X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=pairwiseseqscommand.cpp;fp=pairwiseseqscommand.cpp;h=a4ccbf8f33b34b5dd8eccebf91242249cc465f28;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
new file mode 100644
index 0000000..a4ccbf8
--- /dev/null
+++ b/pairwiseseqscommand.cpp
@@ -0,0 +1,1076 @@
+/*
+ *  pairwiseseqscommand.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 10/20/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "pairwiseseqscommand.h"
+
+//**********************************************************************************************************************
+vector<string> PairwiseSeqsCommand::setParameters(){	
+	try {
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+		CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
+		CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
+		CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
+		CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
+		CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+		CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
+		CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
+		CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
+		CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
+		CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string PairwiseSeqsCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
+		helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
+		helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+		helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
+		helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
+		helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
+		helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
+		helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
+		helpString += "The calc parameter allows you to specify the method of calculating the distances.  Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
+		helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance.  Your options are: T or F. The default is T.\n";
+		helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
+		helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
+		helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed.  The default is false.\n";
+		helpString += "The pairwise.seqs command should be in the following format: \n";
+		helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
+		helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************
+PairwiseSeqsCommand::PairwiseSeqsCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["phylip"] = tempOutNames;
+		outputTypes["column"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
+	try {
+		abort = false; calledHelp = false;   
+	
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+		
+		else {
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters(); 
+			
+			ValidParameters validParameter("pairwise.seqs");
+			map<string, string>::iterator it;
+			
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["phylip"] = tempOutNames;
+			outputTypes["column"] = tempOutNames;
+			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";		}
+			
+
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			
+			if (inputDir == "not found"){	inputDir = "";		}
+
+			fastaFileName = validParameter.validFile(parameters, "fasta", false);
+			if (fastaFileName == "not found") { 				
+				//if there is a current fasta file, use it
+				string filename = m->getFastaFile(); 
+				if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}
+			else { 
+				m->splitAtDash(fastaFileName, fastaFileNames);
+				
+				//go through files and make sure they are good, if not, then disregard them
+				for (int i = 0; i < fastaFileNames.size(); i++) {
+					
+					bool ignore = false;
+					if (fastaFileNames[i] == "current") { 
+						fastaFileNames[i] = m->getFastaFile(); 
+						if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+						else { 	
+							m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; 
+							//erase from file list
+							fastaFileNames.erase(fastaFileNames.begin()+i);
+							i--;
+						}
+					}
+					
+					if (!ignore) {
+					
+						if (inputDir != "") {
+							string path = m->hasPath(fastaFileNames[i]);
+							//if the user has not given a path then, add inputdir. else leave path alone.
+							if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
+						}
+		
+						int ableToOpen;
+						ifstream in;
+
+						ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
+					
+						//if you can't open it, try default location
+						if (ableToOpen == 1) {
+							if (m->getDefaultPath() != "") { //default path is set
+								string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+								ifstream in2;
+								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+								in2.close();
+								fastaFileNames[i] = tryPath;
+							}
+						}
+						
+						//if you can't open it, try output location
+						if (ableToOpen == 1) {
+							if (m->getOutputDir() != "") { //default path is set
+								string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+								ifstream in2;
+								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+								in2.close();
+								fastaFileNames[i] = tryPath;
+							}
+						}
+						
+						in.close();					
+
+						if (ableToOpen == 1) { 
+							m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
+							//erase from file list
+							fastaFileNames.erase(fastaFileNames.begin()+i);
+							i--;
+						}else {
+							m->setFastaFile(fastaFileNames[i]);
+						}
+					}
+				}
+				
+				//make sure there is at least one valid file left
+				if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+			}
+		
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			string temp;
+			temp = validParameter.validFile(parameters, "match", false);		if (temp == "not found"){	temp = "1.0";			}
+			m->mothurConvert(temp, match);  
+			
+			temp = validParameter.validFile(parameters, "mismatch", false);		if (temp == "not found"){	temp = "-1.0";			}
+			m->mothurConvert(temp, misMatch);  
+            if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
+			
+			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-2.0";			}
+			m->mothurConvert(temp, gapOpen);  
+            if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
+			
+			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-1.0";			}
+			m->mothurConvert(temp, gapExtend); 
+            if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
+			
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
+			m->setProcessors(temp);
+			m->mothurConvert(temp, processors);
+			
+			temp = validParameter.validFile(parameters, "cutoff", false);		if(temp == "not found"){	temp = "1.0"; }
+			m->mothurConvert(temp, cutoff); 
+			
+			temp = validParameter.validFile(parameters, "countends", false);	if(temp == "not found"){	temp = "T";	}
+			countends = m->isTrue(temp); 
+			
+			temp = validParameter.validFile(parameters, "compress", false);		if(temp == "not found"){  temp = "F"; }
+			compress = m->isTrue(temp); 
+			
+			align = validParameter.validFile(parameters, "align", false);		if (align == "not found"){	align = "needleman";	}
+			
+			output = validParameter.validFile(parameters, "output", false);		if(output == "not found"){	output = "column"; }
+			if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
+			
+			calc = validParameter.validFile(parameters, "calc", false);			
+			if (calc == "not found") { calc = "onegap";  }
+			else { 
+				 if (calc == "default")  {  calc = "onegap";  }
+			}
+			m->splitAtDash(calc, Estimators);
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+int PairwiseSeqsCommand::execute(){
+	try {
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
+		longestBase = 2000; //will need to update this in driver if we find sequences with more bases.  hardcoded so we don't have the pre-read user fasta file.
+		
+		cutoff += 0.005;
+		
+		for (int s = 0; s < fastaFileNames.size(); s++) {
+			if (m->control_pressed) { outputTypes.clear(); return 0; }
+			
+			m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+			
+			if (outputDir == "") {  outputDir += m->hasPath(fastaFileNames[s]); }
+			
+			ifstream inFASTA;
+			m->openInputFile(fastaFileNames[s], inFASTA);
+			alignDB = SequenceDB(inFASTA); 
+			inFASTA.close();
+			
+			int numSeqs = alignDB.getNumSeqs();
+			int startTime = time(NULL);
+			string outputFile = "";
+				
+			if (output == "lt") { //does the user want lower triangle phylip formatted file 
+				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
+				m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
+			}else if (output == "column") { //user wants column format
+				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
+				outputTypes["column"].push_back(outputFile);
+				m->mothurRemove(outputFile);
+			}else { //assume square
+				outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
+				m->mothurRemove(outputFile);
+				outputTypes["phylip"].push_back(outputFile);
+			}
+			
+			#ifdef USE_MPI
+		
+			int pid, start, end; 
+			int tag = 2001;
+					
+			MPI_Status status; 
+			MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+			
+			//each process gets where it should start and stop in the file
+			if (output != "square") {
+				start = int (sqrt(float(pid)/float(processors)) * numSeqs);
+				end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
+			}else{
+				start = int ((float(pid)/float(processors)) * numSeqs);
+				end = int ((float(pid+1)/float(processors)) * numSeqs);
+			}
+			
+			if (output == "column") {
+				MPI_File outMPI;
+				int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
+
+			char filename[1024];
+				strcpy(filename, outputFile.c_str());
+				
+				MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
+
+				if (pid == 0) { //you are the root process 
+				
+					//do your part
+					string outputMyPart;
+					
+					driverMPI(start, end, outMPI, cutoff); 
+					
+					if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  m->mothurRemove(outputFile); return 0; }
+				
+					//wait on chidren
+					for(int i = 1; i < processors; i++) { 
+						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);   m->mothurRemove(outputFile);  return 0; }
+						
+						char buf[5];
+						MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
+					}
+				}else { //you are a child process
+					//do your part
+					driverMPI(start, end, outMPI, cutoff); 
+					
+					if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile);  return 0; }
+				
+					char buf[5];
+					strcpy(buf, "done"); 
+					//tell parent you are done.
+					MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+				}
+				
+				MPI_File_close(&outMPI);
+				
+			}else { //lower triangle format
+				if (pid == 0) { //you are the root process 
+				
+					//do your part
+					string outputMyPart;
+					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();   m->mothurRemove(outputFile);   return 0; }
+					
+					int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
+					MPI_File outMPI;
+					MPI_File inMPI;
+
+					char filename[1024];
+					strcpy(filename, outputFile.c_str());
+
+					MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+
+					//wait on chidren
+					for(int b = 1; b < processors; b++) { 
+						unsigned long long fileSize;
+						
+						if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile);   return 0; }
+						
+						MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); 
+						
+						string outTemp = outputFile + toString(b) + ".temp";
+
+						char* buf = new char[outTemp.length()];
+						memcpy(buf, outTemp.c_str(), outTemp.length());
+						
+						MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+						delete buf;
+
+						int count = 0;
+						while (count < fileSize) { 
+							char buf2[1];
+							MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
+							MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
+							count += 1;
+						}
+						
+						MPI_File_close(&inMPI); //deleted on close
+					}
+					
+					MPI_File_close(&outMPI);
+				}else { //you are a child process
+					//do your part
+					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) {  return 0; }
+				
+					//tell parent you are done.
+					MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
+				}
+			}
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+	#else		
+					
+		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+			//if you don't need to fork anything
+			if(processors == 1){
+				if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
+				else { driver(0, numSeqs, outputFile, "square");  }
+			}else{ //you have multiple processors
+				
+				for (int i = 0; i < processors; i++) {
+					distlinePair tempLine;
+					lines.push_back(tempLine);
+					if (output != "square") {
+						lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
+						lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+					}else{
+						lines[i].start = int ((float(i)/float(processors)) * numSeqs);
+						lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
+					}
+				}
+				
+				createProcesses(outputFile); 
+			}
+		//#else
+			//ifstream inFASTA;
+			//if (output != "square") {  driver(0, numSeqs, outputFile, cutoff); }
+			//else { driver(0, numSeqs, outputFile, "square");  }
+		//#endif
+		
+	#endif
+			if (m->control_pressed) { outputTypes.clear();   m->mothurRemove(outputFile); return 0; }
+			
+			#ifdef USE_MPI
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+				if (pid == 0) { //only one process should output to screen
+			#endif
+			
+			ifstream fileHandle;
+			fileHandle.open(outputFile.c_str());
+			if(fileHandle) {
+				m->gobble(fileHandle);
+				if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff.");  m->mothurOutEndLine(); }
+			}
+			
+			if (compress) {
+				m->mothurOut("Compressing..."); m->mothurOutEndLine();
+				m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
+				system(("gzip -v " + outputFile).c_str());
+				outputNames.push_back(outputFile + ".gz");
+			}else { outputNames.push_back(outputFile); }
+			
+			#ifdef USE_MPI
+				}
+			#endif
+			
+			m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+			
+			if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
+		}
+		
+		//set phylip file as new current phylipfile
+		string current = "";
+		itTypes = outputTypes.find("phylip");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+		}
+		
+		//set column file as new current columnfile
+		itTypes = outputTypes.find("column");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+		}
+		
+		m->mothurOutEndLine();
+		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
+		m->mothurOutEndLine();
+		
+
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "execute");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+void PairwiseSeqsCommand::createProcesses(string filename) {
+	try {
+        int process = 1;
+		processIDS.clear();
+        
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		
+		
+		//loop through and create all the processes you want
+		while (process != processors) {
+			int pid = fork();
+			
+			if (pid > 0) {
+				processIDS.push_back(pid); 
+				process++;
+			}else if (pid == 0){
+				if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
+				else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
+				exit(0);
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
+				exit(0);
+			}
+		}
+		
+		//parent do my part
+		if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+		else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+		
+		//force parent to wait until all the processes are done
+		for (int i=0;i<processIDS.size();i++) { 
+			int temp = processIDS[i];
+			wait(&temp);
+		}
+#else     
+        //////////////////////////////////////////////////////////////////////////////////////////////////////
+		//Windows version shared memory, so be careful when passing variables through the distanceData struct. 
+		//Above fork() will clone, so memory is separate, but that's not the case with windows, 
+		//that's why the distance calculator was moved inside of the driver to make separate copies.
+		//////////////////////////////////////////////////////////////////////////////////////////////////////
+		
+		vector<pairwiseData*> pDataArray; //[processors-1];
+		DWORD   dwThreadIdArray[processors-1];
+		HANDLE  hThreadArray[processors-1]; 
+		
+		//Create processor-1 worker threads.
+		for( int i=0; i<processors-1; i++ ){
+			string extension = toString(i) + ".temp";
+
+			// Allocate memory for thread data.
+			pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
+			pDataArray.push_back(tempDist);
+			processIDS.push_back(i);
+			
+			if (output != "square") { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);  } 
+            else { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseSquareThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);  }
+		}
+		
+		//do your part
+		if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+		else { driver(lines[0].start, lines[0].end, filename, "square"); }
+		
+		//Wait until all threads have terminated.
+		WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+		
+		//Close all thread handles and free memory allocations.
+		for(int i=0; i < pDataArray.size(); i++){
+			CloseHandle(hThreadArray[i]);
+			delete pDataArray[i];
+		}
+
+#endif
+        
+        //append and remove temp files
+		for (int i=0;i<processIDS.size();i++) { 
+			m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+			m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
+		}
+        
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "createProcesses");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
+	try {
+
+		int startTime = time(NULL);
+        
+        Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+        
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+		
+		//column file
+		ofstream outFile(dFileName.c_str(), ios::trunc);
+		outFile.setf(ios::fixed, ios::showpoint);
+		outFile << setprecision(4);
+		
+		if((output == "lt") && startLine == 0){	outFile << alignDB.getNumSeqs() << endl;	}
+		
+		for(int i=startLine;i<endLine;i++){
+			if(output == "lt")	{	
+				string name = alignDB.get(i).getName();
+				if (name.length() < 10) { //pad with spaces to make compatible
+					while (name.length() < 10) {  name += " ";  }
+				}
+				outFile << name << '\t';	
+			}
+			
+			for(int j=0;j<i;j++){
+				
+				if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
+				
+				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
+				}
+				
+				if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
+				}
+				
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
+
+				
+				distCalculator->calcDist(seqI, seqJ);
+				double dist = distCalculator->getDist();
+				
+				if(dist <= cutoff){
+					if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
+				}
+				if (output == "lt") {  outFile << dist << '\t'; }
+			}
+			
+			if (output == "lt") { outFile << endl; }
+			
+			if(i % 100 == 0){
+				m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+			}
+			
+		}
+		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+		
+		outFile.close();
+        delete alignment;
+        delete distCalculator;
+		
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "driver");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
+	try {
+
+		int startTime = time(NULL);
+        
+        Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+
+		//column file
+		ofstream outFile(dFileName.c_str(), ios::trunc);
+		outFile.setf(ios::fixed, ios::showpoint);
+		outFile << setprecision(4);
+		
+		if(startLine == 0){	outFile << alignDB.getNumSeqs() << endl;	}
+		
+		for(int i=startLine;i<endLine;i++){
+				
+			string name = alignDB.get(i).getName();
+			//pad with spaces to make compatible
+			if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
+				
+			outFile << name << '\t';	
+			
+			for(int j=0;j<alignDB.getNumSeqs();j++){
+				
+				if (m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
+				
+				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
+				}
+				
+				if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
+				}
+				
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
+				
+				distCalculator->calcDist(seqI, seqJ);
+				double dist = distCalculator->getDist();
+								
+				outFile << dist << '\t'; 
+			}
+			
+			outFile << endl; 
+			
+			if(i % 100 == 0){
+				m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+			}
+			
+		}
+		m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+		
+		outFile.close();
+        delete alignment;
+        delete distCalculator;
+		
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "driver");
+		exit(1);
+	}
+}
+#ifdef USE_MPI
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
+	try {
+		MPI_Status status;
+		int startTime = time(NULL);
+        
+        Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+
+		string outputString = "";
+		
+		for(int i=startLine;i<endLine;i++){
+	
+			for(int j=0;j<i;j++){
+				
+				if (m->control_pressed) { delete alignment; delete distCalculator; return 0;  }
+				
+				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
+				}
+				
+				if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
+				}
+				
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
+				
+				distCalculator->calcDist(seqI, seqJ);
+				double dist = distCalculator->getDist();
+				
+				if(dist <= cutoff){
+					 outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); 
+				}
+			}
+			
+			if(i % 100 == 0){
+				//m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+				cout << i << '\t' << (time(NULL) - startTime) << endl;
+			}
+			
+			 
+			//send results to parent
+			int length = outputString.length();
+
+			char* buf = new char[length];
+			memcpy(buf, outputString.c_str(), length);
+			
+			MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+			outputString = "";
+			delete buf;
+			
+		}
+		delete alignment;
+        delete distCalculator;
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
+	try {
+		MPI_Status status;
+		
+		MPI_File outMPI;
+		int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
+
+		char filename[1024];
+		strcpy(filename, file.c_str());
+
+		MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+
+		Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+        
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+
+		
+		string outputString = "";
+		size = 0;
+		
+		if(startLine == 0){	outputString += toString(alignDB.getNumSeqs()) + "\n";	}
+		
+		for(int i=startLine;i<endLine;i++){
+				
+			string name = alignDB.get(i).getName();
+			if (name.length() < 10) { //pad with spaces to make compatible
+				while (name.length() < 10) {  name += " ";  }
+			}
+			outputString += name + "\t";	
+			
+			for(int j=0;j<i;j++){
+				
+				if (m->control_pressed) { delete alignment; delete distCalculator; return 0;  }
+				
+				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
+				}
+				
+				if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
+				}
+				
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
+				
+				distCalculator->calcDist(seqI, seqJ);
+				double dist = distCalculator->getDist();
+				
+				outputString += toString(dist) + "\t"; 
+			}
+			
+			outputString += "\n"; 
+			
+			//send results to parent
+			int length = outputString.length();
+			char* buf = new char[length];
+			memcpy(buf, outputString.c_str(), length);
+			
+			MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+			size += outputString.length();
+			outputString = "";
+			delete buf;
+		}
+		
+		MPI_File_close(&outMPI);
+        delete alignment;
+        delete distCalculator;
+		
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
+	try {
+		MPI_Status status;
+		
+		MPI_File outMPI;
+		int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
+
+		char filename[1024];
+		strcpy(filename, file.c_str());
+
+		MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+		
+		Alignment* alignment;
+        if(align == "gotoh")			{	alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);			}
+		else if(align == "needleman")	{	alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);				}
+		else if(align == "blast")		{	alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);		}
+		else if(align == "noalign")		{	alignment = new NoAlign();													}
+		else {
+			m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
+			m->mothurOutEndLine();
+			alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
+		}
+		
+        ValidCalculators validCalculator;
+        Dist* distCalculator;
+        if (countends) {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")			{	distCalculator = new ignoreGaps();	}
+                else if (Estimators[0] == "eachgap")	{	distCalculator = new eachGapDist();	}
+                else if (Estimators[0] == "onegap")		{	distCalculator = new oneGapDist();	}
+            }
+        }else {
+            if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) { 
+                if (Estimators[0] == "nogaps")		{	distCalculator = new ignoreGaps();					}
+                else if (Estimators[0] == "eachgap"){	distCalculator = new eachGapIgnoreTermGapDist();	}
+                else if (Estimators[0] == "onegap")	{	distCalculator = new oneGapIgnoreTermGapDist();		}
+            }
+        }
+        
+		string outputString = "";
+		size = 0;
+		
+		if(startLine == 0){	outputString += toString(alignDB.getNumSeqs()) + "\n";	}
+		
+		for(int i=startLine;i<endLine;i++){
+				
+			string name = alignDB.get(i).getName();
+			if (name.length() < 10) { //pad with spaces to make compatible
+				while (name.length() < 10) {  name += " ";  }
+			}
+			outputString += name + "\t";	
+			
+			for(int j=0;j<alignDB.getNumSeqs();j++){
+				
+				if (m->control_pressed) {  delete alignment; return 0;  }
+				
+				if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(i).getUnaligned().length()+1);
+				}
+				
+				if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
+					alignment->resize(alignDB.get(j).getUnaligned().length()+1);
+				}
+				
+				Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
+				Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
+				
+				alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
+				seqI.setAligned(alignment->getSeqAAln());
+				seqJ.setAligned(alignment->getSeqBAln());
+				
+				distCalculator->calcDist(seqI, seqJ);
+				double dist = distCalculator->getDist();
+				
+				outputString += toString(dist) + "\t"; 
+			}
+			
+			outputString += "\n"; 
+
+			//send results to parent
+			int length = outputString.length();
+			char* buf = new char[length];
+			memcpy(buf, outputString.c_str(), length);
+			
+			MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+			size += outputString.length();
+			outputString = "";
+			delete buf;
+		}
+		
+		MPI_File_close(&outMPI);
+		
+        delete alignment;
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
+		exit(1);
+	}
+}
+#endif
+/**************************************************************************************************/
+