File: matrixoutputcommand.cpp

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/*
 *  matrixoutputcommand.cpp
 *  Mothur
 *
 *  Created by Sarah Westcott on 5/20/09.
 *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
 *
 */

#include "matrixoutputcommand.h"
#include "subsample.h"

//**********************************************************************************************************************
vector<string> MatrixOutputCommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","phylip",false,true,true); parameters.push_back(pshared);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
        CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
		CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
        CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
        CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
        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, "MatrixOutputCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
string MatrixOutputCommand::getHelpString(){	
	try {
		string helpString = "";
		ValidCalculators validCalculator;
		helpString += "The dist.shared command parameters are shared, groups, calc, output, processors, subsample, iters, mode, and label.  shared is a required, unless you have a valid current file.\n";
		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
		helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
        helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
        helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
		helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
		helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
        helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
		helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
		helpString += "The default value for groups is all the groups in your groupfile.\n";
		helpString += "The default value for calc is jclass and thetayc.\n";
		helpString += validCalculator.printCalc("matrix");
		helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "MatrixOutputCommand", "getHelpString");
		exit(1);
	}
}
//**********************************************************************************************************************
string MatrixOutputCommand::getOutputPattern(string type) {
    try {
        string pattern = "";
        
        if (type == "phylip") {  pattern = "[filename],[calc],[distance],[outputtag],dist-[filename],[calc],[distance],[outputtag],[tag2],dist"; } 
        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
        
        return pattern;
    }
    catch(exception& e) {
        m->errorOut(e, "MatrixOutputCommand", "getOutputPattern");
        exit(1);
    }
}
//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){	
	try {
		abort = true; calledHelp = true; 
		setParameters();
		vector<string> tempOutNames;
		outputTypes["phylip"] = tempOutNames;
	}
	catch(exception& e) {
		m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
		exit(1);
	}
}
//**********************************************************************************************************************

MatrixOutputCommand::MatrixOutputCommand(string option)  {
	try {
		abort = false; calledHelp = false;   
		allLines = 1;
				
		//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();
			map<string,string>::iterator it;
			
			ValidParameters validParameter;
		
			//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;
			
			//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("shared");
				//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["shared"] = inputDir + it->second;		}
				}
			}
			
			sharedfile = validParameter.validFile(parameters, "shared", true);
			if (sharedfile == "not found") { 			
				//if there is a current shared file, use it
				sharedfile = m->getSharedFile(); 
				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
			}else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
			else { m->setSharedFile(sharedfile); }
			
			//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 = "";	
				outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it	
			}
			
			//check for optional parameter and set defaults
			// ...at some point should added some additional type checking...
			label = validParameter.validFile(parameters, "label", false);			
			if (label == "not found") { label = ""; }
			else { 
				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
				else { allLines = 1;  }
			}
			
			output = validParameter.validFile(parameters, "output", false);		if(output == "not found"){	output = "lt"; }
			if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
            
            mode = validParameter.validFile(parameters, "mode", false);		if(mode == "not found"){	mode = "average"; }
			if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
			
			groups = validParameter.validFile(parameters, "groups", false);			
			if (groups == "not found") { groups = ""; }
			else { 
				m->splitAtDash(groups, Groups);
				m->setGroups(Groups);
			}
			
			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
			m->setProcessors(temp);
			m->mothurConvert(temp, processors); 
				
			calc = validParameter.validFile(parameters, "calc", false);			
			if (calc == "not found") { calc = "jclass-thetayc";  }
			else { 
				 if (calc == "default")  {  calc = "jclass-thetayc";  }
			}
			m->splitAtDash(calc, Estimators);
			if (m->inUsersGroups("citation", Estimators)) { 
				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
				//remove citation from list of calcs
				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
			}
            
            temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
			m->mothurConvert(temp, iters); 
            
            temp = validParameter.validFile(parameters, "subsample", false);		if (temp == "not found") { temp = "F"; }
			if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
            else {  
                if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; }  //we will set it to smallest group later 
                else { subsample = false; }
            }
            
            if (subsample == false) { iters = 0; }
            
			if (abort == false) {
			
				ValidCalculators validCalculator;
				
				int i;
				for (i=0; i<Estimators.size(); i++) {
					if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) { 
						if (Estimators[i] == "sharedsobs") { 
							matrixCalculators.push_back(new SharedSobsCS());
						}else if (Estimators[i] == "sharedchao") { 
							matrixCalculators.push_back(new SharedChao1());
						}else if (Estimators[i] == "sharedace") { 
							matrixCalculators.push_back(new SharedAce());
						}else if (Estimators[i] == "jabund") { 	
							matrixCalculators.push_back(new JAbund());
						}else if (Estimators[i] == "sorabund") { 
							matrixCalculators.push_back(new SorAbund());
						}else if (Estimators[i] == "jclass") { 
							matrixCalculators.push_back(new Jclass());
						}else if (Estimators[i] == "sorclass") { 
							matrixCalculators.push_back(new SorClass());
						}else if (Estimators[i] == "jest") { 
							matrixCalculators.push_back(new Jest());
						}else if (Estimators[i] == "sorest") { 
							matrixCalculators.push_back(new SorEst());
						}else if (Estimators[i] == "thetayc") { 
							matrixCalculators.push_back(new ThetaYC());
						}else if (Estimators[i] == "thetan") { 
							matrixCalculators.push_back(new ThetaN());
						}else if (Estimators[i] == "kstest") { 
							matrixCalculators.push_back(new KSTest());
						}else if (Estimators[i] == "sharednseqs") { 
							matrixCalculators.push_back(new SharedNSeqs());
						}else if (Estimators[i] == "ochiai") { 
							matrixCalculators.push_back(new Ochiai());
						}else if (Estimators[i] == "anderberg") { 
							matrixCalculators.push_back(new Anderberg());
						}else if (Estimators[i] == "kulczynski") { 
							matrixCalculators.push_back(new Kulczynski());
						}else if (Estimators[i] == "kulczynskicody") { 
							matrixCalculators.push_back(new KulczynskiCody());
						}else if (Estimators[i] == "lennon") { 
							matrixCalculators.push_back(new Lennon());
						}else if (Estimators[i] == "morisitahorn") { 
							matrixCalculators.push_back(new MorHorn());
						}else if (Estimators[i] == "braycurtis") { 
							matrixCalculators.push_back(new BrayCurtis());
						}else if (Estimators[i] == "whittaker") { 
							matrixCalculators.push_back(new Whittaker());
						}else if (Estimators[i] == "odum") { 
							matrixCalculators.push_back(new Odum());
						}else if (Estimators[i] == "canberra") { 
							matrixCalculators.push_back(new Canberra());
						}else if (Estimators[i] == "structeuclidean") { 
							matrixCalculators.push_back(new StructEuclidean());
						}else if (Estimators[i] == "structchord") { 
							matrixCalculators.push_back(new StructChord());
						}else if (Estimators[i] == "hellinger") { 
							matrixCalculators.push_back(new Hellinger());
						}else if (Estimators[i] == "manhattan") { 
							matrixCalculators.push_back(new Manhattan());
						}else if (Estimators[i] == "structpearson") { 
							matrixCalculators.push_back(new StructPearson());
						}else if (Estimators[i] == "soergel") { 
							matrixCalculators.push_back(new Soergel());
						}else if (Estimators[i] == "spearman") { 
							matrixCalculators.push_back(new Spearman());
						}else if (Estimators[i] == "structkulczynski") { 
							matrixCalculators.push_back(new StructKulczynski());
						}else if (Estimators[i] == "speciesprofile") { 
							matrixCalculators.push_back(new SpeciesProfile());
						}else if (Estimators[i] == "hamming") { 
							matrixCalculators.push_back(new Hamming());
						}else if (Estimators[i] == "structchi2") { 
							matrixCalculators.push_back(new StructChi2());
						}else if (Estimators[i] == "gower") { 
							matrixCalculators.push_back(new Gower());
						}else if (Estimators[i] == "memchi2") { 
							matrixCalculators.push_back(new MemChi2());
						}else if (Estimators[i] == "memchord") { 
							matrixCalculators.push_back(new MemChord());
						}else if (Estimators[i] == "memeuclidean") { 
							matrixCalculators.push_back(new MemEuclidean());
						}else if (Estimators[i] == "mempearson") { 
							matrixCalculators.push_back(new MemPearson());
                        }else if (Estimators[i] == "jsd") {
                                matrixCalculators.push_back(new JSD());
                        }else if (Estimators[i] == "rjsd") {
                            matrixCalculators.push_back(new RJSD());
						}
					}
				}
				
			}
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
		exit(1);
	}
}

//**********************************************************************************************************************

MatrixOutputCommand::~MatrixOutputCommand(){}

//**********************************************************************************************************************

int MatrixOutputCommand::execute(){
	try {
		
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
			
		//if the users entered no valid calculators don't execute command
		if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }
			
		input = new InputData(sharedfile, "sharedfile");
		lookup = input->getSharedRAbundVectors();
		string lastLabel = lookup[0]->getLabel();
		
		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
		set<string> processedLabels;
		set<string> userLabels = labels;
					
		if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0;}
        
        if (subsample) { 
            if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
                subsampleSize = lookup[0]->getNumSeqs();
                for (int i = 1; i < lookup.size(); i++) {
                    int thisSize = lookup[i]->getNumSeqs();
                    
                    if (thisSize < subsampleSize) {	subsampleSize = thisSize;	}
                }
            }else {
                m->clearGroups();
                Groups.clear();
                vector<SharedRAbundVector*> temp;
                for (int i = 0; i < lookup.size(); i++) {
                    if (lookup[i]->getNumSeqs() < subsampleSize) { 
                        m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
                        delete lookup[i];
                    }else { 
                        Groups.push_back(lookup[i]->getGroup()); 
                        temp.push_back(lookup[i]);
                    }
                } 
                lookup = temp;
                m->setGroups(Groups);
            }
            
            if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
        }
        
		numGroups = lookup.size();
        lines.resize(processors);
		for (int i = 0; i < processors; i++) {
			lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
			lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
		}	
        
		if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0;  }
				
		//as long as you are not at the end of the file or done wih the lines you want
		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
		
			if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
		
			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
				process(lookup);
				
				processedLabels.insert(lookup[0]->getLabel());
				userLabels.erase(lookup[0]->getLabel());
			}
			
			if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = lookup[0]->getLabel();
				
				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
				lookup = input->getSharedRAbundVectors(lastLabel);

				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
				process(lookup);
				
				processedLabels.insert(lookup[0]->getLabel());
				userLabels.erase(lookup[0]->getLabel());
				
				//restore real lastlabel to save below
				lookup[0]->setLabel(saveLabel);
			}

			lastLabel = lookup[0]->getLabel();			
			
			//get next line to process
			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
			lookup = input->getSharedRAbundVectors();
		}
		
		if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }

		//output error messages about any remaining user labels
		set<string>::iterator it;
		bool needToRun = false;
		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
			m->mothurOut("Your file does not include the label " + *it);  
			if (processedLabels.count(lastLabel) != 1) {
				m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
				needToRun = true;
			}else {
				m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
			}
		}
		
		if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }

		//run last label if you need to
		if (needToRun == true)  {
			for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  } 
			lookup = input->getSharedRAbundVectors(lastLabel);

			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
			process(lookup);
			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
		}
		
		if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
		
		//reset groups parameter
		m->clearGroups();  
		
		//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); }
		}
		
		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, "MatrixOutputCommand", "execute");
		exit(1);
	}
}
/***********************************************************/
void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
	try {
		
		out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
				
		if (output == "lt") {
            out << simMatrix.size() << endl;
			for (int b = 0; b < simMatrix.size(); b++)	{
				out << lookup[b]->getGroup() << '\t';
				for (int n = 0; n < b; n++)	{
					out << simMatrix[b][n] << '\t'; 
				}
				out << endl;
			}
        }else if (output == "column") {
            for (int b = 0; b < simMatrix.size(); b++)	{
                for (int n = 0; n < b; n++)	{
                    out << lookup[b]->getGroup() << '\t' << lookup[n]->getGroup() << '\t' << simMatrix[b][n] << endl;
                }
            }
		}else{
            out << simMatrix.size() << endl;
			for (int b = 0; b < simMatrix.size(); b++)	{
				out << lookup[b]->getGroup() << '\t';
				for (int n = 0; n < simMatrix[b].size(); n++)	{
					out << simMatrix[b][n] << '\t'; 
				}
				out << endl;
			}
		}
	}
	catch(exception& e) {
		m->errorOut(e, "MatrixOutputCommand", "printSims");
		exit(1);
	}
}
/***********************************************************/
int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
	try {
		vector< vector< vector<seqDist> > > calcDistsTotals;  //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
        vector< vector<seqDist>  > calcDists; calcDists.resize(matrixCalculators.size()); 		
                  
        for (int thisIter = 0; thisIter < iters+1; thisIter++) {
            map<string, string> variables; 
            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
            variables["[distance]"] = thisLookup[0]->getLabel();
            variables["[tag2]"] = "";
            
            vector<SharedRAbundVector*> thisItersLookup = thisLookup;
            
            if (subsample && (thisIter != 0)) {
                SubSample sample;
                vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
                
                //make copy of lookup so we don't get access violations
                vector<SharedRAbundVector*> newLookup;
                for (int k = 0; k < thisItersLookup.size(); k++) {
                    SharedRAbundVector* temp = new SharedRAbundVector();
                    temp->setLabel(thisItersLookup[k]->getLabel());
                    temp->setGroup(thisItersLookup[k]->getGroup());
                    newLookup.push_back(temp);
                }
                
                //for each bin
                for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
                    if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                    for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
                }
                
                tempLabels = sample.getSample(newLookup, subsampleSize);
                thisItersLookup = newLookup;
            }
        
            if(processors == 1){
                driver(thisItersLookup, 0, numGroups, calcDists);
            }else{
                int process = 1;
                vector<int> processIDS;
                
                #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){
                        
                        driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);   
                        
                        string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
                        ofstream outtemp;
                        m->openOutputFile(tempdistFileName, outtemp);
                            
                        for (int i = 0; i < calcDists.size(); i++) {
                            outtemp << calcDists[i].size() << endl;
                                
                            for (int j = 0; j < calcDists[i].size(); j++) {
                                outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
                            }
                        }
                        outtemp.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);
                    }
                }
                
                //parent do your part
                driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);   
                            
                //force parent to wait until all the processes are done
                for (int i = 0; i < processIDS.size(); i++) {
                    int temp = processIDS[i];
                    wait(&temp);
                }
                
                for (int i = 0; i < processIDS.size(); i++) {
                    string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
                    ifstream intemp;
                    m->openInputFile(tempdistFileName, intemp);
                        
                    for (int k = 0; k < calcDists.size(); k++) {
                        int size = 0;
                        intemp >> size; m->gobble(intemp);
                            
                        for (int j = 0; j < size; j++) {
                            int seq1 = 0;
                            int seq2 = 0;
                            float dist = 1.0;
                                
                            intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
                                
                            seqDist tempDist(seq1, seq2, dist);
                            calcDists[k].push_back(tempDist);
                        }
                    }
                    intemp.close();
                    m->mothurRemove(tempdistFileName);
                }
                #else
                //////////////////////////////////////////////////////////////////////////////////////////////////////
                //Windows version shared memory, so be careful when passing variables through the distSharedData struct. 
                //Above fork() will clone, so memory is separate, but that's not the case with windows, 
                //Taking advantage of shared memory to pass results vectors.
                //////////////////////////////////////////////////////////////////////////////////////////////////////
                
                vector<distSharedData*> pDataArray; 
                DWORD   dwThreadIdArray[processors-1];
                HANDLE  hThreadArray[processors-1]; 
                
                //Create processor worker threads.
                for( int i=1; i<processors; i++ ){
                    
                    //make copy of lookup so we don't get access violations
                    vector<SharedRAbundVector*> newLookup;
                    for (int k = 0; k < thisItersLookup.size(); k++) {
                        SharedRAbundVector* temp = new SharedRAbundVector();
                        temp->setLabel(thisItersLookup[k]->getLabel());
                        temp->setGroup(thisItersLookup[k]->getGroup());
                        newLookup.push_back(temp);
                    }
                    
                    //for each bin
                    for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
                    }
                    
                    // Allocate memory for thread data.
                    distSharedData* tempSum = new distSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
                    pDataArray.push_back(tempSum);
                    processIDS.push_back(i);
                    
                    hThreadArray[i-1] = CreateThread(NULL, 0, MyDistSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);   
                }
                
                //parent do your part
                driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);   
                           
                //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-pDataArray[i]->start)) {
                        m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
                    }
                    for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) {  delete pDataArray[i]->thisLookup[j];  } 
                    
                    for (int k = 0; k < calcDists.size(); k++) {
                        int size = pDataArray[i]->calcDists[k].size();
                        for (int j = 0; j < size; j++) {    calcDists[k].push_back(pDataArray[i]->calcDists[k][j]);    }
                    }
                    
                    CloseHandle(hThreadArray[i]);
                    delete pDataArray[i];
                }

                #endif
            }
            
            if (subsample && (thisIter != 0)) {  
                if((thisIter) % 100 == 0){	m->mothurOutJustToScreen(toString(thisIter)+"\n"); 		}
                calcDistsTotals.push_back(calcDists);
                for (int i = 0; i < calcDists.size(); i++) {
                    for (int j = 0; j < calcDists[i].size(); j++) {
                        if (m->debug) {  m->mothurOut("[DEBUG]: Results: iter = " + toString(thisIter) + ", " + thisLookup[calcDists[i][j].seq1]->getGroup() + " - " + thisLookup[calcDists[i][j].seq2]->getGroup() + " distance = " + toString(calcDists[i][j].dist) + ".\n");  }
                    } 
                }
                //clean up memory
                for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
                thisItersLookup.clear();
            }else { //print results for whole dataset
                for (int i = 0; i < calcDists.size(); i++) {
                    if (m->control_pressed) { break; }
                    
                    //initialize matrix
                    vector< vector<double> > matrix; //square matrix to represent the distance
                    matrix.resize(thisLookup.size());
                    for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
                    
                    for (int j = 0; j < calcDists[i].size(); j++) {
                        int row = calcDists[i][j].seq1;
                        int column = calcDists[i][j].seq2;
                        double dist = calcDists[i][j].dist;
                        
                        matrix[row][column] = dist;
                        matrix[column][row] = dist;
                    }
                    
                    variables["[outputtag]"] = output;
                    variables["[calc]"] = matrixCalculators[i]->getName();
                    string distFileName = getOutputFileName("phylip",variables);
                    outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                    
                    ofstream outDist;
                    m->openOutputFile(distFileName, outDist);
                    outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
                    
                    printSims(outDist, matrix);
                    
                    outDist.close();
                }
            }
            for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
		}
		
        if (iters != 0) {
            //we need to find the average distance and standard deviation for each groups distance
            vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals, mode);
            
            //find standard deviation
            vector< vector<seqDist>  > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages);
            
            //print results
            for (int i = 0; i < calcDists.size(); i++) {
                vector< vector<double> > matrix; //square matrix to represent the distance
                matrix.resize(thisLookup.size());
                for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
                
                vector< vector<double> > stdmatrix; //square matrix to represent the stdDev
                stdmatrix.resize(thisLookup.size());
                for (int k = 0; k < thisLookup.size(); k++) {  stdmatrix[k].resize(thisLookup.size(), 0.0); }

            
                for (int j = 0; j < calcAverages[i].size(); j++) {
                    int row = calcAverages[i][j].seq1;
                    int column = calcAverages[i][j].seq2;
                    float dist = calcAverages[i][j].dist;
                    float stdDist = stdDev[i][j].dist;
                    
                    matrix[row][column] = dist;
                    matrix[column][row] = dist;
                    stdmatrix[row][column] = stdDist;
                    stdmatrix[column][row] = stdDist;
                }
                
                map<string, string> variables; 
                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
                variables["[distance]"] = thisLookup[0]->getLabel();
                variables["[outputtag]"] = output;
                variables["[tag2]"] = "ave";
                variables["[calc]"] = matrixCalculators[i]->getName();
                string distFileName = getOutputFileName("phylip",variables);
                outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                ofstream outAve;
                m->openOutputFile(distFileName, outAve);
                outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
                
                printSims(outAve, matrix);
                
                outAve.close();
                
                variables["[tag2]"] = "std";
                distFileName = getOutputFileName("phylip",variables);
                outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                ofstream outSTD;
                m->openOutputFile(distFileName, outSTD);
                outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
                
                printSims(outSTD, stdmatrix);
                
                outSTD.close();

            }
        }
		
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "MatrixOutputCommand", "process");
		exit(1);
	}
}
/**************************************************************************************************/
int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) { 
	try {
		vector<SharedRAbundVector*> subset;
        
		for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
			
			for (int l = 0; l < k; l++) {
				
				if (k != l) { //we dont need to similarity of a groups to itself
					subset.clear(); //clear out old pair of sharedrabunds
					//add new pair of sharedrabunds
					subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
					
					for(int i=0;i<matrixCalculators.size();i++) {
						
						//if this calc needs all groups to calculate the pair load all groups
						if (matrixCalculators[i]->getNeedsAll()) { 
							//load subset with rest of lookup for those calcs that need everyone to calc for a pair
							for (int w = 0; w < thisLookup.size(); w++) {
								if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
							}
						}
						
						vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
						
						if (m->control_pressed) { return 1; }
        
						seqDist temp(l, k, tempdata[0]);
						calcDists[i].push_back(temp);
					}
				}
			}
		}
		
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "MatrixOutputCommand", "driver");
		exit(1);
	}
}
/***********************************************************/