X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=2bb88770ec37651df7ff9da2954926abf3bf5153;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=7a3ad4a1e57e7f3f5dac9539fb2c974cd4e14cbe;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 7a3ad4a..2bb8877 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -10,121 +10,614 @@
 #include "summarycommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
 #include "npshannon.h"
 #include "shannon.h"
+#include "heip.h"
+#include "smithwilson.h"
+#include "shannoneven.h"
 #include "jackknife.h"
+#include "geom.h"
+#include "logsd.h"
+#include "qstat.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "goodscoverage.h"
+#include "coverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
 
 //**********************************************************************************************************************
-
-SummaryCommand::SummaryCommand(){
+vector<string> SummaryCommand::setParameters(){	
 	try {
-		globaldata = GlobalData::getInstance();
-		validCalculator = new ValidCalculators();
-		int i;
-		
-		for (i=0; i<globaldata->Estimators.size(); i++) {
-			if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) { 
-				if(globaldata->Estimators[i] == "sobs"){
-					sumCalculators.push_back(new Sobs());
-				}else if(globaldata->Estimators[i] == "chao"){
-					sumCalculators.push_back(new Chao1());
-				}else if(globaldata->Estimators[i] == "ace"){
-					sumCalculators.push_back(new Ace());
-				}else if(globaldata->Estimators[i] == "jack"){
-					sumCalculators.push_back(new Jackknife());
-				}else if(globaldata->Estimators[i] == "shannon"){
-					sumCalculators.push_back(new Shannon());
-				}else if(globaldata->Estimators[i] == "npshannon"){
-					sumCalculators.push_back(new NPShannon());
-				}else if(globaldata->Estimators[i] == "simpson"){
-					sumCalculators.push_back(new Simpson());
-				}else if(globaldata->Estimators[i] == "bootstrap"){
-					sumCalculators.push_back(new Bootstrap());
-				}
-			}
-		}
+		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
+		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
+		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
+		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
+		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
+		CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
+		CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
 		
-		//reset calc for next command
-		globaldata->setCalc("");
-
+		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 SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SummaryCommand", "setParameters");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 //**********************************************************************************************************************
-
-SummaryCommand::~SummaryCommand(){
-	delete sabund;
-	delete input;
-	delete read;
+string SummaryCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		ValidCalculators validCalculator;
+		helpString += "The summary.single command parameters are list, sabund, rabund, shared, label, calc, abund and groupmode.  list, sabund, rabund or shared is required unless you have a valid current file.\n";
+		helpString += "The summary.single command should be in the following format: \n";
+		helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
+		helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
+		helpString += validCalculator.printCalc("summary");
+		helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
+		helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";
+		helpString += "The label parameter is used to analyze specific labels in your input.\n";
+		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummaryCommand", "getHelpString");
+		exit(1);
+	}
 }
 
+//**********************************************************************************************************************
+SummaryCommand::SummaryCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["summary"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummaryCommand", "SummaryCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
-int SummaryCommand::execute(){
+SummaryCommand::SummaryCommand(string option)  {
 	try {
-	
-		//if the users entered no valid calculators don't execute command
-		if (sumCalculators.size() == 0) { return 0; }
+		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 (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["summary"] = 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;		}
+				}
+				
+				it = parameters.find("rabund");
+				//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["rabund"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("sabund");
+				//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["sabund"] = inputDir + it->second;		}
+				}
+				
+				it = parameters.find("list");
+				//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["list"] = inputDir + it->second;		}
+				}
+			}
+			
+			//check for required parameters
+			listfile = validParameter.validFile(parameters, "list", true);
+			if (listfile == "not open") { listfile = ""; abort = true; }
+			else if (listfile == "not found") { listfile = ""; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
+			
+			sabundfile = validParameter.validFile(parameters, "sabund", true);
+			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
+			else if (sabundfile == "not found") { sabundfile = ""; }
+			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+			
+			rabundfile = validParameter.validFile(parameters, "rabund", true);
+			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
+			else if (rabundfile == "not found") { rabundfile = ""; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
+			
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			else if (sharedfile == "not found") { sharedfile = ""; }
+			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
+			
+			if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
+				//is there are current file available for any of these?
+				//give priority to shared, then list, then rabund, then sabund
+				//if there is a current shared file, use it
+				sharedfile = m->getSharedFile(); 
+				if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+				else { 
+					listfile = m->getListFile(); 
+					if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+					else { 
+						rabundfile = m->getRabundFile(); 
+						if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+						else { 
+							sabundfile = m->getSabundFile(); 
+							if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+							else { 
+								m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single 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 = m->hasPath(inputfile);		}
+
+			//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;  }
+			}
+				
+			calc = validParameter.validFile(parameters, "calc", false);			
+			if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
+			else { 
+				 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
+			}
+			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; } }
+			}
 
-		outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
-		openOutputFile(outputFileName, outputFileHandle);
-		outputFileHandle << "label";
+			string temp;
+			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
+			convert(temp, abund); 
+			
+			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
+			convert(temp, size); 
+			
+			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "T"; }
+			groupMode = m->isTrue(temp);
+			
 	
-		read = new ReadPhilFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummaryCommand", "SummaryCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 
-		for(int i=0;i<sumCalculators.size();i++){
-			if(sumCalculators[i]->getCols() == 1){
-				outputFileHandle << '\t' << sumCalculators[i]->getName();
+int SummaryCommand::execute(){
+	try {
+	
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
+		if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
+		else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
+		
+		if (m->control_pressed) { return 0; }
+		
+		int numLines = 0;
+		int numCols = 0;
+		
+		for (int p = 0; p < inputFileNames.size(); p++) {
+			
+			numLines = 0;
+			numCols = 0;
+			
+			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
+			outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
+			
+			if (inputFileNames.size() > 1) {
+				m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 			}
-			else{
-				outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+			
+			sumCalculators.clear();
+			
+			ValidCalculators validCalculator;
+			
+			for (int i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) { 
+					if(Estimators[i] == "sobs"){
+						sumCalculators.push_back(new Sobs());
+					}else if(Estimators[i] == "chao"){
+						sumCalculators.push_back(new Chao1());
+					}else if(Estimators[i] == "coverage"){
+						sumCalculators.push_back(new Coverage());
+					}else if(Estimators[i] == "geometric"){
+						sumCalculators.push_back(new Geom());
+					}else if(Estimators[i] == "logseries"){
+						sumCalculators.push_back(new LogSD());
+					}else if(Estimators[i] == "qstat"){
+						sumCalculators.push_back(new QStat());
+					}else if(Estimators[i] == "bergerparker"){
+						sumCalculators.push_back(new BergerParker());
+					}else if(Estimators[i] == "bstick"){
+						sumCalculators.push_back(new BStick());
+					}else if(Estimators[i] == "ace"){
+						if(abund < 5)
+							abund = 10;
+						sumCalculators.push_back(new Ace(abund));
+					}else if(Estimators[i] == "jack"){
+						sumCalculators.push_back(new Jackknife());
+					}else if(Estimators[i] == "shannon"){
+						sumCalculators.push_back(new Shannon());
+					}else if(Estimators[i] == "shannoneven"){
+						sumCalculators.push_back(new ShannonEven());
+					}else if(Estimators[i] == "npshannon"){
+						sumCalculators.push_back(new NPShannon());
+					}else if(Estimators[i] == "heip"){
+						sumCalculators.push_back(new Heip());
+					}else if(Estimators[i] == "smithwilson"){
+						sumCalculators.push_back(new SmithWilson());
+					}else if(Estimators[i] == "simpson"){
+						sumCalculators.push_back(new Simpson());
+					}else if(Estimators[i] == "simpsoneven"){
+						sumCalculators.push_back(new SimpsonEven());
+					}else if(Estimators[i] == "invsimpson"){
+						sumCalculators.push_back(new InvSimpson());
+					}else if(Estimators[i] == "bootstrap"){
+						sumCalculators.push_back(new Bootstrap());
+					}else if (Estimators[i] == "nseqs") { 
+						sumCalculators.push_back(new NSeqs());
+					}else if (Estimators[i] == "goodscoverage") { 
+						sumCalculators.push_back(new GoodsCoverage());
+					}else if (Estimators[i] == "efron") { 
+						sumCalculators.push_back(new Efron(size));
+					}else if (Estimators[i] == "boneh") { 
+						sumCalculators.push_back(new Boneh(size));
+					}else if (Estimators[i] == "solow") { 
+						sumCalculators.push_back(new Solow(size));
+					}else if (Estimators[i] == "shen") { 
+						sumCalculators.push_back(new Shen(size, abund));
+					}
+				}
 			}
-		}
-		outputFileHandle << endl;
+			
+			//if the users entered no valid calculators don't execute command
+			if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+			
+			ofstream outputFileHandle;
+			m->openOutputFile(fileNameRoot, outputFileHandle);
+			outputFileHandle << "label";
 		
-		sabund = globaldata->sabund;
-		input = globaldata->ginput;
-		int count = 1;
-		while(sabund != NULL){
+			input = new InputData(inputFileNames[p], format);
+			sabund = input->getSAbundVector();
+			string lastLabel = sabund->getLabel();
 		
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){			
-	
-				cout << sabund->getLabel() << '\t' << count << endl;
+			for(int i=0;i<sumCalculators.size();i++){
+				if(sumCalculators[i]->getCols() == 1){
+					outputFileHandle << '\t' << sumCalculators[i]->getName();
+					numCols++;
+				}
+				else{
+					outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+					numCols += 3;
+				}
+			}
+			outputFileHandle << endl;
+			
+			//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 (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+			
+			while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+				
+				if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+				
+				if(allLines == 1 || labels.count(sabund->getLabel()) == 1){			
+					
+					m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+					processedLabels.insert(sabund->getLabel());
+					userLabels.erase(sabund->getLabel());
+					
+					outputFileHandle << sabund->getLabel();
+					for(int i=0;i<sumCalculators.size();i++){
+						vector<double> data = sumCalculators[i]->getValues(sabund);
+						
+						if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+
+						outputFileHandle << '\t';
+						sumCalculators[i]->print(outputFileHandle);
+					}
+					outputFileHandle << endl;
+					numLines++;
+				}
+				
+				if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+					string saveLabel = sabund->getLabel();
+					
+					delete sabund;
+					sabund = input->getSAbundVector(lastLabel);
+					
+					m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+					processedLabels.insert(sabund->getLabel());
+					userLabels.erase(sabund->getLabel());
+					
+					outputFileHandle << sabund->getLabel();
+					for(int i=0;i<sumCalculators.size();i++){
+						vector<double> data = sumCalculators[i]->getValues(sabund);
+						
+						if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
+						
+						outputFileHandle << '\t';
+						sumCalculators[i]->print(outputFileHandle);
+					}
+					outputFileHandle << endl;
+					numLines++;
+					
+					//restore real lastlabel to save below
+					sabund->setLabel(saveLabel);
+				}		
+				
+				lastLabel = sabund->getLabel();			
+				
+				delete sabund;
+				sabund = input->getSAbundVector();
+			}
 			
+			if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  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();
+				}
+			}
+			
+			//run last label if you need to
+			if (needToRun == true)  {
+				if (sabund != NULL) {	delete sabund;	}
+				sabund = input->getSAbundVector(lastLabel);
+				
+				m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 				outputFileHandle << sabund->getLabel();
 				for(int i=0;i<sumCalculators.size();i++){
 					vector<double> data = sumCalculators[i]->getValues(sabund);
+					
+					if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
+
 					outputFileHandle << '\t';
 					sumCalculators[i]->print(outputFileHandle);
 				}
 				outputFileHandle << endl;
+				numLines++;
+				delete sabund;
 			}
-		
-			sabund = input->getSAbundVector();
-			count++;
+			
+			outputFileHandle.close();
+			
+			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+
+			
+			delete input;  
+			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 		}
-	
+		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }  return 0;  }
+		
+		//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
+		if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
+		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }  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 SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SummaryCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
+//**********************************************************************************************************************
+vector<string> SummaryCommand::parseSharedFile(string filename) {
+	try {
+		vector<string> filenames;
+		
+		map<string, ofstream*> filehandles;
+		map<string, ofstream*>::iterator it3;
+		
+		input = new InputData(filename, "sharedfile");
+		vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+		
+		string sharedFileRoot = m->getRootName(filename);
+		
+		//clears file before we start to write to it below
+		for (int i=0; i<lookup.size(); i++) {
+			remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+			filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
+		}
+		
+		ofstream* temp;
+		for (int i=0; i<lookup.size(); i++) {
+			temp = new ofstream;
+			filehandles[lookup[i]->getGroup()] = temp;
+			groups.push_back(lookup[i]->getGroup());
+		}
 
+		while(lookup[0] != NULL) {
+		
+			for (int i = 0; i < lookup.size(); i++) {
+				RAbundVector rav = lookup[i]->getRAbundVector();
+				m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+				rav.print(*(filehandles[lookup[i]->getGroup()]));
+				(*(filehandles[lookup[i]->getGroup()])).close();
+			}
+		
+			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+			lookup = input->getSharedRAbundVectors();
+		}
+		
+		//free memory
+		for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+			delete it3->second;
+		}
+		
+		delete input;
+
+		return filenames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummaryCommand", "parseSharedFile");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
+	try {
+		
+		ofstream out;
+		string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
+		
+		//open combined file
+		m->openOutputFile(combineFileName, out);
+		
+		//open each groups summary file
+		string newLabel = "";
+		map<string, vector<string> > files;
+		for (int i=0; i<outputNames.size(); i++) {
+			vector<string> thisFilesLines;
+			
+			ifstream temp;
+			m->openInputFile(outputNames[i], temp);
+			
+			//read through first line - labels
+			string tempLabel;
+			if (i == 0) { //we want to save the labels to output below
+				for (int j = 0; j < numCols+1; j++) {  
+					temp >> tempLabel; 
+					
+					if (j == 1) {  newLabel += "group\t" + tempLabel + '\t';
+					}else{  newLabel += tempLabel + '\t';	}
+				}
+			}else{  for (int j = 0; j < numCols+1; j++) {  temp >> tempLabel;  }  }
+			
+			m->gobble(temp);
+			
+			//for each label
+			for (int k = 0; k < numLines; k++) {
+				
+				string thisLine = "";
+				string tempLabel;
+					
+				for (int j = 0; j < numCols+1; j++) {  
+					temp >> tempLabel; 
+						
+					//save for later
+					if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";	}
+					else{  thisLine += tempLabel + "\t";	}
+				}
+					
+				thisLine += "\n";
+				
+				thisFilesLines.push_back(thisLine);
+					
+				m->gobble(temp);
+			}
+				
+			files[outputNames[i]] = thisFilesLines;
+			
+			temp.close();
+			remove(outputNames[i].c_str());
+		}
+		
+		//output label line to new file
+		out << newLabel << endl;
+		
+		//for each label
+		for (int k = 0; k < numLines; k++) {
+		
+			//grab summary data for each group
+			for (int i=0; i<outputNames.size(); i++) {
+				out << files[outputNames[i]][k];
+			}
+		}	
+		
+		outputNames.clear();
+		
+		out.close();
+		
+		//return combine file name
+		return combineFileName;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************