X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;fp=collectcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=7ad41367f795abe7aeeda1052a8211daf72aeaf4;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
deleted file mode 100644
index 7ad4136..0000000
--- a/collectcommand.cpp
+++ /dev/null
@@ -1,593 +0,0 @@
-/*
- *  collectcommand.cpp
- *  Dotur
- *
- *  Created by Sarah Westcott on 1/2/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "collectcommand.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 "smithwilson.h"
-#include "heip.h"
-#include "shannoneven.h"
-#include "jackknife.h"
-#include "geom.h"
-#include "qstat.h"
-#include "logsd.h"
-#include "bergerparker.h"
-#include "bstick.h"
-#include "goodscoverage.h"
-#include "efron.h"
-#include "boneh.h"
-#include "solow.h"
-#include "shen.h"
-#include "coverage.h"
-
-
-//**********************************************************************************************************************
-vector<string> CollectCommand::setParameters(){	
-	try {
-		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 pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-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 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) {
-		m->errorOut(e, "CollectCommand", "setParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-string CollectCommand::getHelpString(){	
-	try {
-		string helpString = "";
-		ValidCalculators validCalculator;
-		helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
-		helpString += "The collect.single command should be in the following format: \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 += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
-		helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
-		helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
-		helpString += validCalculator.printCalc("single");
-		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, "CollectCommand", "getHelpString");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-CollectCommand::CollectCommand(){	
-	try {
-		abort = true; calledHelp = true; 
-		setParameters();
-		vector<string> tempOutNames;
-		outputTypes["sobs"] = tempOutNames;
-		outputTypes["chao"] = tempOutNames;
-		outputTypes["nseqs"] = tempOutNames;
-		outputTypes["coverage"] = tempOutNames;
-		outputTypes["ace"] = tempOutNames;
-		outputTypes["jack"] = tempOutNames;
-		outputTypes["shannon"] = tempOutNames;
-		outputTypes["shannoneven"] = tempOutNames;
-		outputTypes["npshannon"] = tempOutNames;
-		outputTypes["heip"] = tempOutNames;
-		outputTypes["smithwilson"] = tempOutNames;
-		outputTypes["simpson"] = tempOutNames;
-		outputTypes["simpsoneven"] = tempOutNames;
-		outputTypes["invsimpson"] = tempOutNames;
-		outputTypes["bootstrap"] = tempOutNames;
-		outputTypes["geometric"] = tempOutNames;
-		outputTypes["qstat"] = tempOutNames;
-		outputTypes["logseries"] = tempOutNames;
-		outputTypes["bergerparker"] = tempOutNames;
-		outputTypes["bstick"] = tempOutNames;
-		outputTypes["goodscoverage"] = tempOutNames;
-		outputTypes["efron"] = tempOutNames;
-		outputTypes["boneh"] = tempOutNames;
-		outputTypes["solow"] = tempOutNames;
-		outputTypes["shen"] = tempOutNames;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CollectCommand", "CollectCommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-CollectCommand::CollectCommand(string option)  {
-	try {
-		abort = false; calledHelp = false;   
-		allLines = 1;
-		
-		//allow user to run help
-		if(option == "help") { help(); calledHelp = true; abort = 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["sobs"] = tempOutNames;
-			outputTypes["chao"] = tempOutNames;
-			outputTypes["nseqs"] = tempOutNames;
-			outputTypes["coverage"] = tempOutNames;
-			outputTypes["ace"] = tempOutNames;
-			outputTypes["jack"] = tempOutNames;
-			outputTypes["shannon"] = tempOutNames;
-			outputTypes["shannoneven"] = tempOutNames;
-			outputTypes["npshannon"] = tempOutNames;
-			outputTypes["heip"] = tempOutNames;
-			outputTypes["smithwilson"] = tempOutNames;
-			outputTypes["simpson"] = tempOutNames;
-			outputTypes["simpsoneven"] = tempOutNames;
-			outputTypes["invsimpson"] = tempOutNames;
-			outputTypes["bootstrap"] = tempOutNames;
-			outputTypes["geometric"] = tempOutNames;
-			outputTypes["qstat"] = tempOutNames;
-			outputTypes["logseries"] = tempOutNames;
-			outputTypes["bergerparker"] = tempOutNames;
-			outputTypes["bstick"] = tempOutNames;
-			outputTypes["goodscoverage"] = tempOutNames;
-			outputTypes["efron"] = tempOutNames;
-			outputTypes["boneh"] = tempOutNames;
-			outputTypes["solow"] = tempOutNames;
-			outputTypes["shen"] = 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 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 = "";		}
-			
-			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;
-							}
-						}
-					}
-				}
-			}
-			
-			//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;  }
-			}
-			
-			//NOTE: if you add new calc options, don't forget to add them to the parameter initialize in setParameters or the gui won't be able to use them
-			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; } }
-			}
-
-			string temp;
-			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			m->mothurConvert(temp, freq); 
-			
-			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			m->mothurConvert(temp, abund); 
-			
-			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			m->mothurConvert(temp, size); 
-		}
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CollectCommand", "CollectCommand");
-		exit(1);
-	}			
-}
-//**********************************************************************************************************************
-
-int CollectCommand::execute(){
-	try {
-		
-		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-	
-		if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
-		else {  inputFileNames = parseSharedFile(sharedfile);  format = "rabund"; }
-	
-		for (int p = 0; p < inputFileNames.size(); p++) {
-			
-			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  m->clearGroups();  return 0; }
-			
-			if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
-			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
-			//globaldata->inputFileName = inputFileNames[p];
-		
-			if (inputFileNames.size() > 1) {
-				m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
-			}
-		
-			ValidCalculators validCalculator;
-			
-			for (int i=0; i<Estimators.size(); i++) {
-				if (validCalculator.isValidCalculator("single", Estimators[i]) == true) { 
-					if (Estimators[i] == "sobs") { 
-						cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
-						outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
-					}else if (Estimators[i] == "chao") { 
-						cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
-						outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
-					}else if (Estimators[i] == "nseqs") { 
-						cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
-						outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
-					}else if (Estimators[i] == "coverage") { 
-						cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
-						outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
-					}else if (Estimators[i] == "ace") { 
-						cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
-						outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
-					}else if (Estimators[i] == "jack") { 
-						cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
-						outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
-					}else if (Estimators[i] == "shannon") { 
-						cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
-						outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
-					}else if (Estimators[i] == "shannoneven") { 
-						cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
-						outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
-					}else if (Estimators[i] == "npshannon") { 
-						cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"npshannon")));
-						outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon");
-					}else if (Estimators[i] == "heip") { 
-						cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
-						outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
-					}else if (Estimators[i] == "smithwilson") { 
-						cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
-						outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
-					}else if (Estimators[i] == "simpson") { 
-						cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
-						outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
-					}else if (Estimators[i] == "simpsoneven") { 
-						cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
-						outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
-					}else if (Estimators[i] == "invsimpson") { 
-						cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
-						outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
-					}else if (Estimators[i] == "bootstrap") { 
-						cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
-						outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
-					}else if (Estimators[i] == "geometric") { 
-						cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
-						outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
-					}else if (Estimators[i] == "qstat") { 
-						cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
-						outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
-					}else if (Estimators[i] == "logseries") { 
-						cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
-						outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
-					}else if (Estimators[i] == "bergerparker") { 
-						cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
-						outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
-					}else if (Estimators[i] == "bstick") { 
-						cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
-						outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
-					}else if (Estimators[i] == "goodscoverage") { 
-						cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
-						outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
-					}else if (Estimators[i] == "efron") {
-						cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
-						outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
-					}else if (Estimators[i] == "boneh") {
-						cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
-						outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
-					}else if (Estimators[i] == "solow") {
-						cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
-						outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
-					}else if (Estimators[i] == "shen") {
-						cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
-						outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
-					}
-				}
-			}
-		
-			//if the users entered no valid calculators don't execute command
-			if (cDisplays.size() == 0) { 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<cDisplays.size();i++){	delete cDisplays[i];	}
-				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
-				delete input;  
-				delete order; 
-				m->clearGroups();
-				return 0;
-			}
-
-
-			while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-			
-				if (m->control_pressed) { 
-					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
-					delete input;  
-					delete order; 
-					m->clearGroups();
-					return 0;
-				}
-
-				
-				if(allLines == 1 || labels.count(order->getLabel()) == 1){
-				
-					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-					cCurve = new Collect(order, cDisplays);
-					cCurve->getCurve(freq);
-					delete cCurve;
-					
-					processedLabels.insert(order->getLabel());
-					userLabels.erase(order->getLabel());
-					
-					
-				}
-				//you have a label the user want that is smaller than this label and the last label has not already been processed 
-				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();
-					cCurve = new Collect(order, cDisplays);
-					cCurve->getCurve(freq);
-					delete cCurve;
-					
-					
-					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());
-			}
-			
-			
-			if (m->control_pressed) { 
-					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
-					delete input;  
-					m->clearGroups();
-					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 (order != NULL) {	delete order;	}
-				order = (input->getOrderVector(lastLabel));
-				
-				m->mothurOut(order->getLabel()); m->mothurOutEndLine();
-				
-				cCurve = new Collect(order, cDisplays);
-				cCurve->getCurve(freq);
-				delete cCurve;
-				
-				if (m->control_pressed) { 
-					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear(); 
-					delete input;  
-					delete order;
-					m->clearGroups();
-					return 0;
-				}
-				delete order;
-			}
-			
-			for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-			cDisplays.clear();
-			delete input;  
-		}
-		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} return 0; }
-				
-		m->mothurOutEndLine();
-		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
-		m->mothurOutEndLine();
-
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "CollectCommand", "execute");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-vector<string> CollectCommand::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++) {
-			m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
-			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, "CollectCommand", "parseSharedFile");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-