aligncommand.cpp

/*
 *  aligncommand.cpp
 *  Mothur
 *
 *  Created by Sarah Westcott on 5/15/09.
 *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
 *
 *	This version of nast does everything I think that the greengenes nast server does and then some.  I have added the 
 *	feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment 
 *	method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch 
 *	(non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
 *	allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
 *	provide a better alignment because of the banding method employed by blast (I'm not sure about this).
 *
 */

#include "aligncommand.h"
#include "referencedb.h"

//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){	
	try {
		CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
		CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate);
		CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "","",false,false,true); parameters.push_back(psearch);
		CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
		CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
		CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign);
		CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
		CommandParameter pgapopen("gapopen", "Number", "", "-5.0", "", "", "","",false,false); parameters.push_back(pgapopen);
		CommandParameter pgapextend("gapextend", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapextend);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
		CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pflip);
		CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
		CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(pthreshold);
		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, "AlignCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
string AlignCommand::getHelpString(){	
	try {
		string helpString = "";
		helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
		helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
		helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
		helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.";
		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.";
		helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
		helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
		helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
		helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0.";
		helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -2.0.";
		helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.";
		helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.";
		helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
		helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
		helpString += "The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.";
		helpString += "The align.seqs command should be in the following format:";
		helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
		helpString += "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)";
		helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "getHelpString");
		exit(1);
	}
}
//**********************************************************************************************************************
string AlignCommand::getOutputPattern(string type) {
    try {
        string pattern = "";
        
        if (type == "fasta") {  pattern = "[filename],align"; } //makes file like: amazon.align
        else if (type == "alignreport") {  pattern = "[filename],align.report"; }
        else if (type == "accnos") {  pattern = "[filename],flip.accnos"; }
        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
        
        return pattern;
    }
    catch(exception& e) {
        m->errorOut(e, "AlignCommand", "getOutputPattern");
        exit(1);
    }
}
//**********************************************************************************************************************
AlignCommand::AlignCommand(){	
	try {
		abort = true; calledHelp = true; 
		setParameters();
		vector<string> tempOutNames;
		outputTypes["fasta"] = tempOutNames;
		outputTypes["alignreport"] = tempOutNames;
		outputTypes["accnos"] = tempOutNames;
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "AlignCommand");
		exit(1);
	}
}
//**********************************************************************************************************************
AlignCommand::AlignCommand(string option)  {
	try {
		abort = false; calledHelp = false;  
		ReferenceDB* rdb = ReferenceDB::getInstance();
		
		//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("align.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["fasta"] = tempOutNames;
			outputTypes["alignreport"] = tempOutNames;
			outputTypes["accnos"] = 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 = "";		}
			else {
				string path;

				it = parameters.find("reference");

				//user has given a template file
				if(it != parameters.end()){ 
					path = m->hasPath(it->second);
					//if the user has not given a path then, add inputdir. else leave path alone.
					if (path == "") {	parameters["reference"] = inputDir + it->second;		}
				}
			}

			candidateFileName = validParameter.validFile(parameters, "fasta", false);
			if (candidateFileName == "not found") { 
				//if there is a current fasta file, use it
				string filename = m->getFastaFile(); 
				if (filename != "") { candidateFileNames.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 candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
			}else { 
				m->splitAtDash(candidateFileName, candidateFileNames);
				
				//go through files and make sure they are good, if not, then disregard them
				for (int i = 0; i < candidateFileNames.size(); i++) {
					//candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
					
					bool ignore = false;
					if (candidateFileNames[i] == "current") { 
						candidateFileNames[i] = m->getFastaFile(); 
						if (candidateFileNames[i] != "") {  m->mothurOut("Using " + candidateFileNames[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
							candidateFileNames.erase(candidateFileNames.begin()+i);
							i--;
						}
					}
					
					if (!ignore) {
					
						if (inputDir != "") {
							string path = m->hasPath(candidateFileNames[i]);
							//if the user has not given a path then, add inputdir. else leave path alone.
							if (path == "") {	candidateFileNames[i] = inputDir + candidateFileNames[i];		}
						}
		
						int ableToOpen;
						ifstream in;
						ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
						in.close();	
						
						//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(candidateFileNames[i]);
								m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
								ifstream in2;
								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
								in2.close();
								candidateFileNames[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(candidateFileNames[i]);
								m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
								ifstream in2;
								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
								in2.close();
								candidateFileNames[i] = tryPath;
							}
						}
						
										

						if (ableToOpen == 1) { 
							m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
							//erase from file list
							candidateFileNames.erase(candidateFileNames.begin()+i);
							i--;
						}else {
							m->setFastaFile(candidateFileNames[i]);
						}
					}
				}
				
				//make sure there is at least one valid file left
				if (candidateFileNames.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, "ksize", false);		if (temp == "not found"){	temp = "8";				}
			m->mothurConvert(temp, kmerSize); 
			
			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);  
			
			temp = validParameter.validFile(parameters, "gapopen", false);		if (temp == "not found"){	temp = "-5.0";			}
			m->mothurConvert(temp, gapOpen);  
			
			temp = validParameter.validFile(parameters, "gapextend", false);	if (temp == "not found"){	temp = "-2.0";			}
			m->mothurConvert(temp, gapExtend); 
			
			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
			m->setProcessors(temp);
			m->mothurConvert(temp, processors); 
			
			temp = validParameter.validFile(parameters, "flip", false);			if (temp == "not found"){	temp = "f";				}
			flip = m->isTrue(temp); 
			
			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
			save = m->isTrue(temp); 
			rdb->save = save; 
			if (save) { //clear out old references
				rdb->clearMemory();
			}
			
			//this has to go after save so that if the user sets save=t and provides no reference we abort
			templateFileName = validParameter.validFile(parameters, "reference", true);
			if (templateFileName == "not found") { 
				//check for saved reference sequences
				if (rdb->referenceSeqs.size() != 0) {
					templateFileName = "saved";
				}else {
					m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command."); 
					m->mothurOutEndLine();
					abort = true; 
				}
			}else if (templateFileName == "not open") { abort = true; }	
			else {	if (save) {	rdb->setSavedReference(templateFileName);	}	}
			
			temp = validParameter.validFile(parameters, "threshold", false);	if (temp == "not found"){	temp = "0.50";			}
			m->mothurConvert(temp, threshold); 
			
			search = validParameter.validFile(parameters, "search", false);		if (search == "not found"){	search = "kmer";		}
			if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
			
			align = validParameter.validFile(parameters, "align", false);		if (align == "not found"){	align = "needleman";	}
			if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }

		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "AlignCommand");
		exit(1);
	}
}
//**********************************************************************************************************************
AlignCommand::~AlignCommand(){	

	if (abort == false) {
		for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
		delete templateDB;
	}
}
//**********************************************************************************************************************

int AlignCommand::execute(){
	try {
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}

		templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
		
		for (int s = 0; s < candidateFileNames.size(); s++) {
			if (m->control_pressed) { outputTypes.clear(); return 0; }
			
			m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
			
			if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
            map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s]));
			string alignFileName = getOutputFileName("fasta", variables);  
			string reportFileName = getOutputFileName("alignreport", variables);
			string accnosFileName = getOutputFileName("accnos", variables);
            
			bool hasAccnos = true;
			
			int numFastaSeqs = 0;
			for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
			int start = time(NULL);
		
#ifdef USE_MPI	
				int pid, numSeqsPerProcessor; 
				int tag = 2001;
				vector<unsigned long long> MPIPos;
				MPIWroteAccnos = false;
			
				MPI_Status status; 
				MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
				MPI_Comm_size(MPI_COMM_WORLD, &processors); 

				MPI_File inMPI;
				MPI_File outMPIAlign;
				MPI_File outMPIReport;
				MPI_File outMPIAccnos;
				
				int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
				int inMode=MPI_MODE_RDONLY; 
				
				char outAlignFilename[1024];
				strcpy(outAlignFilename, alignFileName.c_str());
				
				char outReportFilename[1024];
				strcpy(outReportFilename, reportFileName.c_str());
				
				char outAccnosFilename[1024];
				strcpy(outAccnosFilename, accnosFileName.c_str());
				
				char inFileName[1024];
				strcpy(inFileName, candidateFileNames[s].c_str());
				
				MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
				MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
				MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
				MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
				
				if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
				
				if (pid == 0) { //you are the root process 
					
					MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
					
					//send file positions to all processes
					for(int i = 1; i < processors; i++) { 
						MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
						MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
					}
					
					//figure out how many sequences you have to align
					numSeqsPerProcessor = numFastaSeqs / processors;
					int startIndex =  pid * numSeqsPerProcessor;
					if(pid == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; 	}
					
					//align your part
					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
					
					if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }

					for (int i = 1; i < processors; i++) {
						bool tempResult;
						MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
						if (tempResult != 0) { MPIWroteAccnos = true; }
					}
				}else{ //you are a child process
					MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
					MPIPos.resize(numFastaSeqs+1);
					MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);

					
					//figure out how many sequences you have to align
					numSeqsPerProcessor = numFastaSeqs / processors;
					int startIndex =  pid * numSeqsPerProcessor;
					if(pid == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; 	}
					
					
					//align your part
					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
					
					if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }

					MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); 
				}
				
				//close files 
				MPI_File_close(&inMPI);
				MPI_File_close(&outMPIAlign);
				MPI_File_close(&outMPIReport);
				MPI_File_close(&outMPIAccnos);
				
				//delete accnos file if blank
				if (pid == 0) {
					//delete accnos file if its blank else report to user
					if (MPIWroteAccnos) { 
						m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
						if (!flip) {
							m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); 
						}else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
						m->mothurOutEndLine();
					}else { 
						//MPI_Info info;
						//MPI_File_delete(outAccnosFilename, info);
						hasAccnos = false;	
						m->mothurRemove(accnosFileName); 
					}
				}
				
#else

			vector<unsigned long long> positions; 
		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
			positions = m->divideFile(candidateFileNames[s], processors);
			for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(new linePair(positions[i], positions[(i+1)]));	}
		#else
			if (processors == 1) {
				lines.push_back(new linePair(0, 1000));
			}else {
				positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); 
				if (positions.size() < processors) { processors = positions.size(); }
                
				//figure out how many sequences you have to process
				int numSeqsPerProcessor = numFastaSeqs / processors;
				for (int i = 0; i < processors; i++) {
					int startIndex =  i * numSeqsPerProcessor;
					if(i == (processors - 1)){	numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; 	}
					lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
				}
			}
		#endif
			
			if(processors == 1){
				numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
			}else{
				numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
			}
				
			if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear();  return 0; }
			
			//delete accnos file if its blank else report to user
			if (m->isBlank(accnosFileName)) {  m->mothurRemove(accnosFileName);  hasAccnos = false; }
			else { 
				m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
				if (!flip) {
					m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); 
				}else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
				m->mothurOutEndLine();
			}

#endif		


		#ifdef USE_MPI
			MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
					
			if (pid == 0) { //only one process should output to screen
		#endif

			outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
			outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
			if (hasAccnos)	{	outputNames.push_back(accnosFileName);	outputTypes["accnos"].push_back(accnosFileName);  }
			
		#ifdef USE_MPI
			}
		#endif

			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
			m->mothurOutEndLine();
			m->mothurOutEndLine();
		}
		
		//set align file as new current fastafile
		string currentFasta = "";
		itTypes = outputTypes.find("fasta");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
		}
		
		m->mothurOutEndLine();
		m->mothurOut("Output File Names: "); 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, "AlignCommand", "execute");
		exit(1);
	}
}

//**********************************************************************************************************************
int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
	try {
		ofstream alignmentFile;
		m->openOutputFile(alignFName, alignmentFile);
		
		ofstream accnosFile;
		m->openOutputFile(accnosFName, accnosFile);
		
		NastReport report(reportFName);
		
		ifstream inFASTA;
		m->openInputFile(filename, inFASTA);

		inFASTA.seekg(filePos->start);

		bool done = false;
		int count = 0;
		
		//moved this into driver to avoid deep copies in windows paralellized version
		Alignment* alignment;
		int longestBase = templateDB->getLongestBase();
		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);
		}
	
		while (!done) {
			
			if (m->control_pressed) {  break; }
			
			Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
			report.setCandidate(candidateSeq);

			int origNumBases = candidateSeq->getNumBases();
			string originalUnaligned = candidateSeq->getUnaligned();
			int numBasesNeeded = origNumBases * threshold;
	
			if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
				if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
					alignment->resize(candidateSeq->getUnaligned().length()+1);
				}
				Sequence temp = templateDB->findClosestSequence(candidateSeq);
				Sequence* templateSeq = &temp;
				
				float searchScore = templateDB->getSearchScore();
								
				Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
		
				Sequence* copy;
				
				Nast* nast2;
				bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
												//since nast does not make a copy of hte sequence passed, and it is used by the reporter below
												//you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
												//so this bool tells you if you need to delete it
												
				//if there is a possibility that this sequence should be reversed
				if (candidateSeq->getNumBases() < numBasesNeeded) {
					
					string wasBetter =  "";
					//if the user wants you to try the reverse
					if (flip) {
				
						//get reverse compliment
						copy = new Sequence(candidateSeq->getName(), originalUnaligned);
						copy->reverseComplement();
						
						//rerun alignment
						Sequence temp2 = templateDB->findClosestSequence(copy);
						Sequence* templateSeq2 = &temp2;
						
						searchScore = templateDB->getSearchScore();
						
						nast2 = new Nast(alignment, copy, templateSeq2);
			
						//check if any better
						if (copy->getNumBases() > candidateSeq->getNumBases()) {
							candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
							templateSeq = templateSeq2; 
							delete nast;
							nast = nast2;
							needToDeleteCopy = true;
							wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
						}else{  
							wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
							delete nast2;
							delete copy;	
						}
					}
					
					//create accnos file with names
					accnosFile << candidateSeq->getName() << wasBetter << endl;
				}
				
				report.setTemplate(templateSeq);
				report.setSearchParameters(search, searchScore);
				report.setAlignmentParameters(align, alignment);
				report.setNastParameters(*nast);
	
				alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
				
				report.print();
				delete nast;
				if (needToDeleteCopy) {   delete copy;   }
				
				count++;
			}
			delete candidateSeq;
			
			#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; }
			#endif
			
			//report progress
			if((count) % 100 == 0){	m->mothurOutJustToScreen(toString(count) + "\n"); 		}
			
		}
		//report progress
		if((count) % 100 != 0){	m->mothurOutJustToScreen(toString(count) + "\n"); 		}
		
		delete alignment;
		alignmentFile.close();
		inFASTA.close();
		accnosFile.close();
		
		return count;
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "driver");
		exit(1);
	}
}
//**********************************************************************************************************************
#ifdef USE_MPI
int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& MPIPos){
	try {
		string outputString = "";
		MPI_Status statusReport; 
		MPI_Status statusAlign; 
		MPI_Status statusAccnos; 
		MPI_Status status; 
		int pid;
		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
	
		NastReport report;
		
		if (pid == 0) {
			outputString = report.getHeaders();
			int length = outputString.length();
            
			char* buf = new char[length];
			memcpy(buf, outputString.c_str(), length);
		
			MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);

            delete buf;
		}
		
		Alignment* alignment;
		int longestBase = templateDB->getLongestBase();
		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);
		}
		
		
		for(int i=0;i<num;i++){
		
			if (m->control_pressed) { delete alignment; return 0; }

			//read next sequence
			int length = MPIPos[start+i+1] - MPIPos[start+i];

			char* buf4 = new char[length];
			//memcpy(buf4, outputString.c_str(), length);

			MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
			
			string tempBuf = buf4;

			delete buf4;

			if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
	
			istringstream iss (tempBuf,istringstream::in);

			Sequence* candidateSeq = new Sequence(iss);  
			report.setCandidate(candidateSeq);

			int origNumBases = candidateSeq->getNumBases();
			string originalUnaligned = candidateSeq->getUnaligned();
			int numBasesNeeded = origNumBases * threshold;
	
			if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
				if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
					alignment->resize(candidateSeq->getUnaligned().length()+1);
				}
								
				Sequence temp = templateDB->findClosestSequence(candidateSeq);
				Sequence* templateSeq = &temp;
				
				float searchScore = templateDB->getSearchScore();
								
				Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
				Sequence* copy;
				
				Nast* nast2;
				bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
												//since nast does not make a copy of hte sequence passed, and it is used by the reporter below
												//you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
												//so this bool tells you if you need to delete it
												
				//if there is a possibility that this sequence should be reversed
				if (candidateSeq->getNumBases() < numBasesNeeded) {
					
					string wasBetter = "";
					//if the user wants you to try the reverse
					if (flip) {
						//get reverse compliment
						copy = new Sequence(candidateSeq->getName(), originalUnaligned);
						copy->reverseComplement();
						
						//rerun alignment
						Sequence temp2 = templateDB->findClosestSequence(copy);
						Sequence* templateSeq2 = &temp2;
						
						searchScore = templateDB->getSearchScore();
						
						nast2 = new Nast(alignment, copy, templateSeq2);
			
						//check if any better
						if (copy->getNumBases() > candidateSeq->getNumBases()) {
							candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
							templateSeq = templateSeq2; 
							delete nast;
							nast = nast2;
							needToDeleteCopy = true;
							wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
						}else{  
							wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
							delete nast2;
							delete copy;	
						}
					}
					
					//create accnos file with names
					outputString = candidateSeq->getName() + wasBetter + "\n";
					
					//send results to parent
					int length = outputString.length();

					char* buf = new char[length];
					memcpy(buf, outputString.c_str(), length);
				
					MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
					delete buf;
					MPIWroteAccnos = true;
				}
				
				report.setTemplate(templateSeq);
				report.setSearchParameters(search, searchScore);
				report.setAlignmentParameters(align, alignment);
				report.setNastParameters(*nast);
	
				outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
				
				//send results to parent
				int length = outputString.length();
				char* buf2 = new char[length];
				memcpy(buf2, outputString.c_str(), length);
				
				MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
				
				delete buf2;

				outputString = report.getReport();
				
				//send results to parent
				length = outputString.length();
				char* buf3 = new char[length];
				memcpy(buf3, outputString.c_str(), length);
				
				MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
				
				delete buf3;
				delete nast;
				if (needToDeleteCopy) {   delete copy;   }
			}
			delete candidateSeq;
			
			//report progress
			if((i+1) % 100 == 0){	cout << (toString(i+1)) << endl;		}
		}
		//report progress
		if((num) % 100 != 0){	cout << (toString(num)) << endl;		}
		
		return 1;
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "driverMPI");
		exit(1);
	}
}
#endif
/**************************************************************************************************/

int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
	try {
		int num = 0;
		processIDS.resize(0);
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
		int process = 1;
		
		//loop through and create all the processes you want
		while (process != processors) {
			int pid = fork();
			
			if (pid > 0) {
				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
				process++;
			}else if (pid == 0){
				num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
				
				//pass numSeqs to parent
				ofstream out;
				string tempFile = alignFileName + toString(getpid()) + ".num.temp";
				m->openOutputFile(tempFile, out);
				out << num << endl;
				out.close();
				
				exit(0);
			}else { 
				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
				exit(0);
			}
		}
		
		//do my part
		num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
		
		//force parent to wait until all the processes are done
		for (int i=0;i<processIDS.size();i++) { 
			int temp = processIDS[i];
			wait(&temp);
		}
		
		vector<string> nonBlankAccnosFiles;
		if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
		else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
			
		for (int i = 0; i < processIDS.size(); i++) {
			ifstream in;
			string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
			m->openInputFile(tempFile, in);
			if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
			in.close(); m->mothurRemove(tempFile);
			
			m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
			m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
			
			appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
			m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
			
			if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
				nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
			}else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp"));  }
			
		}
		
		//append accnos files
		if (nonBlankAccnosFiles.size() != 0) { 
			rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
			
			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
				m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
				m->mothurRemove(nonBlankAccnosFiles[h]);
			}
		}else { //recreate the accnosfile if needed
			ofstream out;
			m->openOutputFile(accnosFName, out);
			out.close();
		}
#else
		//////////////////////////////////////////////////////////////////////////////////////////////////////
		//Windows version shared memory, so be careful when passing variables through the alignData struct. 
		//Above fork() will clone, so memory is separate, but that's not the case with windows, 
		//////////////////////////////////////////////////////////////////////////////////////////////////////
		
		vector<alignData*> pDataArray; 
		DWORD   dwThreadIdArray[processors-1];
		HANDLE  hThreadArray[processors-1]; 
		
		//Create processor worker threads.
		for( int i=0; i<processors-1; i++ ){
			//copy templateDb
			//AlignmentDB* tempDB = new AlignmentDB(*templateDB);
			
			// Allocate memory for thread data.
			string extension = "";
			if (i != 0) { extension = toString(i) + ".temp"; }
			
			alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
			pDataArray.push_back(tempalign);
			processIDS.push_back(i);
				
			//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
			//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
			hThreadArray[i] = CreateThread(NULL, 0, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
		}
		
		//need to check for line ending error
		ifstream inFASTA;
		m->openInputFile(filename, inFASTA);
		inFASTA.seekg(lines[processors-1]->start-1);
		char c = inFASTA.peek();
		
		if (c != '>') { //we need to move back
			lines[processors-1]->start--; 
		}
		
		//using the main process as a worker saves time and memory
		//do my part - do last piece because windows is looking for eof
		num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
		
		//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++){
            if (pDataArray[i]->count != pDataArray[i]->end) {
                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
            }
			num += pDataArray[i]->count;
			CloseHandle(hThreadArray[i]);
			delete pDataArray[i];
		}
		
		vector<string> nonBlankAccnosFiles;
		if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
		else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
		
		for (int i = 1; i < processors; i++) {
			m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
			m->mothurRemove((alignFileName + toString(i) + ".temp"));
			
			appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
			m->mothurRemove((reportFileName + toString(i) + ".temp"));
			
			if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
				nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
			}else { m->mothurRemove((accnosFName + toString(i) + ".temp"));  }
		}
		
		//append accnos files
		if (nonBlankAccnosFiles.size() != 0) { 
			rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
			
			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
				m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
				m->mothurRemove(nonBlankAccnosFiles[h]);
			}
		}else { //recreate the accnosfile if needed
			ofstream out;
			m->openOutputFile(accnosFName, out);
			out.close();
		}	
#endif	
		
		return num;
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "createProcesses");
		exit(1);
	}
}
//**********************************************************************************************************************

void AlignCommand::appendReportFiles(string temp, string filename) {
	try{
		
		ofstream output;
		ifstream input;
		m->openOutputFileAppend(filename, output);
		m->openInputFile(temp, input);

		while (!input.eof())	{	char c = input.get(); if (c == 10 || c == 13){	break;	}	} // get header line
				
        char buffer[4096];        
        while (!input.eof()) {
            input.read(buffer, 4096);
            output.write(buffer, input.gcount());
        }
		
		input.close();
		output.close();
	}
	catch(exception& e) {
		m->errorOut(e, "AlignCommand", "appendReportFiles");
		exit(1);
	}
}
//**********************************************************************************************************************