X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=566fd10c8ef9ff90849896982343e6970bdeaba5;hb=e88ba6b7a994a8502030d38cc5cc542994694d4d;hp=3eedb2ecd99ff2a68342c23ab617639c3c82e312;hpb=fb5a52d8d7896ba00c9ccc6add22ed89c5fb2ad7;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 3eedb2e..566fd10 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -9,240 +9,451 @@
 
 #include "unifracunweightedcommand.h"
 
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"groups","iters","distance","random", "processors","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "UnifracUnweightedCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+UnifracUnweightedCommand::UnifracUnweightedCommand(){	
+	try {
+		globaldata = GlobalData::getInstance();
+		abort = true; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["unweighted"] = tempOutNames;
+		outputTypes["uwsummary"] = tempOutNames;
+		outputTypes["phylip"] = tempOutNames;
+		outputTypes["column"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "UnifracUnweightedCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"tree","group"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "UnifracUnweightedCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 /***********************************************************/
-UnifracUnweightedCommand::UnifracUnweightedCommand() {
+UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
+		abort = false; calledHelp = false;   
+		Groups.clear();
+			
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
-		T = globaldata->gTree;
-		tmap = globaldata->gTreemap;
-		unweightedFile = globaldata->getTreeFile() + ".unweighted";
-		openOutputFile(unweightedFile, out);
-		sumFile = globaldata->getTreeFile() + ".uwsummary";
-		openOutputFile(sumFile, outSum);
-		distFile = globaldata->getTreeFile() + ".uwdistrib";
-		openOutputFile(distFile, outDist);
-
-		//if the user has not entered specific groups to analyze then do them all
-		if (globaldata->Groups.size() != 0) {
-			//check that groups are valid
-			for (int i = 0; i < globaldata->Groups.size(); i++) {
-				if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
-					cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
-					// erase the invalid group from globaldata->Groups
-					globaldata->Groups.erase (globaldata->Groups.begin()+i);
-				}
+		else {
+			//valid paramters for this command
+			string Array[] =  {"groups","iters","distance","random", "processors","outputdir","inputdir"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+		
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["unweighted"] = tempOutNames;
+			outputTypes["uwsummary"] = tempOutNames;
+			outputTypes["phylip"] = tempOutNames;
+			outputTypes["column"] = tempOutNames;
+			
+			if (globaldata->gTree.size() == 0) {//no trees were read
+				m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted command."); m->mothurOutEndLine(); abort = true;  }
+			
+			//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(globaldata->inputFileName); //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 = ""; }
+			else { 
+				m->splitAtDash(groups, Groups);
+				globaldata->Groups = Groups;
+			}
+				
+			itersString = validParameter.validFile(parameters, "iters", false);				if (itersString == "not found") { itersString = "1000"; }
+			convert(itersString, iters); 
+			
+			string temp = validParameter.validFile(parameters, "distance", false);			
+			if (temp == "not found") { phylip = false; outputForm = ""; }
+			else{
+				if ((temp == "lt") || (temp == "column") || (temp == "square")) {  phylip = true;  outputForm = temp; }
+				else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
+			}
+			
+			temp = validParameter.validFile(parameters, "random", false);					if (temp == "not found") { temp = "f"; }
+			random = m->isTrue(temp);
+			
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = "1";				}
+			convert(temp, processors); 
+			
+			if (!random) {  iters = 0;  } //turn off random calcs
+			
+			//if user selects distance = true and no groups it won't calc the pairwise
+			if ((phylip) && (Groups.size() == 0)) {
+				groups = "all";
+				m->splitAtDash(groups, Groups);
+				globaldata->Groups = Groups;
+			}
+		
+			if (abort == false) {
+				T = globaldata->gTree;
+				tmap = globaldata->gTreemap;
+				sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
+				outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
+				m->openOutputFile(sumFile, outSum);
+				
+				util = new SharedUtil();
+				util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");	//sets the groups the user wants to analyze
+				util->getCombos(groupComb, globaldata->Groups, numComp);
+				
+				if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+				
+				unweighted = new Unweighted(tmap);
+				
 			}
 			
-			//if the user only entered invalid groups
-			if (globaldata->Groups.size() == 0) { 
-				cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl; 
-			}		
 		}
-
-		convert(globaldata->getIters(), iters);  //how many random trees to generate
-		unweighted = new Unweighted(tmap);
-
+		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void UnifracUnweightedCommand::help(){
+	try {
+		m->mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
+		m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance, processors and random.  No parameters are required.\n");
+		m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group.\n");
+		m->mothurOut("The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
+		m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n");
+		m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n");
+		m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
+		m->mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
+		m->mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
+		m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
+		m->mothurOut("The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+	}
+	catch(exception& e) {
+		m->errorOut(e, "UnifracUnweightedCommand", "help");
 		exit(1);
 	}
 }
+
+
 /***********************************************************/
 int UnifracUnweightedCommand::execute() {
 	try {
 		
-		//get unweighted for users tree
-		userData.resize(1,0);  //data[0] = unweightedscore 
-		randomData.resize(1,0); //data[0] = unweightedscore
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		//format output
-		outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-		outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
+		int start = time(NULL);
 		
+		userData.resize(numComp,0);  //data[0] = unweightedscore 
+		randomData.resize(numComp,0); //data[0] = unweightedscore
 		//create new tree with same num nodes and leaves as users
-		randT = new Tree();
- 			
+		
+		if (numComp < processors) { processors = numComp;  }
+		
+		outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
+		m->mothurOut("Tree#\tGroups\tUWScore\tUWSig"); m->mothurOutEndLine();
+		
 		//get pscores for users trees
 		for (int i = 0; i < T.size(); i++) {
-			cout << "Processing tree " << i+1 << endl;
-			userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
+			if (m->control_pressed) { 
+				outSum.close();
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }
+				return 0; 
+			}
 			
-			//update uscoreFreq
-			it = uscoreFreq.find(userData[0]);
-			if (it == uscoreFreq.end()) {//new score
-				uscoreFreq[userData[0]] = 1;
-			}else{ uscoreFreq[userData[0]]++; }
+			counter = 0;
 			
-			//add users score to valid scores
-			validScores[userData[0]] = userData[0];
+			if (random)  {  
+				output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted", itersString);
+				outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
+				outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
+			}
 			
-			//saves users score
-			utreeScores.push_back(userData[0]);
 			
-			//copy T[i]'s info.
-			randT->getCopy(T[i]); 
+			//get unweighted for users tree
+			rscoreFreq.resize(numComp);  
+			rCumul.resize(numComp);  
+			utreeScores.resize(numComp);  
+			UWScoreSig.resize(numComp); 
+
+			userData = unweighted->getValues(T[i], processors, outputDir);  //userData[0] = unweightedscore
+		
+			if (m->control_pressed) { if (random) { delete output;  } outSum.close();  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }return 0; }
 			
-			//get unweighted scores for random trees
+			//output scores for each combination
+			for(int k = 0; k < numComp; k++) {
+				//saves users score
+				utreeScores[k].push_back(userData[k]);
+				
+				//add users score to validscores
+				validScores[userData[k]] = userData[k];
+			}
+		
+			//get unweighted scores for random trees - if random is false iters = 0
 			for (int j = 0; j < iters; j++) {
-				//create a random tree with same topology as T[i], but different labels
-				randT->assembleRandomUnifracTree();
-				//get pscore of random tree
-				randomData = unweighted->getValues(randT);
-			
-				//add trees unweighted score to map of scores
-				it2 = rscoreFreq.find(randomData[0]);
-				if (it2 != rscoreFreq.end()) {//already have that score
-					rscoreFreq[randomData[0]]++;
-				}else{//first time we have seen this score
-					rscoreFreq[randomData[0]] = 1;
-				}
+		
+				//we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
+				randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
+				
+				if (m->control_pressed) { if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+			
+				for(int k = 0; k < numComp; k++) {	
+					//add trees unweighted score to map of scores
+					map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
+					if (it != rscoreFreq[k].end()) {//already have that score
+						rscoreFreq[k][randomData[k]]++;
+					}else{//first time we have seen this score
+						rscoreFreq[k][randomData[k]] = 1;
+					}
 				
-				//add randoms score to validscores
-				validScores[randomData[0]] = randomData[0];
+					//add randoms score to validscores
+					validScores[randomData[k]] = randomData[k];
+				}
 				
-				//output info to uwdistrib file
-				outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
+				//report progress
+//				m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();	
 			}
-			
-			saveRandomScores(); //save all random scores for unweighted file
-			
-			//find the signifigance of the score
-			float rcumul = 1.0000;
-			for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { 
-				rCumul[it->first] = rcumul;
-				//get percentage of random trees with that info
-				rscoreFreq[it->first] /= iters; 
-				rcumul-= it->second;  
+	
+			for(int a = 0; a < numComp; a++) {
+				float rcumul = 1.0000;
 				
+				if (random) {
+					//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+					for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
+						//make rscoreFreq map and rCumul
+						map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
+						rCumul[a][it->first] = rcumul;
+						//get percentage of random trees with that info
+						if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
+						else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+					}
+					UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+				}else		{	UWScoreSig[a].push_back(0.0);						}
+	
 			}
 			
-			//save the signifigance of the users score for printing later
-			UWScoreSig.push_back(rCumul[userData[0]]);
+			if (m->control_pressed) { if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0;  }
 			
+			//print output files
+			printUWSummaryFile(i);
+			if (random)  {	printUnweightedFile();	delete output;	}
+			if (phylip) {	createPhylipFile(i);		}
 			
-			//clear random data
-			rscoreFreq.clear();  //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
-			rCumul.clear();
+			rscoreFreq.clear(); 
+			rCumul.clear();  
+			validScores.clear(); 
+			utreeScores.clear();  
+			UWScoreSig.clear(); 
 		}
 		
-		float ucumul = 1.0000;
-		float rcumul = 1.0000;
-		//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
-		for (it = validScores.begin(); it != validScores.end(); it++) { 
-			it2 = uscoreFreq.find(it->first);
-			//make uCumul map
-			uCumul[it->first] = ucumul;
-			//user data has that score 
-			if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul-= it2->second;  }
-			else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
-						
-			//make rscoreFreq map and rCumul
-			it2 = totalrscoreFreq.find(it->first);
-			rCumul[it->first] = rcumul;
-			//get percentage of random trees with that info
-			if (it2 != totalrscoreFreq.end()) {  totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second;  }
-			else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
-			
-		}
+
+		outSum.close();
 		
-		printUnweightedFile();
-		printUWSummaryFile();
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }	return 0; }
 		
-		delete randT;
+		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
+		
+		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 UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "UnifracUnweightedCommand", "execute");
 		exit(1);
 	}
 }
 /***********************************************************/
 void UnifracUnweightedCommand::printUnweightedFile() {
 	try {
-		//column headers
-		
-		out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-				
-		//format output
-		out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-		
-		//print each line
-		for (it = validScores.begin(); it != validScores.end(); it++) { 
-			out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << totalrscoreFreq[it->first] << '\t' << rCumul[it->first] << endl; 
-		} 
-		
-		out.close();
+		vector<double> data;
+		vector<string> tags;
 		
+		tags.push_back("Score");
+		tags.push_back("RandFreq"); tags.push_back("RandCumul");
+			
+		for(int a = 0; a < numComp; a++) {
+			output->initFile(groupComb[a], tags);
+			//print each line
+			for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
+				data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);						
+				output->output(data);
+				data.clear();
+			} 
+			output->resetFile();
+		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
 		exit(1);
 	}
 }
 
 /***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
 	try {
-		//column headers
-		outSum << "Tree#" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
-		
+				
 		//format output
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
-		
+			
 		//print each line
-		for (int i = 0; i< T.size(); i++) {
-			outSum << setprecision(6) << i+1 << '\t' << '\t' << utreeScores[i] << '\t' << UWScoreSig[i] << endl; 
+
+		for(int a = 0; a < numComp; a++) {
+			outSum << i+1 << '\t';
+			m->mothurOut(toString(i+1) + "\t");
+			
+			if (random) {
+				if (UWScoreSig[a][0] > (1/(float)iters)) {
+					outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+					cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; 
+					m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t" + toString(UWScoreSig[a][0])+ "\n"); 
+				}else {
+					outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+					cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; 
+					m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters))) + "\n"); 
+				}
+			}else{
+				outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+				cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl; 
+				m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00\n");
+			}
 		}
 		
-		outSum.close();
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
 		exit(1);
 	}
 }
 /***********************************************************/
-void UnifracUnweightedCommand::saveRandomScores() {
+void UnifracUnweightedCommand::createPhylipFile(int i) {
 	try {
-		for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { 
-			//does this score already exist in the total map
-			it2 = totalrscoreFreq.find(it->first);
-			//if yes then add them
-			if (it2 != totalrscoreFreq.end()) { 
-				totalrscoreFreq[it->first] += rscoreFreq[it->first];
-			}else{ //its a new score
-				totalrscoreFreq[it->first] = rscoreFreq[it->first];
+		string phylipFileName;
+		if ((outputForm == "lt") || (outputForm == "square")) {
+			phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.phylip.dist";
+			outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
+		}else { //column
+			phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.column.dist";
+			outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); 
+		}
+		
+		ofstream out;
+		m->openOutputFile(phylipFileName, out);
+		
+		if ((outputForm == "lt") || (outputForm == "square")) {
+			//output numSeqs
+			out << globaldata->Groups.size() << endl;
+		}
+		
+		//make matrix with scores in it
+		vector< vector<float> > dists;	dists.resize(globaldata->Groups.size());
+		for (int i = 0; i < globaldata->Groups.size(); i++) {
+			dists[i].resize(globaldata->Groups.size(), 0.0);
+		}
+		
+		//flip it so you can print it
+		int count = 0;
+		for (int r=0; r<globaldata->Groups.size(); r++) { 
+			for (int l = 0; l < r; l++) {
+				dists[r][l] = utreeScores[count][0];
+				dists[l][r] = utreeScores[count][0];
+				count++;
+			}
+		}
+		
+		//output to file
+		for (int r=0; r<globaldata->Groups.size(); r++) { 
+			//output name
+			string name = globaldata->Groups[r];
+			if (name.length() < 10) { //pad with spaces to make compatible
+				while (name.length() < 10) {  name += " ";  }
+			}
+			
+			if (outputForm == "lt") {
+				out << name << '\t';
+			
+				//output distances
+				for (int l = 0; l < r; l++) {	out  << dists[r][l] << '\t';  }
+				out << endl;
+			}else if (outputForm == "square") {
+				out << name << '\t';
+				
+				//output distances
+				for (int l = 0; l < globaldata->Groups.size(); l++) {	out  << dists[r][l] << '\t';  }
+				out << endl;
+			}else{
+				//output distances
+				for (int l = 0; l < r; l++) {	
+					string otherName = globaldata->Groups[l];
+					if (otherName.length() < 10) { //pad with spaces to make compatible
+						while (otherName.length() < 10) {  otherName += " ";  }
+					}
+					
+					out  << name << '\t' << otherName << dists[r][l] << endl;  
+				}
 			}
 		}
+		out.close();
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the UnifracUnweightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
 		exit(1);
 	}
 }
+/***********************************************************/
+
+
 
-/***********************************************************/
\ No newline at end of file