						m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
 					}
 					
 					//append output files
 					for(int i=1;i<processors;i++){
 						m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
-						remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
+						m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
 					}
 					
 					if (m->control_pressed) { 
-						remove(outputFileName.c_str()); 
-						remove(accnosFileName.c_str());
-						for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} outputTypes.clear();
+						m->mothurRemove(outputFileName); 
+						m->mothurRemove(accnosFileName);
+						for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();
 						for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 						delete chimera;
 						return 0;
@@ -436,15 +438,16 @@ int ChimeraCcodeCommand::execute(){
 				}
 
 			#else
+				lines.push_back(new linePair(0, 1000));
 				numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 				
-				if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
+				if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
 				
 			#endif
 	
 			m->appendFiles(outputFileName, tempHeader);
 		
-			remove(outputFileName.c_str());
+			m->mothurRemove(outputFileName);
 			rename(tempHeader.c_str(), outputFileName.c_str());
 		#endif
 		
@@ -521,8 +524,8 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
 			}
 			delete candidateSeq;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				unsigned long int pos = inFASTA.tellg();
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
 				if (inFASTA.eof()) { break; }
@@ -547,7 +550,7 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
+int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
 	try {
 				
 		MPI_Status status; 
@@ -608,7 +611,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 0;
 		int num = 0;
 		
@@ -648,7 +651,7 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename,
 			string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 			m->openInputFile(tempFile, in);
 			if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
-			in.close(); remove(tempFile.c_str());
+			in.close(); m->mothurRemove(tempFile);
 		}
 		
 		return num;