X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=a0b80ecbbf77ef9e8b95b90b558656148651f9fc;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=713ae9af7346dbcdffe38e3f38f9f93b1129984d;hpb=72a92a86c30876883e8af2af9803a3ecf38bdea7;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 713ae9a..a0b80ec 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,491 +1,173 @@
-#include <iostream>
-#include <iomanip>
-#include <string>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-
-using namespace std;
 
+/*
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
-#include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
-#include <exception>
-#include <iostream>
+#include "sharedlistvector.h"
+#include "inputdata.h"
+#include "fullmatrix.h"
 
 /*******************************************************/
 
-/******************************************************/
+/******************************************************
 GlobalData* GlobalData::getInstance() {
-	if( _uniqueInstance == 0 ) {
+	if( _uniqueInstance == 0) {
 		_uniqueInstance = new GlobalData();
 	}
 	return _uniqueInstance;
 }
 /*******************************************************/
 
-/******************************************************/
-
-ListVector* GlobalData::getListVector()		{	return gListVector;		}
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setListVector(ListVector* lv){
-	try {
-		if(gListVector != NULL){	delete gListVector;	}
-		gListVector = new ListVector(*lv);
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-}
-
-/*******************************************************/
-
-/******************************************************/
-
-SparseMatrix* GlobalData::getSparseMatrix()	{	return gSparseMatrix;	}
-/*******************************************************/
-
-/******************************************************/
-void GlobalData::setSparseMatrix(SparseMatrix* sm){
-	try{
-		if(gSparseMatrix != NULL){	delete gSparseMatrix;	}
-		gSparseMatrix = new SparseMatrix(*sm);
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
-}
-/*******************************************************/
-
-/******************************************************/
-//This function parses through the option string of the command to remove its parameters
-void GlobalData::parseGlobalData(string commandString, string optionText){
-	try {
-		allLines = 1;
-		commandName = commandString; //save command name to be used by other classes
-		
-		//clears out data from previous read
-		if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
-			clear();
-		}
-		
-		//saves help request
-		if (commandName =="help") {
-			helpRequest = optionText;
-		}
-		
-		string key, value;		
-		//reads in parameters and values
-		if((optionText != "") && (commandName != "help")){
-			while((optionText.find_first_of(',') != -1)) {  //while there are parameters
-				splitAtComma(value, optionText);
-				splitAtEquals(key, value);
-				
-				if (key == "phylip" )	{ phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";	}
-				if (key == "column" )	{ columnfile = value; inputFileName = value; fileroot = value; format = "column";	}
-				if (key == "list" )		{ listfile = value; inputFileName = value; fileroot = value; format = "list";		}
-				if (key == "rabund" )	{ rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";	}
-				if (key == "sabund" )	{ sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";	} 
-				if (key == "fasta" )	{ fastafile = value; inputFileName = value; fileroot = value; format = "fasta";		} 
-				if (key == "treefile" )		{ treefile = value; inputFileName = value; fileroot = value; format = "tree";		}
-				if (key == "name" )		{ namefile = value;		}
-				if (key == "order" )	{ orderfile = value;	}
-				if (key == "group" )	{ groupfile = value;	}
-				if (key == "cutoff" )		{ cutoff = value;		}
-				if (key == "precision" )	{ precision = value;	}
-				if (key == "iters" )		{ iters = value;		}
-				if (key == "jumble" )		{ jumble = value;		}
-				if (key == "freq" )			{ freq = value;			}
-				if (key == "method" )		{ method = value;		}
-				if (key == "fileroot" )		{ fileroot = value;		}
-				
-				if (key == "single") {//stores estimators in a vector
-					singleEstimators.clear(); //clears out old values
-					if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
-					splitAtDash(value, singleEstimators);
-				}
-				if (key == "rarefaction") {//stores estimators in a vector
-					rareEstimators.clear(); //clears out old values
-					if (value == "default") { value = "rarefraction"; }
-					splitAtDash(value, rareEstimators);
-				}
-				if (key == "shared") {//stores estimators in a vector
-					sharedEstimators.clear(); //clears out old values
-					if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
-					splitAtDash(value, sharedEstimators);
-				}
-				if (key == "summary") { //stores summaries to be used in a vector
-					summaryEstimators.clear();
-					if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
-					splitAtDash(value, summaryEstimators);
-				}
-				if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
-					sharedSummaryEstimators.clear();
-					if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
-					splitAtDash(value, sharedSummaryEstimators);
-				}
-				if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
-					sharedRareEstimators.clear();
-					if (value == "default") { value = "sharedobserved"; }
-					splitAtDash(value, sharedRareEstimators);
-				}
-				if (key == "line") {//stores lines to be used in a vector
-					lines.clear();
-					line = value;
-					splitAtDash(value, lines);
-					allLines = 0;
-				}
-				if (key == "label") {//stores lines to be used in a vector
-					labels.clear();
-					label = value;
-					splitAtDash(value, labels);
-					allLines = 0;
-				}
-			}
-			
-			//saves the last parameter
-			value = optionText;
-			splitAtEquals(key, value);
-			if (key == "phylip" )	{ phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";	}
-			if (key == "column" )	{ columnfile = value; inputFileName = value; fileroot = value; format = "column";	}
-			if (key == "list" )		{ listfile = value; inputFileName = value; fileroot = value; format = "list";		}
-			if (key == "rabund" )	{ rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";	}
-			if (key == "sabund" )	{ sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";	}
-			if (key == "fasta" )	{ fastafile = value; inputFileName = value; fileroot = value; format = "fasta";		}
-			if (key == "treefile" )		{ treefile = value; inputFileName = value; fileroot = value; format = "tree";		}  
-			if (key == "name" )		{ namefile = value;		}
-			if (key == "order" )	{ orderfile = value;	}
-			if (key == "group" )	{ groupfile = value;	}
-			if (key == "cutoff" )		{ cutoff = value;		}
-			if (key == "precision" )	{ precision = value;	}
-			if (key == "iters" )		{ iters = value;		}
-			if (key == "jumble" )		{ jumble = value;		}
-			if (key == "freq" )			{ freq = value;			}
-			if (key == "method" )		{ method = value;		}
-			if (key == "fileroot" )		{ fileroot = value;		}
-
-			if (key == "single") {//stores estimators in a vector
-				singleEstimators.clear(); //clears out old values
-				if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
-				splitAtDash(value, singleEstimators);
-			}
-			if (key == "rarefaction") {//stores estimators in a vector
-				rareEstimators.clear(); //clears out old values
-				if (value == "default") { value = "rarefraction"; }
-				splitAtDash(value, rareEstimators);
-			}
-			if (key == "shared") {//stores estimators in a vector
-				sharedEstimators.clear(); //clears out old values
-				if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
-				splitAtDash(value, sharedEstimators);
-			}
-			if (key == "summary") { //stores summaries to be used in a vector
-				summaryEstimators.clear();
-				if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
-				splitAtDash(value, summaryEstimators);
-			}
-			if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
-				sharedSummaryEstimators.clear();
-				if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
-				splitAtDash(value, sharedSummaryEstimators);
-			}
-			if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
-				sharedRareEstimators.clear();
-				if (value == "default") { value = "sharedobserved"; }
-				splitAtDash(value, sharedRareEstimators);
-			}
-			
-			if (key == "line") {//stores lines to be used in a vector
-				lines.clear();
-				line = value;
-				splitAtDash(value, lines);
-				allLines = 0;
-			}
-			if (key == "label") {//stores lines to be used in a vector
-				labels.clear();
-				label = value;
-				splitAtDash(value, labels);
-				allLines = 0;
-			}
-		}
-		
-		//set format for shared
-		if ((listfile != "") && (groupfile != "")) { format = "shared"; }
-				
-		//input defaults
-		if (commandName == "collect.single") {
-			if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
-		}
-		if (commandName == "rarefaction.single") {
-			if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }	
-		}
-		if (commandName == "collect.shared") {
-			if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }	
-		}
-		if (commandName == "summary.single") {
-			if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
-		}
-		if (commandName == "summary.shared") {
-			if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
-		}
-		if (commandName == "rarefaction.shared") {
-			if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
-		}
-
-
-		//if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
-		if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
-			if (listfile != "") { format = "list"; }
-			else if (sabundfile != "") { format = "sabund"; }
-			else if (rabundfile != "") { format = "rabund"; }
-		}
-				
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
-}
-/*******************************************************/
-
-/******************************************************/
+/******************************************************
 // These functions give you the option parameters of the commands
-string GlobalData::getPhylipFile()		{	return phylipfile;	}
-string GlobalData::getColumnFile()		{	return columnfile;	}
-string GlobalData::getListFile()		{	return listfile;	}
-string GlobalData::getRabundFile()		{	return rabundfile;	}
-string GlobalData::getSabundFile()		{	return sabundfile;	}
-string GlobalData::getNameFile()		{	return namefile;	}
-string GlobalData::getGroupFile()		{	return groupfile;	}
-string GlobalData::getOrderFile()		{	return orderfile;	}
-string GlobalData::getTreeFile()		{	return treefile;	}
-string GlobalData::getFastaFile()		{	return fastafile;	}
-string GlobalData::getCutOff()			{	return cutoff;		}
-string GlobalData::getFormat()			{	return format;		}
-string GlobalData::getPrecision()		{	return precision;	}
-string GlobalData::getMethod()			{	return method;		}
-string GlobalData::getFileRoot()		{	return fileroot;	}
-string GlobalData::getIters()			{	return iters;		}
-string GlobalData::getJumble()			{	return jumble;		}
-string GlobalData::getFreq()			{	return freq;		}
-void GlobalData::setListFile(string file)	{	listfile = file;	inputFileName = file;}
-void GlobalData::setRabundFile(string file)	{	rabundfile = file;	inputFileName = file;}
-void GlobalData::setSabundFile(string file)	{	sabundfile = file;	inputFileName = file;}
-void GlobalData::setPhylipFile(string file)	{	phylipfile = file;    inputFileName = file;}
-void GlobalData::setColumnFile(string file)	{	columnfile = file;    inputFileName = file;}
-//void GlobalData::setGroupFile(string file)	{	groupfile = file;	}
-void GlobalData::setNameFile(string file)	{	namefile = file;	}
-void GlobalData::setFormat(string Format)	{	format = Format; 	}
-
-
-/*******************************************************/
-
-/******************************************************/
-
+string GlobalData::getPhylipFile()		{	return phylipfile;		}
+string GlobalData::getColumnFile()		{	return columnfile;		}
+string GlobalData::getListFile()		{	return listfile;		}
+string GlobalData::getRabundFile()		{	return rabundfile;		}
+string GlobalData::getSabundFile()		{	return sabundfile;		}
+string GlobalData::getNameFile()		{	return namefile;		}
+string GlobalData::getGroupFile()		{	return groupfile;		}
+string GlobalData::getOrderFile()		{	return orderfile;		}
+string GlobalData::getOrderGroupFile()	{	return ordergroup;		}
+string GlobalData::getTreeFile()		{	return treefile;		}
+string GlobalData::getSharedFile()		{	return sharedfile;		}	
+string GlobalData::getRelAbundFile()	{	return relAbundfile;	}	
+string GlobalData::getFormat()			{	return format;			}
+
+void GlobalData::setListFile(string file)		{	listfile = file;	inputFileName = file;					}
+void GlobalData::setTreeFile(string file)		{	treefile = file;	inputFileName = file;					}
+void GlobalData::setRabundFile(string file)		{	rabundfile = file;	inputFileName = file;					}
+void GlobalData::setSabundFile(string file)		{	sabundfile = file;	inputFileName = file;					}
+void GlobalData::setPhylipFile(string file)		{	phylipfile = file;    inputFileName = file;					}
+void GlobalData::setColumnFile(string file)		{	columnfile = file;    inputFileName = file;					}
+void GlobalData::setGroupFile(string file)		{	groupfile = file;											}
+void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file;					}
+void GlobalData::setRelAbundFile(string file)	{	relAbundfile = file;	inputFileName = file;				}
+void GlobalData::setNameFile(string file)		{	namefile = file;		}
+void GlobalData::setOrderFile(string file)		{	orderfile = file;		}
+void GlobalData::setOrderGroupFile(string file)	{	ordergroup = file;		}
+void GlobalData::setFormat(string Format)		{	format = Format;		}
+
+
+/*******************************************************/
+
+/******************************************************
 GlobalData::GlobalData() {
+	m = MothurOut::getInstance();
 	//option definitions should go here...
-	helpRequest = "";
 	clear();
+	gListVector = NULL;		
+	gSparseMatrix = NULL;	
+	ginput = NULL;
+	gorder = NULL;
+	glist = NULL;
+	gSharedList = NULL;
+	sabund = NULL;
+	rabund = NULL;
+	gGroupmap = NULL;
+	gMatrix = NULL;
+	gTreemap = NULL;
+	gSequenceDB = NULL;
+	nameMap = NULL;
+	saveNextLabel = "";
 }
 /*******************************************************/
 
-/******************************************************/
-
+/******************************************************
 void GlobalData::clear() {
 	//option definitions should go here...
-	phylipfile		=	"";
-	columnfile		=	"";
+	phylipfile		=	""; //do we need this?
+	columnfile		=	""; //do we need this?
 	listfile		=	"";
 	rabundfile		=	"";
 	sabundfile		=	"";
-	namefile		=	"";
-	groupfile		=	""; 
+	namefile		=	""; //do we need this?
+	groupfile		=	""; //do we need this?
 	orderfile		=	"";
-	fastafile		=   "";
+	ordergroup		=	"";
+//	fastafile		=   ""; //do we need this?
 	treefile		=	"";
-	cutoff			=	"10.00";
-	format			=	"";
-	precision		=	"100";
-	iters			=	"1000"; 
-	line			=   "";
-	label			=	"";
-	jumble			=	"1";
-	freq			=	"100";
-	method			=	"furthest";
-	fileroot		=	"";
-	single			=	"sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
-	rarefaction		=	"rarefaction";
-	shared			=	"sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
-	sharedsummary	=   "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
-	summary			=	"summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
-	sharedrarefaction = "sharedobserved";
+	sharedfile		=	"";
+	relAbundfile	=	"";
+	format = "";
+	saveNextLabel = "";
 }
-/*******************************************************/
 
-/******************************************************/
 
-GlobalData::~GlobalData() {
-	_uniqueInstance = 0;
-	if(gListVector != NULL)		{	delete gListVector;		}
-	if(gSparseMatrix != NULL)	{	delete gSparseMatrix;	}
-	if(gorder != NULL)			{	delete gorder;		}
-}
 /*******************************************************/
 
-/******************************************************/
-//This function parses the estimator options and puts them in a vector
-void GlobalData::splitAtDash(string& estim, vector<string>& container) {
-	try {
-		string individual;
-		
-		while (estim.find_first_of('-') != -1) {
-			individual = estim.substr(0,estim.find_first_of('-'));
-			if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-				estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-				container.push_back(individual);
-			}
-		}
-		//get last one
-		container.push_back(estim);
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
+/******************************************************
+void GlobalData::newRead() {
+	try{	
+			//remove old file names
+			clear();
+			
+			//free memory
+			if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
 
-}
-/*******************************************************/
+			if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
 
-/******************************************************/
-//This function parses the label options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<string>& container) {
-	try {
-		string individual;
-		
-		while (estim.find_first_of('-') != -1) {
-			individual = estim.substr(0,estim.find_first_of('-'));
-			if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-				estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-				container.insert(individual);
-			}
-		}
-		//get last one
-		container.insert(estim);
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
+			if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
 
-}
-/*******************************************************/
+			if (ginput != NULL) { delete ginput; ginput = NULL;}
 
-/******************************************************/
-//This function parses the line options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<int>& container) {
-	try {
-		string individual;
-		int lineNum;
-		
-		while (estim.find_first_of('-') != -1) {
-			individual = estim.substr(0,estim.find_first_of('-'));
-			if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
-				estim = estim.substr(estim.find_first_of('-')+1, estim.length());
-				convert(individual, lineNum); //convert the string to int
-				container.insert(lineNum);
-			}
-		}
-		//get last one
-		convert(estim, lineNum); //convert the string to int
-		container.insert(lineNum);
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
+			if (gorder != NULL) { delete gorder; gorder = NULL; }
 
-}
-/*******************************************************/
+			if (glist != NULL) { delete glist; glist = NULL;}
 
-/******************************************************/
+			if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
 
-//This function splits up the various option parameters
-void GlobalData::splitAtComma(string& prefix, string& suffix){
-	try {
-		prefix = suffix.substr(0,suffix.find_first_of(','));
-		if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
-			suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
-		}
+			if (sabund != NULL) { delete sabund; sabund = NULL;}
+
+			if (rabund != NULL) { delete rabund; rabund = NULL; }
+
+			if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
+
+			if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
+
+			if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+			
+			if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
+
+
+			gTree.clear();
+			Treenames.clear();
+			labels.clear(); Groups.clear();
+			allLines = 1;
+			runParse = true;
+			names.clear();
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GlobalData", "newRead");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
-/*******************************************************/
 
-/******************************************************/
-//This function separates the key value from the option value i.e. distfile = "96_..."
-void GlobalData::splitAtEquals(string& key, string& value){		
+//******************************************************/
+
+/*****************************************************
+GlobalData::~GlobalData() {
+	_uniqueInstance = 0;
 	try {
-		if(value.find_first_of('=') != -1){
-			key = value.substr(0,value.find_first_of('='));
-			if ((value.find_first_of('=')+1) <= value.length()) {
-				value = value.substr(value.find_first_of('=')+1, value.length());
-			}
-		}else{
-			key = value;
-			value = 1;
-		}
+		if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
+		if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
+		if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
+		if (ginput != NULL) { delete ginput; ginput = NULL;}
+		if (gorder != NULL) { delete gorder; gorder = NULL; }
+		if (glist != NULL) { delete glist; glist = NULL;}
+		if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
+		if (sabund != NULL) { delete sabund; sabund = NULL;}
+		if (rabund != NULL) { delete rabund; rabund = NULL; }
+		if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
+		if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
+		if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+		if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GlobalData", "~GlobalData");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 /*******************************************************/
 
-/******************************************************/
+/*******************************************************/
+
+