X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=libshuffcommand.cpp;h=46f1a53a475767d379059ca431f0d01e8596afa8;hp=9ab9108f23ca4d63c3479bb8c6a27d27e08704ea;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=cd10743907df223b7dd5b3a3deb20fde758b8ed7

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 9ab9108..46f1a53 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -7,353 +7,562 @@
  *
  */
 
-#include "libshuffcommand.h"
+/* This class is designed to implement an integral form of the Cramer-von Mises statistic.
+	you may refer to the "Integration of Microbial Ecology and Statistics: A Test To Compare Gene Libraries" 
+	paper in Applied and Environmental Microbiology, Sept. 2004, p. 5485-5492 0099-2240/04/$8.00+0  
+	DOI: 10.1128/AEM.70.9.5485-5492.2004 Copyright 2004 American Society for Microbiology for more information. */
 
-//**********************************************************************************************************************
 
+#include "libshuffcommand.h"
+#include "libshuff.h"
+#include "slibshuff.h"
+#include "dlibshuff.h"
 
-LibShuffCommand::LibShuffCommand(){
-	try {
-		globaldata = GlobalData::getInstance();
-		convert(globaldata->getCutOff(), cutOff);
-		convert(globaldata->getIters(), iters);
-		convert(globaldata->getStep(), step);
-		form = globaldata->getForm();
-		matrix = globaldata->gMatrix;
-		coverageFile = getRootName(globaldata->getPhylipFile()) + "coverage";
-		summaryFile = getRootName(globaldata->getPhylipFile()) + "slsummary";
-		openOutputFile(coverageFile, out);
-		openOutputFile(summaryFile, outSum);
-		
-		//set the groups to be analyzed
-		setGroups();
 
-		//file headers for coverage file
-		out << "D" << '\t';
-		for (int i = 0; i < groupComb.size(); i++) {
-			out << "C" + groupComb[i] << '\t';
-		}
-		
-		for (int i = 0; i < numGroups; i++) {
-			for (int j = 0; j < numGroups; j++) {
-				//don't output AA to AA
-				if (i != j) {
-					out << "Delta" + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
-				}
-			}
-		}
-		out << endl;
 
-		numComp = numGroups*numGroups;
-		
-		coverage = new Coverage();
+//**********************************************************************************************************************
+vector<string> LibShuffCommand::setParameters(){	
+	try {
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","coverage-libshuffsummary",false,true,true); parameters.push_back(pphylip);
+		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		CommandParameter piters("iters", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(piters);
+		CommandParameter pstep("step", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pstep);
+		CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pcutoff);
+		CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "","",false,false); parameters.push_back(pform);
+		CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "LibShuffCommand", "setParameters");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LibShuffCommand class function LibShuffCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+string LibShuffCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		helpString += "The libshuff command parameters are phylip, group, sim, groups, iters, step, form and cutoff.  phylip and group parameters are required, unless you have valid current files.\n";
+		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
+		helpString += "The group names are separated by dashes.  The iters parameter allows you to specify how many random matrices you would like compared to your matrix.\n";
+		helpString += "The step parameter allows you to specify change in distance you would like between each output if you are using the discrete form.\n";
+		helpString += "The form parameter allows you to specify if you would like to analyze your matrix using the discrete or integral form. Your options are integral or discrete.\n";
+		helpString += "The libshuff command should be in the following format: libshuff(groups=yourGroups, iters=yourIters, cutOff=yourCutOff, form=yourForm, step=yourStep).\n";
+		helpString += "Example libshuff(groups=A-B-C, iters=500, form=discrete, step=0.01, cutOff=2.0).\n";
+		helpString += "The default value for groups is all the groups in your groupfile, iters is 10000, cutoff is 1.0, form is integral and step is 0.01.\n";
+		helpString += "The libshuff command output two files: .coverage and .slsummary their descriptions are in the manual.\n";
+		helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e.yourIters).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "LibShuffCommand", "getHelpString");
 		exit(1);
-	}	
-			
+	}
 }
-
 //**********************************************************************************************************************
-
-LibShuffCommand::~LibShuffCommand(){
-	delete coverage;
+string LibShuffCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "coverage") {  pattern = "[filename],libshuff.coverage"; } 
+        else if (type == "libshuffsummary") {  pattern = "[filename],libshuff.summary"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "LibShuffCommand", "getOutputPattern");
+        exit(1);
+    }
 }
-
 //**********************************************************************************************************************
+LibShuffCommand::LibShuffCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["coverage"] = tempOutNames;
+		outputTypes["libshuffsummary"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
+		exit(1);
+	}
+}
 
-int LibShuffCommand::execute(){
+//**********************************************************************************************************************
+LibShuffCommand::LibShuffCommand(string option)  {
 	try {
-		//deltaValues[0] = scores for the difference between AA and AB.
-		//cValues[0][0][0] = AA at distance 0.0, cValues[0][0][1] = AB at distance 0.0, cValues[0][0][2] = AC at distance 0.0, cValues[0][1][0] = BA at distance 0.0, cValues[0][1][1] = BB...
-		Progress* reading;
-		reading = new Progress("Comparing to random:", iters);
-		
-		sumDelta.resize(numComp-numGroups, 0.0);
+		abort = false; calledHelp = false;   
 		
-		matrix->setBounds();
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
-		//load distances
-		if (form != "discrete") { matrix->getDist(dist); }
 		else {
-			float f = 0.0;
-			while (f <= cutOff) {
-				dist.push_back(f);
-				f += step;
+			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;  }
 			}
-		}
-	
-		/*****************************/
-		//get values for users matrix
-		/*****************************/
 			
-		//clear out old Values
-		deltaValues.clear();
-		deltaValues.resize(dist.size());			
-		
-		coverage->getValues(matrix, cValues, dist, "user");
-		
-		//loop through each distance and load rsumdelta
-		for (int p = 0; p < cValues.size(); p++) {	
-			//find delta values
-			int count = 0;
-			for (int i = 0; i < numGroups; i++) {
-				for (int j = 0; j < numGroups; j++) {
-					//don't save AA to AA
-					if (i != j) {
-						//(Caa - Cab)^2
-						deltaValues[p].push_back( (abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])) ); 
-						sumDelta[count] += deltaValues[p][count];
-						count++;
-					}
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["coverage"] = tempOutNames;
+			outputTypes["libshuffsummary"] = tempOutNames;
+			
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("phylip");
+				//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["phylip"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("group");
+				//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["group"] = inputDir + it->second;		}
 				}
 			}
-		}
 			
-		printCoverageFile();
+			//check for required parameters
+			phylipfile = validParameter.validFile(parameters, "phylip", true);
+			if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+			else if (phylipfile == "not found") { 
+				phylipfile = m->getPhylipFile(); 
+				if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+				else { 
+					m->mothurOut("You must provide a phylip file."); m->mothurOutEndLine(); 
+					abort = true;
+				} 
+			}else { m->setPhylipFile(phylipfile); }	
 			
-		/*******************************************************************************/
-		//create and score random matrixes finding the sumDelta values for summary file
-		/******************************************************************************/
-
-		//initialize rsumDelta
-		rsumDelta.resize(numComp-numGroups);
-		for (int l = 0; l < rsumDelta.size(); l++) {
-			for (int w = 0; w < iters; w++) {
-				rsumDelta[l].push_back(0.0);
+			//check for required parameters
+			groupfile = validParameter.validFile(parameters, "group", true);
+			if (groupfile == "not open") { groupfile = ""; abort = true; }
+			else if (groupfile == "not found") { 
+				groupfile = m->getGroupFile(); 
+				if (groupfile != "") {  m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+				else { 
+					m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); 
+					abort = true;
+				} 
+			}else { m->setGroupFile(groupfile); }	
+			
+			//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(phylipfile); //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...
+			groups = validParameter.validFile(parameters, "groups", false);			
+			if (groups == "not found") { groups = ""; savegroups = groups; }
+			else { 
+				savegroups = groups;
+				m->splitAtDash(groups, Groups);
+				m->setGroups(Groups);
+			}
+				
+			string temp;
+			temp = validParameter.validFile(parameters, "iters", false);				if (temp == "not found") { temp = "10000"; }
+			m->mothurConvert(temp, iters); 
+			
+			temp = validParameter.validFile(parameters, "cutoff", false);				if (temp == "not found") { temp = "1.0"; }
+			m->mothurConvert(temp, cutOff); 
+			
+			temp = validParameter.validFile(parameters, "step", false);				if (temp == "not found") { temp = "0.01"; }
+			m->mothurConvert(temp, step); 
+			
+			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
+			sim = m->isTrue(temp); 
+			
+			userform = validParameter.validFile(parameters, "form", false);			if (userform == "not found") { userform = "integral"; }
+			
 		}
 		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "LibShuffCommand", "LibShuffCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+int LibShuffCommand::execute(){
+	try {
+		
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
+		//read files
+		groupMap = new GroupMap(groupfile);
+		int error = groupMap->readMap();
+		if (error == 1) { delete groupMap; return 0; }
 		
-		for (int m = 0; m < iters; m++) {
-			//generate random matrix in getValues
-			//values for random matrix
+		ifstream in;
+		m->openInputFile(phylipfile, in);
+		matrix = new FullMatrix(in, groupMap, sim); //reads the matrix file
+		in.close();
 		
-			coverage->getValues(matrix, cValues, dist, "random");
+		if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+		
+		//if files don't match...
+		if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {  
+			m->mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences.");  m->mothurOutEndLine();				
+			//create new group file
+			if(outputDir == "") { outputDir += m->hasPath(groupfile); }
 			
-			//loop through each distance and load rsumdelta
-			for (int p = 0; p < cValues.size(); p++) {
-				//find delta values
-				int count = 0;
-				for (int i = 0; i < numGroups; i++) {
-					for (int j = 0; j < numGroups; j++) {
-						//don't save AA to AA
-						if (i != j) {
-							//(Caa - Cab)^2
-							rsumDelta[count][m] += ((abs(cValues[p][i][i]-cValues[p][i][j]) * abs(cValues[p][i][i]-cValues[p][i][j])));
-							count++;
-						}
-					}
-				}
+			string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
+			outputNames.push_back(newGroupFile);
+			ofstream outGroups;
+			m->openOutputFile(newGroupFile, outGroups);
+			
+			for (int i = 0; i < matrix->getNumSeqs(); i++) {
+				if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
 				
+				Names temp = matrix->getRowInfo(i);
+				outGroups << temp.seqName << '\t' << temp.groupName << endl;
 			}
-//cout << "iter " << m << endl;
-			//clear out old Values
-			reading->update(m);
-			cValues.clear();
+			outGroups.close();
 			
-//cout << "random sum delta for iter " << m << endl;
-//for (int i = 0; i < rsumDelta.size(); i++) {
-//	cout << setprecision(6) << rsumDelta[i][m] << '\t';
-//}
-//cout << endl;
-
+			m->mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); m->mothurOutEndLine();
+			
+			//read new groupfile
+			delete groupMap; 
+			groupfile = newGroupFile;
+			
+			groupMap = new GroupMap(groupfile);
+			groupMap->readMap();
+			
+			if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
 		}
 		
-		reading->finish();
-		delete reading;
-				
-		/**********************************************************/
-		//find the signifigance of the user matrix' sumdelta values
-		/**********************************************************/
+			
+		setGroups();								//set the groups to be analyzed and sorts them
+		
+		if (numGroups < 2) { m->mothurOut("[ERROR]: libshuff requires at least 2 groups, you only have " + toString(numGroups) + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
 		
-		for (int t = 0; t < rsumDelta.size(); t++) {
-			//sort rsumDelta t
-			sort(rsumDelta[t].begin(), rsumDelta[t].end());
+		if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+		
+		/********************************************************************************************/
+		//this is needed because when we read the matrix we sort it into groups in alphabetical order
+		//the rest of the command and the classes used in this command assume specific order
+		/********************************************************************************************/
+		matrix->setGroups(groupMap->getNamesOfGroups());
+		vector<int> sizes;
+		for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {   sizes.push_back(groupMap->getNumSeqs((groupMap->getNamesOfGroups())[i]));  }
+		matrix->setSizes(sizes);
 			
-			//the index of the score higher than yours is returned 
-			//so if you have 1000 random matrices the index returned is 100 
-			//then there are 900 matrices with a score greater then you. 
-			//giving you a signifigance of 0.900
-			int index = findIndex(sumDelta[t], t);    
 			
-			//the signifigance is the number of trees with the users score or higher 
-			sumDeltaSig.push_back((iters-index)/(float)iters);
+		if(userform == "discrete"){
+			form = new DLibshuff(matrix, iters, step, cutOff);
+		}
+		else{
+			form = new SLibshuff(matrix, iters, cutOff);
+		}
+	
+		savedDXYValues = form->evaluateAll();
+		savedMinValues = form->getSavedMins();
+		
+		if (m->control_pressed) {  delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
+	
+		pValueCounts.resize(numGroups);
+		for(int i=0;i<numGroups;i++){
+			pValueCounts[i].assign(numGroups, 0);
+		}
+	
+		if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; return 0; }
+				
+		Progress* reading = new Progress();
+		
+		for(int i=0;i<numGroups-1;i++) {
+			for(int j=i+1;j<numGroups;j++) {
+				
+				if (m->control_pressed) {  outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
 
+				reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
+				int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
+				int spotj = groupMap->groupIndex[groupNames[j]];
+	
+				for(int p=0;p<iters;p++) {	
+					
+					if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+					
+					form->randomizeGroups(spoti,spotj); 
+					if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj])	{	pValueCounts[i][j]++;	}
+					if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti])	{	pValueCounts[j][i]++;	}
+					
+					if (m->control_pressed) {  outputTypes.clear(); delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+					
+					reading->update(p);			
+				}
+				form->resetGroup(spoti);
+				form->resetGroup(spotj);
+			}
 		}
 		
+		if (m->control_pressed) { outputTypes.clear();  delete form; m->clearGroups(); delete matrix; delete groupMap; delete reading; return 0; }
+	
+		reading->finish();
+		delete reading;
+
+		m->mothurOutEndLine();
 		printSummaryFile();
-		
+		printCoverageFile();
+				
 		//clear out users groups
-		globaldata->Groups.clear();
+		m->clearGroups();
+		delete form;
+		
+		delete matrix; delete groupMap;
+		
+		if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
+
+		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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "LibShuffCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LibShuffCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
+
 //**********************************************************************************************************************
-void LibShuffCommand::printCoverageFile() {
+
+int LibShuffCommand::printCoverageFile() {
 	try {
-		//format output
-		out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-		
-		//loop through each distance 
-		for (int p = 0; p < cValues.size(); p++) {
-			out << setprecision(6) << dist[p] << '\t';
-			//print out coverage values
-			for (int i = 0; i < numGroups; i++) {
-				for (int j = 0; j < numGroups; j++) {
-					out << cValues[p][i][j] << '\t';
+
+		ofstream outCov;
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+		summaryFile = getOutputFileName("coverage", variables);
+		m->openOutputFile(summaryFile, outCov);
+		outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
+		outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
+		//cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+		
+		map<double,vector<int> > allDistances;
+		map<double,vector<int> >::iterator it;
+
+		vector<vector<int> > indices(numGroups);
+		int numIndices = numGroups * numGroups;
+		
+		int index = 0;
+		for(int i=0;i<numGroups;i++){
+			indices[i].assign(numGroups,0);
+			for(int j=0;j<numGroups;j++){
+				indices[i][j] = index++;
+				
+				int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
+				int spotj = groupMap->groupIndex[groupNames[j]];
+				
+				for(int k=0;k<savedMinValues[spoti][spotj].size();k++){
+					
+					if(m->control_pressed)  { outCov.close(); return 0; }
+					
+					if(allDistances[savedMinValues[spoti][spotj][k]].size() != 0){
+						allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]]++;
+					}
+					else{
+						allDistances[savedMinValues[spoti][spotj][k]].assign(numIndices, 0);
+						allDistances[savedMinValues[spoti][spotj][k]][indices[i][j]] = 1;
+					}
 				}
 			}
-			
-			for (int h = 0; h < deltaValues[p].size(); h++) {
-				out << deltaValues[p][h] << '\t';
+		}
+		it=allDistances.begin();
+		
+		//cout << setprecision(8);
+
+		vector<int> prevRow = it->second;
+		it++;
+		
+		for(;it!=allDistances.end();it++){
+			for(int i=0;i<it->second.size();i++){
+				it->second[i] += prevRow[i];
+			}
+			prevRow = it->second;
+		}
+		
+		vector<int> lastRow = allDistances.rbegin()->second;
+		outCov << setprecision(8);
+		
+		outCov << "dist";
+		for (int i = 0; i < numGroups; i++){
+			outCov << '\t' << groupNames[i];
+		}
+		for (int i=0;i<numGroups;i++){
+			for(int j=i+1;j<numGroups;j++){
+				if(m->control_pressed)  { outCov.close(); return 0; }
+				outCov << '\t' << groupNames[i] << '-' << groupNames[j] << '\t';
+				outCov << groupNames[j] << '-' << groupNames[i];
 			}
-			
-			out << endl;
 		}
+		outCov << endl;
 		
+		for(it=allDistances.begin();it!=allDistances.end();it++){
+			outCov << it->first << '\t';
+			for(int i=0;i<numGroups;i++){
+				outCov << it->second[indices[i][i]]/(float)lastRow[indices[i][i]] << '\t';
+			}
+			for(int i=0;i<numGroups;i++){
+				for(int j=i+1;j<numGroups;j++){
+					if(m->control_pressed)  { outCov.close(); return 0; }
+					
+					outCov << it->second[indices[i][j]]/(float)lastRow[indices[i][j]] << '\t';
+					outCov << it->second[indices[j][i]]/(float)lastRow[indices[j][i]] << '\t';
+				}
+			}
+			outCov << endl;
+		}
+		outCov.close();
+		
+		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "LibShuffCommand", "printCoverageFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LibShuffCommand class function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 } 
+
 //**********************************************************************************************************************
-void LibShuffCommand::printSummaryFile() {
+
+int LibShuffCommand::printSummaryFile() {
 	try {
-		//format output
+
+		ofstream outSum;
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+		summaryFile = getOutputFileName("libshuffsummary",variables);
+		m->openOutputFile(summaryFile, outSum);
+		outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
+
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
+		cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 		
-		for (int i = 0; i < numGroups; i++) {
-			for (int j = 0; j < numGroups; j++) {
-				//don't output AA to AA
-				if (i != j) {
-					outSum << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
-					cout << "Delta " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t'<< "DeltaSig " + globaldata->Groups[i] + "-" + globaldata->Groups[j] << '\t';
+		cout << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+		m->mothurOutJustToLog("Comparison\tdCXYScore\tSignificance"); m->mothurOutEndLine();
+		outSum << setw(20) << left << "Comparison" << '\t' << setprecision(8) << "dCXYScore" << '\t' << "Significance" << endl;
+	
+		int precision = (int)log10(iters);
+		for(int i=0;i<numGroups;i++){
+			for(int j=i+1;j<numGroups;j++){
+				if(m->control_pressed)  { outSum.close(); return 0; }
+				
+				int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
+				int spotj = groupMap->groupIndex[groupNames[j]];
+				
+				if(pValueCounts[i][j]){
+					cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+					m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((pValueCounts[i][j]/(float)iters))); m->mothurOutEndLine();
+					outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << setprecision(precision) << pValueCounts[i][j]/(float)iters << endl;
+				}
+				else{
+					cout << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+					m->mothurOutJustToLog(groupNames[i]+"-"+groupNames[j] + "\t" + toString(savedDXYValues[spoti][spotj]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
+					outSum << setw(20) << left << groupNames[i]+'-'+groupNames[j] << '\t' << setprecision(8) << savedDXYValues[spoti][spotj] << '\t' << '<' <<setprecision(precision) << 1/(float)iters << endl;
+				}
+				if(pValueCounts[j][i]){
+					cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+					m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((pValueCounts[j][i]/(float)iters))); m->mothurOutEndLine();
+					outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << setprecision (precision) << pValueCounts[j][i]/(float)iters << endl;
+				}
+				else{
+					cout << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
+					m->mothurOutJustToLog(groupNames[j]+"-"+groupNames[i] + "\t" + toString(savedDXYValues[spotj][spoti]) + "\t" + toString((1/(float)iters))); m->mothurOutEndLine();
+					outSum << setw(20) << left << groupNames[j]+'-'+groupNames[i] << '\t' << setprecision(8) << savedDXYValues[spotj][spoti] << '\t' << '<' <<setprecision (precision) << 1/(float)iters << endl;
 				}
-			}
-		}
-		outSum << endl;
-		cout << endl;
-		
-		//print out delta values
-		for (int i = 0; i < sumDelta.size(); i++) {
-			if (sumDeltaSig[i] > (1/(float)iters)) {
-				outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
-				cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << sumDeltaSig[i] << '\t';
-			}else {
-				outSum << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
-				cout << setprecision(6) << sumDelta[i] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << '\t';
 			}
 		}
 		
-		outSum << endl;
-		cout << endl;
-	
+		outSum.close();
+		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "LibShuffCommand", "printSummaryFile");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LibShuffCommand class function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 } 
 
 //**********************************************************************************************************************
+
 void LibShuffCommand::setGroups() {
 	try {
+		vector<string> myGroups = m->getGroups();
 		//if the user has not entered specific groups to analyze then do them all
-		if (globaldata->Groups.size() == 0) {
-			numGroups = globaldata->gGroupmap->getNumGroups();
+		if (m->getNumGroups() == 0) {
+			numGroups = groupMap->getNumGroups();
 			for (int i=0; i < numGroups; i++) { 
-				globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+				myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 			}
-		}else {
-			if (globaldata->getGroups() != "all") {
+		} else {
+			if (savegroups != "all") {
 				//check that groups are valid
-				for (int i = 0; i < globaldata->Groups.size(); i++) {
-					if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
-						cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+				for (int i = 0; i < myGroups.size(); i++) {
+					if (groupMap->isValidGroup(myGroups[i]) != true) {
+						m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 						// erase the invalid group from globaldata->Groups
-						globaldata->Groups.erase (globaldata->Groups.begin()+i);
+						myGroups.erase(myGroups.begin()+i);
 					}
 				}
 			
 				//if the user only entered invalid groups
-				if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) { 
-					numGroups = globaldata->gGroupmap->getNumGroups();
+				if ((myGroups.size() == 0) || (myGroups.size() == 1)) { 
+					numGroups = groupMap->getNumGroups();
 					for (int i=0; i < numGroups; i++) { 
-						globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+						myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 					}
-					cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; 
-				}else { numGroups = globaldata->Groups.size(); }
-			}else { //users wants all groups
-				numGroups = globaldata->gGroupmap->getNumGroups();
-				globaldata->Groups.clear();
+					m->mothurOut("When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
+				} else { numGroups = myGroups.size(); }
+			} else { //users wants all groups
+				numGroups = groupMap->getNumGroups();
+				myGroups.clear();
 				for (int i=0; i < numGroups; i++) { 
-					globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+					myGroups.push_back((groupMap->getNamesOfGroups())[i]);
 				}
 			}
 		}
-		
+
 		//sort so labels match
-		sort(globaldata->Groups.begin(), globaldata->Groups.end());
+		sort(myGroups.begin(), myGroups.end());
 		
-		// number of comparisons i.e. with groups A,B,C = AA, AB, AC, BA, BB, BC...;
-		for (int i=0; i<numGroups; i++) { 
-			for (int l = 0; l < numGroups; l++) {
-				//set group comparison labels
-				groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
-			}
-		}
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LibShuffCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
-/***********************************************************/
-int LibShuffCommand::findIndex(float score, int index) {
-	try{
-		for (int i = 0; i < rsumDelta[index].size(); i++) {
-			if (rsumDelta[index][i] >= score)	{	return i;	}
-		}
-		return rsumDelta[index].size();
+		//sort
+		//sort(groupMap->namesOfGroups.begin(), groupMap->namesOfGroups.end());
+		
+		for (int i = 0; i < (groupMap->getNamesOfGroups()).size(); i++) {  groupMap->groupIndex[(groupMap->getNamesOfGroups())[i]] = i;  }
+
+		groupNames = myGroups;
+		m->setGroups(myGroups);
+
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the LibShuffCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "LibShuffCommand", "setGroups");
 		exit(1);
 	}
 }
 
 /***********************************************************/
-