X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=8f8d1ad5da1addc5dac09f68c6dec5a5b99c1568;hb=5a1e62397b91f57d0d3aff635891df04b8999a88;hp=d7afc40b352229484d2f350f1ad190631a5ab7ed;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index d7afc40..8f8d1ad 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,362 +1,46 @@
+
+
 #include "globaldata.hpp"
-#include "tree.h"
-#include "sparsematrix.hpp"
+#include "sharedlistvector.h"
+#include "inputdata.h"
+#include "fullmatrix.h"
 
 /*******************************************************/
 
 /******************************************************/
 GlobalData* GlobalData::getInstance() {
-	if( _uniqueInstance == 0 ) {
+	if( _uniqueInstance == 0) {
 		_uniqueInstance = new GlobalData();
 	}
 	return _uniqueInstance;
 }
 /*******************************************************/
 
-/******************************************************/
-//This function parses through the option string of the command to remove its parameters
-void GlobalData::parseGlobalData(string commandString, string optionText){
-	try {
-		commandName = commandString; //save command name to be used by other classes
-		
-		//set all non filename paramters to default
-		reset();
-		
-		//clears out data from previous read
-		if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
-			clear();
-			gGroupmap = NULL;
-			gListVector = NULL;
-			gSparseMatrix = NULL;
-			gTree.clear();
-			Treenames.clear();
-			labels.clear(); lines.clear(); Groups.clear();
-			allLines = 1;
-		}
-		
-		//saves help request
-		if (commandName =="help") {
-			helpRequest = optionText;
-		}
-		
-		if (commandName == "libshuff") {
-			iters = "10000";
-			cutoff = "1.0";
-		}
-		
-		//set default value for cutoff
-		if (commandName == "dist.seqs") {	cutoff = "1.0";		}
-
-		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 == "nexus" )	{ nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";		} 
-				if (key == "clustal" )	{ clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
-				if (key == "tree" )		{ treefile = value; inputFileName = value; fileroot = value; format = "tree";		}
-				if (key == "shared" )	{ sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";	}
-				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 == "abund" )        { abund = value;        }
-				if (key == "random" )		{ randomtree = value;	}
-				if (key == "calc")			{ calc = value;			}
-				if (key == "step")			{ step = value;			}
-				if (key == "form")			{ form = value;			}
-				if (key == "sorted")		{ sorted = value;		}
-				if (key == "vertical")		{ vertical = value;		}
-				if (key == "trump")		    { trump = value;		}
-				if (key == "hard")			{ hard = value;		}
-				if (key == "soft")		    { soft = value;		    }
-				if (key == "scale")			{ scale = value;		}
-				if (key == "countends" )	{ countends = value;	}
-				if (key == "processors" )	{ processors = value;	}
-				if (key == "size" )         { size = value;         }
-				if (key == "candidate")		{ candidatefile = value;	}
-				if (key == "search")		{ search = value;		}
-				if (key == "ksize")			{ ksize = value;		}
-				if (key == "align")		    { align = value;		}
-				if (key == "match")			{ match = value;		}
-				if (key == "mismatch")		{ mismatch = value;	    }
-				if (key == "gapopen")		{ gapopen = value;		}
-				if (key == "gapextend" )	{ gapextend = value;	}
-				if (key == "start" )		{ startPos = value;	}
-				if (key == "end" )			{ endPos = value;	}
-				if (key == "maxambig" )		{ maxAmbig = value;	}
-				if (key == "maxhomop" )		{ maxHomoPolymer = value;	}
-				if (key == "minlength" )	{ minLength = value;	}
-				if (key == "maxlength" )	{ maxLength = value;	}
-				
-				if (key == "line") {//stores lines to be used in a vector
-					lines.clear();
-					labels.clear();
-					line = value;
-					label = "";
-					if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
-					else { allLines = 1;  }
-				}
-			
-				if (key == "label") {//stores lines to be used in a vector
-					labels.clear();
-					lines.clear();
-					label = value;
-					line = "";
-					if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
-					else { allLines = 1;  }
-				}
-
-				if (key == "groups") {//stores groups to be used in a vector
-					Groups.clear();
-					groups = value;
-					splitAtDash(value, Groups);
-				}
-
-			}
-			
-			//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 == "nexus" )	{ nexusfile = value; inputFileName = value; fileroot = value; format = "nexus";		}
-			if (key == "clustal" )	{ clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; } 
-			if (key == "tree" )		{ treefile = value; inputFileName = value; fileroot = value; format = "tree";		} 
-			if (key == "shared" )	{ sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile";	}
-			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 == "abund" )        { abund = value;        }
-			if (key == "random" )		{ randomtree = value;	}
-			if (key == "calc")			{ calc = value;			}
-			if (key == "step")			{ step = value;			}
-			if (key == "form")			{ form = value;			}
-			if (key == "sorted")		{ sorted = value;		}
-			if (key == "vertical")		{ vertical = value;		}
-			if (key == "trump")		    { trump = value;		}
-			if (key == "hard")			{ hard = value;		}
-			if (key == "soft")		    { soft = value;		    }
-			if (key == "scale")			{ scale = value;		}
-			if (key == "countends" )	{ countends = value;	}
-			if (key == "processors" )	{ processors = value;	}
-			if (key == "size" )         { size = value;         }
-			if (key == "candidate")		{ candidatefile = value;	}
-			if (key == "search")		{ search = value;		}
-			if (key == "ksize")			{ ksize = value;		}
-			if (key == "align")		    { align = value;		}
-			if (key == "match")			{ match = value;		}
-			if (key == "mismatch")		{ mismatch = value;	    }
-			if (key == "gapopen")		{ gapopen = value;		}
-			if (key == "gapextend" )	{ gapextend = value;	}
-			if (key == "start" )		{ startPos = value;	}
-			if (key == "end" )			{ endPos = value;	}
-			if (key == "maxambig" )		{ maxAmbig = value;	}
-			if (key == "maxhomop" )		{ maxHomoPolymer = value;	}
-			if (key == "minlength" )	{ minLength = value;	}
-			if (key == "maxlength" )	{ maxLength = value;	}
-
-
-			if (key == "line") {//stores lines to be used in a vector
-				lines.clear();
-				labels.clear();
-				line = value;
-				label = "";
-				if (line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
-				else { allLines = 1;  }
-			}
-			
-			if (key == "label") {//stores lines to be used in a vector
-				labels.clear();
-				lines.clear();
-				label = value;
-				line = "";
-				if (label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
-				else { allLines = 1;  }
-			}
-			
-			if (key == "groups") {//stores groups to be used in a vector
-					Groups.clear();
-					groups = value;
-					splitAtDash(value, Groups);
-			}
-		}
-		
-		//set format for shared
-		if ((listfile != "") && (groupfile != "")) { format = "shared"; }
-		if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
-				
-		//input defaults for calculators
-		if (commandName == "collect.single") {
-
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "rarefaction.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "collect.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "summary.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "summary.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "rarefaction.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "dist.seqs") {
-			if ((calc == "default") || (calc == "")) {  calc = "onegap";	}
-			if (countends == "")	{ countends = "T"; }
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if (commandName == "venn") {
-			if ((calc == "default") || (calc == "")) { 
-				if (format == "list") { calc = "sobs"; }
-				else { calc = "sharedsobs"; }
-			}
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
-			if ((calc == "default") || (calc == "")) { 
-				calc = "jclass-thetayc";
-			}
-			Estimators.clear();
-			splitAtDash(calc, Estimators); 
-		}
-		
-		if(commandName == "filter.seqs"){
-			if(trump == "" && vertical == "" && hard == "" && soft == ""){
-				trump = '.';
-			}
-
-		}
-
-		//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::getSharedFile()		{	return sharedfile;	}
-string GlobalData::getFastaFile()		{	return fastafile;	}
-string GlobalData::getNexusFile()		{	return nexusfile;	}
-string GlobalData::getClustalFile()     {   return clustalfile; }
-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;		}
-string GlobalData::getAbund()           {   return abund;       }
-string GlobalData::getRandomTree()		{	return randomtree;	}
-string GlobalData::getGroups()			{	return groups;		}
-string GlobalData::getStep()			{	return step;		}
-string GlobalData::getForm()			{	return form;		}
-string GlobalData::getSorted()			{	return sorted;		}
-string GlobalData::getVertical()		{   return vertical;    }
-string GlobalData::getTrump()			{   return trump;       }
-string GlobalData::getSoft()			{   return soft;		}
-string GlobalData::getHard()			{   return hard;		}
-string GlobalData::getScale()			{	return scale;		}
-string GlobalData::getCountEnds()		{   return countends;	}
-string GlobalData::getProcessors()		{	return processors;	}
-string GlobalData::getSize()            {   return size;        }
-string GlobalData::getCandidateFile()	{	return candidatefile;}
-string GlobalData::getSearch()			{	return search;		}
-string GlobalData::getKSize()			{	return ksize;		}
-string GlobalData::getAlign()			{	return align;		}
-string GlobalData::getMatch()			{	return match;		}
-string GlobalData::getMismatch()		{	return mismatch;	}
-string GlobalData::getGapopen()			{	return gapopen;		}
-string GlobalData::getGapextend()		{	return gapextend;	}
-string GlobalData::getStartPos()		{	return startPos;	}
-string GlobalData::getEndPos()			{	return endPos;		}
-string GlobalData::getMaxAmbig()		{	return maxAmbig;	}
-string GlobalData::getMaxHomoPolymer()	{	return maxHomoPolymer;	}
-string GlobalData::getMinLength()		{	return minLength;	}
-string GlobalData::getMaxLength()		{	return maxLength;	}
-
+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::getSharedFile()		{	return sharedfile;		}	
+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; fileroot = file;	}
+void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file;					}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
+void GlobalData::setOrderFile(string file)		{	orderfile = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
-void GlobalData::setRandomTree(string Random)	{	randomtree = Random;	}
-void GlobalData::setGroups(string g)			{	groups = g;				}
-void GlobalData::setCalc(string Calc)			{	calc = Calc;			}
-void GlobalData::setCountEnds(string e)			{   countends = e;			}
-void GlobalData::setProcessors(string p)		{	processors = p;			}
 
 
 /*******************************************************/
@@ -364,257 +48,114 @@ void GlobalData::setProcessors(string p)		{	processors = p;			}
 /******************************************************/
 GlobalData::GlobalData() {
 	//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;
 }
 /*******************************************************/
 
 /******************************************************/
 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		=   "";
-	nexusfile		=   "";
-	clustalfile		=   "";
+//	fastafile		=   ""; //do we need this?
 	treefile		=	"";
 	sharedfile		=	"";
-	candidatefile	=	"";
-	cutoff			=	"10.00";
-	format			=	"";
-	precision		=	"100";
-	iters			=	"1000"; 
-	line			=   "";
-	label			=	"";
-	groups			=	"";
-	jumble			=	"1";	//0 means don't jumble, 1 means jumble.
-	randomtree		=	"";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
-	freq			=	"100";
-	method			=	"furthest";
-	fileroot		=	"";
-	abund           =   "10";
-	step			=	"0.01";
-	form			=	"integral";
-	sorted			=	"T";  //F means don't sort, T means sort.
-	vertical        =   "F";		
-	trump           =	"";		
-	hard			=   "";		
-	soft            =   "";	
-	scale			=	"log10";
-	countends		=   "T";  //yes
-	processors		=	"1";
-	size            =   "0";
-	search			=	"kmer";
-	ksize			=	"8";
-	align			=	"needleman";
-	match			=	"1.0";
-	mismatch		=	"-1.0";
-	gapopen			=	"-1.0";
-	gapextend		=	"-2.0";
-	startPos		=	"-1";
-	endPos			=	"-1";
-	maxAmbig		=	"-1";
-	maxHomoPolymer	=	"-1";
-	minLength		=	"-1";
-	maxLength		=	"-1";
-	
 }
 
-//*******************************************************/
 
-/******************************************************/
-void GlobalData::reset() {
-	cutoff			=	"10.00";
-	precision		=	"100";
-	iters			=	"1000"; 
-	groups			=	"";
-	jumble			=	"1";	//0 means don't jumble, 1 means jumble.
-	sorted			=	"T";  //F means don't sort, T means sort.
-	randomtree		=	"";  //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
-	freq			=	"100";
-	method			=	"furthest";
-	calc			=	"";
-	abund			=   "10";
-	step			=	"0.01";
-	form			=	"integral";
-	countends		=   "T";
-	processors		=	"1";
-	size            =   "0";
-	search			=	"kmer";
-	ksize			=	"8";
-	align			=	"needleman";
-	match			=	"1.0";
-	mismatch		=	"-1.0";
-	gapopen			=	"-1.0";
-	gapextend		=	"-2.0";
-	vertical        =   "";		
-	trump           =   "";		
-	hard			=   "";		
-	soft            =   "";	
-	startPos		=	"-1";
-	endPos			=	"-1";
-	maxAmbig		=	"-1";
-	maxHomoPolymer	=	"-1";
-	minLength		=	"-1";
-	maxLength		=	"-1";
-	
-}
 /*******************************************************/
 
 /******************************************************/
-GlobalData::~GlobalData() {
-	_uniqueInstance = 0;
-	if(gListVector != NULL)		{	delete gListVector;		}
-	if(gSparseMatrix != NULL)	{	delete gSparseMatrix;	}
-	if(gorder != NULL)			{	delete gorder;		}
-}
-/*******************************************************/
+void GlobalData::newRead() {
+	try{	
+			//remove old file names
+			clear();
+			
+			//free memory
+			if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
 
-/*******************************************************/
-void GlobalData::parseTreeFile() {
-	//Why is THIS in GlobalData??? - PDS
-	
-	//only takes names from the first tree and assumes that all trees use the same names.
-	try {
-		string filename = treefile;
-		ifstream filehandle;
-		openInputFile(filename, filehandle);
-		int c, comment;
-		comment = 0;
-		
-		//if you are not a nexus file 
-		if ((c = filehandle.peek()) != '#') {  
-			while((c = filehandle.peek()) != ';') { 
-				while ((c = filehandle.peek()) != ';') {
-					// get past comments
-					if(c == '[') {
-						comment = 1;
-					}
-					if(c == ']'){
-						comment = 0;
-					}
-					if((c == '(') && (comment != 1)){ break; }
-					filehandle.get();
-				}
+			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;}
 
-				readTreeString(filehandle); 
-			}
-		//if you are a nexus file
-		}else if ((c = filehandle.peek()) == '#') {
-			string holder = "";
-					
-			// get past comments
-			while(holder != "translate" && holder != "Translate"){	
-				if(holder == "[" || holder == "[!"){
-					comment = 1;
-				}
-				if(holder == "]"){
-					comment = 0;
-				}
-				filehandle >> holder; 
-	
-				//if there is no translate then you must read tree string otherwise use translate to get names
-				if(holder == "tree" && comment != 1){	
-					//pass over the "tree rep.6878900 = "
-					while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
+			if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 
-					if (c == EOF ) { break; }
-					filehandle.putback(c);  //put back first ( of tree.
-					readTreeString(filehandle);	
-					break;
-				}
-			}
+			if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
 			
-			//use nexus translation rather than parsing tree to save time
-			if ((holder == "translate") || (holder == "Translate")) {
+			if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 
-				string number, name, h;
-				h = ""; // so it enters the loop the first time
-				while((h != ";") && (number != ";")) { 
-					filehandle >> number;
-					filehandle >> name;
-	
-					//c = , until done with translation then c = ;
-					h = name.substr(name.length()-1, name.length()); 
-					name.erase(name.end()-1);  //erase the comma
-					Treenames.push_back(number);
-				}
-				if (number == ";") { Treenames.pop_back(); }  //in case ';' from translation is on next line instead of next to last name
-			}
-		}
-		
+
+			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 parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "GlobalData", "newRead");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
 }
-/*******************************************************/
 
-/*******************************************************/
-void GlobalData::readTreeString(ifstream& filehandle)	{
-	try {
-		int c;
-		string name; //k
-		
-		while((c = filehandle.peek()) != ';') { 
-				//if you are a name
-			if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
-				name = "";
-				c = filehandle.get();
-	//		k = c;
-//cout << k << endl;
-				while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {			
-					name += c;
-					c = filehandle.get();
-		//	k = c;
-//cout << " in name while " << k << endl;
-				}
-				
-//cout << "name = " << name << endl;
-				Treenames.push_back(name);
-				filehandle.putback(c);
-//k = c;
-//cout << " after putback" <<  k << endl;
-			} 
-			
-			if (c  == ':') { //read until you reach the end of the branch length
-				while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
-					c = filehandle.get();
-				//	k = c;
-	//cout << " in branch while " << k << endl;
-				}
-				filehandle.putback(c);
-			}
-			c = filehandle.get();
-			if (c == ';') { break; }
-		//	k = c;
-//cout << k << endl;
+//******************************************************/
 
-		}
+/******************************************************/
+GlobalData::~GlobalData() {
+	_uniqueInstance = 0;
+	try {
+		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 parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "GlobalData", "~GlobalData");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		
-}	
-
+}
 /*******************************************************/
 
 /*******************************************************/