X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerapintailcommand.cpp;h=c5c678e78a344eed06ea0308c0df6178e7f22a51;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=01a905f40d4c69514230ad033367cc02982cd3db;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 01a905f..c5c678e 100644
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -69,6 +69,27 @@ string ChimeraPintailCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraPintailCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "chimera") {  outputFileName =  "pintail.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "pintail.accnos"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChimeraPintailCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraPintailCommand::ChimeraPintailCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -225,13 +246,13 @@ ChimeraPintailCommand::ChimeraPintailCommand(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, "increment", false);		if (temp == "not found") { temp = "25"; }
-			convert(temp, increment);
+			m->mothurConvert(temp, increment);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -392,17 +413,16 @@ int ChimeraPintailCommand::execute(){
 					}
 				}
 			}
-			
 			chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
 			
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 			string outputFileName, accnosFileName;
 			if (maskfile != "") {
-				outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";
-				accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos";
+				outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("chimera");
+				accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("accnos");
 			}else {
-				outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.chimeras";
-				accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.accnos";
+				outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+				accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
 			}
 			
 			if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0;	}
@@ -417,7 +437,7 @@ int ChimeraPintailCommand::execute(){
 		#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
@@ -487,14 +507,15 @@ int ChimeraPintailCommand::execute(){
 				MPI_File_close(&outMPIAccnos);
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 		#else
-			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);
@@ -532,6 +553,7 @@ int ChimeraPintailCommand::execute(){
 				}
 
 			#else
+				lines.push_back(new linePair(0, 1000));
 				numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 				
 				if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); 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];  }  lines.clear(); delete chimera; return 0; }
@@ -610,8 +632,8 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
 			}
 			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; }
@@ -636,7 +658,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
+int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
 	try {
 				
 		MPI_Status status; 
@@ -696,7 +718,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
 
 int ChimeraPintailCommand::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;