X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=208544adf1bd7ec2f0f59603c4eb86840275cf80;hb=afcbef163b4f32d0ff25a834cb9af8eef8d06ffa;hp=e228dbe7bcdef90bc829098091a8e1794c1d5114;hpb=016a30dacbe75869aef5fdb58d2d1bf9eb8f9b33;p=mothur.git

diff --git a/summarycommand.cpp b/summarycommand.cpp
index e228dbe..208544a 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -14,8 +14,13 @@
 #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"
@@ -31,21 +36,20 @@
 
 //**********************************************************************************************************************
 
-SummaryCommand::SummaryCommand(string option){
+SummaryCommand::SummaryCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
 		abort = false;
 		allLines = 1;
-		lines.clear();
 		labels.clear();
 		Estimators.clear();
 		
 		//allow user to run help
-		if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+		if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"line","label","calc","abund","size"};
+			string Array[] =  {"label","calc","abund","size","outputdir","groupmode","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -59,31 +63,27 @@ SummaryCommand::SummaryCommand(string option){
 			}
 			
 			//make sure the user has already run the read.otu command
-			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the summary.single command." << endl; abort = true; }
+			if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.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 = "";	
+				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...
-			line = validParameter.validFile(parameters, "line", false);				
-			if (line == "not found") { line = "";  }
-			else { 
-				if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
-				else { allLines = 1;  }
-			}
-			
 			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; }
 			else { 
-				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+				if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 				else { allLines = 1;  }
 			}
 			
-			//make sure user did not use both the line and label parameters
-			if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
-			//if the user has not specified any line or labels use the ones from read.otu
-			else if((line == "") && (label == "")) {  
+			//if the user has not specified any labels use the ones from read.otu
+			if(label == "") {  
 				allLines = globaldata->allLines; 
 				labels = globaldata->labels; 
-				lines = globaldata->lines;
 			}
 				
 			calc = validParameter.validFile(parameters, "calc", false);			
@@ -91,7 +91,7 @@ SummaryCommand::SummaryCommand(string option){
 			else { 
 				 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 			}
-			splitAtDash(calc, Estimators);
+			m->splitAtDash(calc, Estimators);
 
 			string temp;
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
@@ -99,108 +99,43 @@ SummaryCommand::SummaryCommand(string option){
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
 			convert(temp, size); 
-	
-			if (abort == false) {
 			
-				validCalculator = new ValidCalculators();
-				int i;
-				
-				for (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] == "npshannon"){
-							sumCalculators.push_back(new NPShannon());
-						}else if(Estimators[i] == "simpson"){
-							sumCalculators.push_back(new Simpson());
-						}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));
-						}
-					}
-				}
-			}
+			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "F"; }
+			groupMode = m->isTrue(temp);
+			
+	
 		}
-
-				
 	}
 	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", "SummaryCommand");
 		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);
-	}	
 }
 //**********************************************************************************************************************
 
 void SummaryCommand::help(){
 	try {
-		cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
-		cout << "The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";
-		cout << "The summary.single command parameters are label, line, calc, abund.  No parameters are required, but you may not use " << "\n";
-		cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
-		cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
-		cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
+		m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
+		m->mothurOut("The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
+		m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode.  No parameters are required.\n");
+		m->mothurOut("The summary.single command should be in the following format: \n");
+		m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
+		m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
 		validCalculator->printCalc("summary", cout);
-		cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\n";
-		cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
-		cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+		m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
+		m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=False).\n");
+		m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SummaryCommand", "help");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SummaryCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 //**********************************************************************************************************************
 
-SummaryCommand::~SummaryCommand(){
-	if (abort == false) {
-		delete input;  globaldata->ginput = NULL;
-		delete read;
-		delete validCalculator;
-		globaldata->sabund = NULL;
-	}
-}
+SummaryCommand::~SummaryCommand(){}
 
 //**********************************************************************************************************************
 
@@ -209,121 +144,375 @@ int SummaryCommand::execute(){
 	
 		if (abort == true) { return 0; }
 		
-		int count = 1;
+		vector<string> outputNames;
 		
-		//if the users entered no valid calculators don't execute command
-		if (sumCalculators.size() == 0) { return 0; }
-
-		outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
-		openOutputFile(outputFileName, outputFileHandle);
-		outputFileHandle << "label";
-	
-		read = new ReadOTUFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
+		string hadShared = "";
+		if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
+		else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 		
-		sabund = globaldata->sabund;
-		string lastLabel = sabund->getLabel();
-		input = globaldata->ginput;
+		if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
+		
+		int numLines = 0;
+		int numCols = 0;
 		
-		for(int i=0;i<sumCalculators.size();i++){
-			if(sumCalculators[i]->getCols() == 1){
-				outputFileHandle << '\t' << sumCalculators[i]->getName();
+		for (int p = 0; p < inputFileNames.size(); p++) {
+			
+			numLines = 0;
+			numCols = 0;
+			
+			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
+			globaldata->inputFileName = inputFileNames[p];
+			outputNames.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();
+			
+			validCalculator = new ValidCalculators();
+			
+			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 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;
-		set<int> userLines = lines;
-		
-		while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
-			if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){			
-	
-				cout << sabund->getLabel() << '\t' << count << endl;
-				processedLabels.insert(sabund->getLabel());
-				userLabels.erase(sabund->getLabel());
-				userLines.erase(count);
+			//if the users entered no valid calculators don't execute command
+			if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
+			
+			ofstream outputFileHandle;
+			m->openOutputFile(fileNameRoot, outputFileHandle);
+			outputFileHandle << "label";
+			
+			read = new ReadOTUFile(globaldata->inputFileName);	
+			read->read(&*globaldata); 
+			
+			sabund = globaldata->sabund;
+			string lastLabel = sabund->getLabel();
+			input = globaldata->ginput;
+			
+			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) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }  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 validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+			
+			while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+				
+				if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } 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 validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; 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) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } 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 validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
 
+						outputFileHandle << '\t';
+						sumCalculators[i]->print(outputFileHandle);
+					}
+					outputFileHandle << endl;
+					numLines++;
+				}
 				
-				outputFileHandle << sabund->getLabel();
-				for(int i=0;i<sumCalculators.size();i++){
-					vector<double> data = sumCalculators[i]->getValues(sabund);
-					outputFileHandle << '\t';
-					sumCalculators[i]->print(outputFileHandle);
+				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) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } 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 validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; 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) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } 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 validCalculator; delete read;  delete input; globaldata->ginput = NULL; 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();
 				}
-				outputFileHandle << endl;
 			}
 			
-			if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
-				delete sabund;
+			//run last label if you need to
+			if (needToRun == true)  {
+				if (sabund != NULL) {	delete sabund;	}
 				sabund = input->getSAbundVector(lastLabel);
 				
-				cout << sabund->getLabel() << '\t' << count << endl;
-				processedLabels.insert(sabund->getLabel());
-				userLabels.erase(sabund->getLabel());
-				
+				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) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } 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 validCalculator; delete read; delete sabund; globaldata->sabund = NULL; delete input; globaldata->ginput = NULL; return 0;  }
+
 					outputFileHandle << '\t';
 					sumCalculators[i]->print(outputFileHandle);
 				}
 				outputFileHandle << endl;
-			}		
+				numLines++;
+				delete sabund;
+			}
+			
+			outputFileHandle.close();
+			
+			if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } 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 validCalculator; delete read;  delete input; globaldata->ginput = NULL; return 0;  }
 
-			lastLabel = sabund->getLabel();			
 			
-			delete sabund;
-			sabund = input->getSAbundVector();
-			count++;
+			delete input;  globaldata->ginput = NULL;
+			delete read;
+			delete validCalculator;
+			globaldata->sabund = NULL;
+			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 		}
 		
-		//output error messages about any remaining user labels
-		set<string>::iterator it;
-		bool needToRun = false;
-		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-			cout << "Your file does not include the label "<< *it; 
-			if (processedLabels.count(lastLabel) != 1) {
-				cout << ". I will use " << lastLabel << "." << endl;
-				needToRun = true;
-			}else {
-				cout << ". Please refer to " << lastLabel << "." << endl;
+		if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
+		
+		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 ((hadShared != "") && (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) {
+		m->errorOut(e, "SummaryCommand", "execute");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SummaryCommand::parseSharedFile(string filename) {
+	try {
+		vector<string> filenames;
+		
+		map<string, ofstream*> filehandles;
+		map<string, ofstream*>::iterator it3;
+		
+				
+		//read first line
+		read = new ReadOTUFile(filename);	
+		read->read(&*globaldata); 
+			
+		input = globaldata->ginput;
+		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 read;
+		delete input;
+		globaldata->ginput = NULL;
+
+		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(globaldata->inputFileName)) + "groups.summary";
 		
-		//run last line if you need to
-		if (needToRun == true)  {
-			delete sabund;
-			sabund = input->getSAbundVector(lastLabel);
+		//open combined file
+		m->openOutputFile(combineFileName, out);
+		
+		//open each groups summary file
+		string newLabel = "";
+		ifstream* temp;
+		map<string, ifstream*> filehandles;
+		for (int i=0; i<outputNames.size(); i++) {
+			temp = new ifstream;
+			filehandles[outputNames[i]] = temp;
+			m->openInputFile(outputNames[i], *(temp));
 			
-			cout << sabund->getLabel() << '\t' << count << endl;
-			outputFileHandle << sabund->getLabel();
-			for(int i=0;i<sumCalculators.size();i++){
-				vector<double> data = sumCalculators[i]->getValues(sabund);
-				outputFileHandle << '\t';
-				sumCalculators[i]->print(outputFileHandle);
-			}
-			outputFileHandle << endl;
-			delete sabund;
+			//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));
 		}
 		
-		outputFileHandle.close();
+		//output label line to new file
+		out << newLabel << endl;
+		
+		//for each label
+		for (int i = 0; i < numLines; i++) {
+		
+			//grab summary data for each group
+			for (int i=0; i<outputNames.size(); i++) {
+				string tempLabel;
+				
+				for (int j = 0; j < numCols+1; j++) {  
+					*(filehandles[outputNames[i]]) >> tempLabel; 
+					
+					//print to combined file
+					if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t';	}
+					else{  out << tempLabel << '\t';	}
+				}
+				
+				out << endl;
+				m->gobble(*(filehandles[outputNames[i]]));
+			}
+		}	
+		
+		//close each groups summary file
+		for (int i=0; i<outputNames.size(); i++) {  (*(filehandles[outputNames[i]])).close();  remove(outputNames[i].c_str());  }
+		outputNames.clear();
+		
+		out.close();
+		
+		//return combine file name
+		return combineFileName;
 		
-		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", "createGroupSummaryFile");
 		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);
-	}		
 }
-
 //**********************************************************************************************************************