X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=1c04bc4384fb632db099867821b6ffb3b4d79e95;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=c2204e7a573969a2f4d1d80f41eb9defb3c53070;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index c2204e7..1c04bc4 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -10,105 +10,500 @@
 #include "rarefactcommand.h"
 #include "ace.h"
 #include "sobs.h"
+#include "nseqs.h"
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "heip.h"
+#include "smithwilson.h"
+#include "invsimpson.h"
 #include "npshannon.h"
+#include "shannoneven.h"
 #include "shannon.h"
 #include "jackknife.h"
-
-//**********************************************************************************************************************
+#include "coverage.h"
 
 
-RareFactCommand::RareFactCommand(){
+//**********************************************************************************************************************
+vector<string> RareFactCommand::setParameters(){	
 	try {
-		globaldata = GlobalData::getInstance();
-		string fileNameRoot;
-		fileNameRoot = getRootName(globaldata->inputFileName);
-		int i;
-		for (i=0; i<globaldata->rareEstimators.size(); i++) {
-			if (globaldata->rareEstimators[i] == "sobs") { 
-				rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
-			}else if (globaldata->rareEstimators[i] == "chao") { 
-				rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
-			}else if (globaldata->rareEstimators[i] == "ace") { 
-				rDisplays.push_back(new RareDisplay(new Ace(), new ThreeColumnFile(fileNameRoot+"r_ace")));
-			}else if (globaldata->rareEstimators[i] == "jack") { 
-				rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
-			}else if (globaldata->rareEstimators[i] == "shannon") { 
-				rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
-			}else if (globaldata->rareEstimators[i] == "npshannon") { 
-				rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
-			}else if (globaldata->rareEstimators[i] == "simpson") { 
-				rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
-			}else if (globaldata->rareEstimators[i] == "bootstrap") { 
-				rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_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 pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
+		CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+		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 RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RareFactCommand", "setParameters");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+string RareFactCommand::getHelpString(){	
+	try {
+		ValidCalculators validCalculator;
+		string helpString = "";
+		helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
+		helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
+		helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+		helpString += "The rarefaction.single command should be in the following format: \n";
+		helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
+		helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
+		helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
+		validCalculator.printCalc("rarefaction");
+		helpString += "The label parameter is used to analyze specific labels in your input.\n";
+		helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactCommand", "getHelpString");
 		exit(1);
-	}	
-			
+	}
 }
 
 //**********************************************************************************************************************
-
-RareFactCommand::~RareFactCommand(){
-	delete order;
-	delete input;
-	delete rCurve;
-	delete read;
+RareFactCommand::RareFactCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["rarefaction"] = tempOutNames;
+		outputTypes["r_chao"] = tempOutNames;
+		outputTypes["r_ace"] = tempOutNames;
+		outputTypes["r_jack"] = tempOutNames;
+		outputTypes["r_shannon"] = tempOutNames;
+		outputTypes["r_shannoneven"] = tempOutNames;
+		outputTypes["r_heip"] = tempOutNames;
+		outputTypes["r_smithwilson"] = tempOutNames;
+		outputTypes["r_npshannon"] = tempOutNames;
+		outputTypes["r_simpson"] = tempOutNames;
+		outputTypes["r_simpsoneven"] = tempOutNames;
+		outputTypes["r_invsimpson"] = tempOutNames;
+		outputTypes["r_bootstrap"] = tempOutNames;
+		outputTypes["r_coverage"] = tempOutNames;
+		outputTypes["r_nseqs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactCommand", "RareFactCommand");
+		exit(1);
+	}
 }
+//**********************************************************************************************************************
+RareFactCommand::RareFactCommand(string option)  {
+	try {
+		abort = false; calledHelp = false;   
+		allLines = 1;
+						
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+		
+		else {
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			map<string,string>::iterator it;
+			
+			ValidParameters validParameter;
+		
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["rarefaction"] = tempOutNames;
+			outputTypes["r_chao"] = tempOutNames;
+			outputTypes["r_ace"] = tempOutNames;
+			outputTypes["r_jack"] = tempOutNames;
+			outputTypes["r_shannon"] = tempOutNames;
+			outputTypes["r_shannoneven"] = tempOutNames;
+			outputTypes["r_heip"] = tempOutNames;
+			outputTypes["r_smithwilson"] = tempOutNames;
+			outputTypes["r_npshannon"] = tempOutNames;
+			outputTypes["r_simpson"] = tempOutNames;
+			outputTypes["r_simpsoneven"] = tempOutNames;
+			outputTypes["r_invsimpson"] = tempOutNames;
+			outputTypes["r_bootstrap"] = tempOutNames;
+			outputTypes["r_coverage"] = tempOutNames;
+			outputTypes["r_nseqs"] = 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; }
+			
+			sabundfile = validParameter.validFile(parameters, "sabund", true);
+			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
+			else if (sabundfile == "not found") { sabundfile = ""; }
+			else {  format = "sabund"; inputfile = 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; }
+			
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			else if (sharedfile == "not found") { sharedfile = ""; }
+			else {  format = "sharedfile"; inputfile = 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";  }
+			else { 
+				 if (calc == "default")  {  calc = "sobs";  }
+			}
+			m->splitAtDash(calc, Estimators);
 
+			string temp;
+			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
+			convert(temp, freq); 
+			
+			temp = validParameter.validFile(parameters, "abund", false);			if (temp == "not found") { temp = "10"; }
+			convert(temp, abund); 
+			
+			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
+			convert(temp, nIters); 
+			
+			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
+			m->setProcessors(temp);
+			convert(temp, processors);
+		}
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactCommand", "RareFactCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 int RareFactCommand::execute(){
 	try {
-		int count = 1;
-		read = new ReadPhilFile(globaldata->inputFileName);	
-		read->read(&*globaldata); 
-
-		order = globaldata->gorder;
-		input = globaldata->ginput;
 	
-		while(order != NULL){
+		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; }
 		
-			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+		for (int p = 0; p < inputFileNames.size(); p++) {
 			
-				rCurve = new Rarefact(order, rDisplays);
-				convert(globaldata->getFreq(), freq);
-				convert(globaldata->getIters(), nIters);
-				rCurve->getCurve(freq, nIters);
+			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+						
+			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  m->Groups.clear();  return 0; }
 			
-				delete rCurve;
+			if (inputFileNames.size() > 1) {
+				m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+			}
+			int i;
+			ValidCalculators validCalculator;
+			
+			  
+			for (i=0; i<Estimators.size(); i++) {
+				if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) { 
+					if (Estimators[i] == "sobs") { 
+						rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
+						outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
+					}else if (Estimators[i] == "chao") { 
+						rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+						outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
+					}else if (Estimators[i] == "ace") { 
+						if(abund < 5)
+							abund = 10;
+						rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
+						outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
+					}else if (Estimators[i] == "jack") { 
+						rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+						outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
+					}else if (Estimators[i] == "shannon") { 
+						rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+						outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
+					}else if (Estimators[i] == "shannoneven") { 
+						rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
+						outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
+					}else if (Estimators[i] == "heip") { 
+						rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
+						outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
+					}else if (Estimators[i] == "smithwilson") { 
+						rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
+						outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
+					}else if (Estimators[i] == "npshannon") { 
+						rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+						outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
+					}else if (Estimators[i] == "simpson") { 
+						rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+						outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
+					}else if (Estimators[i] == "simpsoneven") { 
+						rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
+						outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
+					}else if (Estimators[i] == "invsimpson") { 
+						rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
+						outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
+					}else if (Estimators[i] == "bootstrap") { 
+						rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+						outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
+					}else if (Estimators[i] == "coverage") { 
+						rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
+						outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
+					}else if (Estimators[i] == "nseqs") { 
+						rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+						outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
+					}
+				}
+			}
+			
+			
+			//if the users entered no valid calculators don't execute command
+			if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}  return 0; }
+			
+			input = new InputData(inputFileNames[p], format);			
+			order = input->getOrderVector();
+			string lastLabel = order->getLabel();
+			
+			//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+			set<string> processedLabels;
+			set<string> userLabels = labels;
+			
+			if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			
+			//as long as you are not at the end of the file or done wih the lines you want
+			while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+				
+				if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+
+				
+				if(allLines == 1 || labels.count(order->getLabel()) == 1){
+					
+					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+					rCurve = new Rarefact(order, rDisplays, processors);
+					rCurve->getCurve(freq, nIters);
+					delete rCurve;
+					
+					processedLabels.insert(order->getLabel());
+					userLabels.erase(order->getLabel());
+				}
+				
+				if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+					string saveLabel = order->getLabel();
+					
+					delete order;
+					order = (input->getOrderVector(lastLabel));
+					
+					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+					rCurve = new Rarefact(order, rDisplays, processors);
+					rCurve->getCurve(freq, nIters);
+					delete rCurve;
+					
+					processedLabels.insert(order->getLabel());
+					userLabels.erase(order->getLabel());
+					
+					//restore real lastlabel to save below
+					order->setLabel(saveLabel);
+				}
+				
+				lastLabel = order->getLabel();		
+				
+				delete order;
+				order = (input->getOrderVector());
+			}
 			
-				cout << order->getLabel() << '\t' << count << endl;
+			if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}  delete input;   for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+
+			//output error messages about any remaining user labels
+			set<string>::iterator it;
+			bool needToRun = false;
+			for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+				m->mothurOut("Your file does not include the label " + *it);
+				if (processedLabels.count(lastLabel) != 1) {
+					m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+					needToRun = true;
+				}else {
+					m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+				}
 			}
+			
+			if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}  delete input;   for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+
+			//run last label if you need to
+			if (needToRun == true)  {
+				if (order != NULL) {	delete order;	}
+				order = (input->getOrderVector(lastLabel));
+				
+				m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+				rCurve = new Rarefact(order, rDisplays, processors);
+				rCurve->getCurve(freq, nIters);
+				delete rCurve;
+				
+				delete order;
+			}
+			
+			
+			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
+			rDisplays.clear();
+			delete input;  
+		}
 		
-			order = (input->getOrderVector());
-			count++;
 		
-		}
-	
-		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
+		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 RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "RareFactCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
+//**********************************************************************************************************************
+vector<string> RareFactCommand::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;
+		m->Groups.clear();
 
+		return filenames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareFactCommand", "parseSharedFile");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
+
+
+