X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=a3dc757cba2e9adf6aecc051f3a03d9875b92026;hb=e7fe6dd9db877b98c362f9524c3130bbbd037200;hp=e58d19181d156e00dff0190388552858a32dbbde;hpb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index e58d191..a3dc757 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,95 +1,52 @@
-#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 "sparsematrix.hpp"
 
 /*******************************************************/
 
 /******************************************************/
 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
 		
+		//set all non filename paramters to default
+		reset();
+		
 		//clears out data from previous read
-		if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
+		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") {
+		if(commandName =="help") {
 			helpRequest = optionText;
 		}
 		
+		if(commandName == "libshuff") {
+			iters = "10000";
+			cutoff = "1.0";
+		}
+		
+		//set default value for cutoff and phylip
+		if (commandName == "dist.seqs") {	cutoff = "1.0";	  phylipfile = "F";	}
+
 		string key, value;		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
@@ -97,71 +54,74 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				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 == "tree" )		{ 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 == "randomtree" )	{ randomtree = value;	}
-				if (key == "groups" )		{ groups = 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 set
+				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 == "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 == "flip"	)		{	flip = value;			}
+				if(key == "oligos"	)		{	oligoFile = value;		}
+					
+				if(key == "line") {//stores lines to be used in a vector
 					lines.clear();
+					labels.clear();
 					line = value;
 					label = "";
-					splitAtDash(value, lines);
-					allLines = 0;
+					if(line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+					else { allLines = 1;  }
 				}
-				if (key == "label") {//stores labels to be used in a set
+			
+				if(key == "label") {//stores lines to be used in a vector
 					labels.clear();
+					lines.clear();
 					label = value;
 					line = "";
-					splitAtDash(value, labels);
-					allLines = 0;
+					if(label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+					else { allLines = 1;  }
 				}
-				if (key == "groups") {//stores groups to be used in a vector
+
+				if(key == "groups") {//stores groups to be used in a vector
 					Groups.clear();
 					groups = value;
 					splitAtDash(value, Groups);
@@ -169,114 +129,158 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 
 			}
 			
-			//saves the last parameter
+			//saves the last parameter ==> this seems silly...
 			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 == "tree" )		{ 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 == "randomtree" )	{ randomtree = value;	}
-			if (key == "groups" )		{ groups = 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 == "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 == "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 == "flip"	)	{	flip = value;			}
+			if(key == "oligos"	)	{	oligoFile = value;		}
 			
-			if (key == "line") {//stores lines to be used in a vector
+
+			if(key == "line") {//stores lines to be used in a vector
 				lines.clear();
+				labels.clear();
 				line = value;
 				label = "";
-				splitAtDash(value, lines);
-				allLines = 0;
+				if(line != "all") {  splitAtDash(value, lines);  allLines = 0;  }
+				else { allLines = 1;  }
 			}
-			if (key == "label") {//stores lines to be used in a vector
+			
+			if(key == "label") {//stores lines to be used in a vector
 				labels.clear();
+				lines.clear();
 				label = value;
 				line = "";
-				splitAtDash(value, labels);
-				allLines = 0;
+				if(label != "all") {  splitAtDash(value, labels);  allLines = 0;  }
+				else { allLines = 1;  }
 			}
-			if (key == "groups") {//stores groups to be used in a vector
+			
+			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"; }
-				
-		//input defaults
-		if (commandName == "collect.single") {
-			if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
+		if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
+		
+		//set default value for cutoff
+		if (commandName == "dist.seqs") {	format = "fasta";  inputFileName = fastafile;  fileroot = fastafile;	}
+						
+		//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 == "rarefaction.single") {
-			if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }	
+		if(commandName == "summary.single") {
+			if((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
 		}
-		if (commandName == "collect.shared") {
-			if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }	
+		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 == "summary.single") {
-			if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
+		if(commandName == "rarefaction.shared") {
+			if((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
 		}
-		if (commandName == "summary.shared") {
-			if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
+		if(commandName == "dist.seqs") {
+			if((calc == "default") || (calc == "")) {  calc = "onegap";	}
+			if(countends == "")	{ countends = "T"; }
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
 		}
-		if (commandName == "rarefaction.shared") {
-			if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
+		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"; }
+		//ifyou 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";
@@ -286,55 +290,91 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		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;		}
-string GlobalData::getRandomTree()		{	return randomtree;	}
-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;		}
+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::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::getFlip()			{	return flip;			}
+string GlobalData::getOligosFile()		{	return oligoFile;		}
+
+
+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::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file; fileroot = file;	}
 void GlobalData::setNameFile(string file)		{	namefile = 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;			}
 
 
 /*******************************************************/
 
 /******************************************************/
-
 GlobalData::GlobalData() {
 	//option definitions should go here...
 	helpRequest = "";
 	clear();
+	gListVector = NULL;		
+	gSparseMatrix = NULL;	
 }
 /*******************************************************/
 
 /******************************************************/
-
 void GlobalData::clear() {
 	//option definitions should go here...
 	phylipfile		=	"";
@@ -347,6 +387,8 @@ void GlobalData::clear() {
 	orderfile		=	"";
 	fastafile		=   "";
 	treefile		=	"";
+	sharedfile		=	"";
+	candidatefile	=	"";
 	cutoff			=	"10.00";
 	format			=	"";
 	precision		=	"100";
@@ -355,21 +397,85 @@ void GlobalData::clear() {
 	label			=	"";
 	groups			=	"";
 	jumble			=	"1";	//0 means don't jumble, 1 means jumble.
-	randomtree		=	"0";  //0 means user will enter some user trees, 1 means they just want the random tree distribution.
+	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		=	"";
-	single			=	"sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
-	rarefaction		=	"sobs";
-	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";
+	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";
+	flip			=	"0";
+	oligoFile		=	"";
 }
-/*******************************************************/
+
+//*******************************************************/
 
 /******************************************************/
+void GlobalData::reset() {
+	label			=	"";
+	line			=   "";
+	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";
+	flip			=	"0";
+	oligoFile		=	"";
+	
+}
+/*******************************************************/
 
+/******************************************************/
 GlobalData::~GlobalData() {
 	_uniqueInstance = 0;
 	if(gListVector != NULL)		{	delete gListVector;		}
@@ -378,139 +484,145 @@ GlobalData::~GlobalData() {
 }
 /*******************************************************/
 
-/******************************************************/
-//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);
-	}
-
-}
 /*******************************************************/
-
-/******************************************************/
-//This function parses the label options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<string>& container) {
+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 individual;
+		string filename = treefile;
+		ifstream filehandle;
+		openInputFile(filename, filehandle);
+		int c, comment;
+		comment = 0;
 		
-		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);
+		//ifyou 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();
+				}
+
+				readTreeString(filehandle); 
+			}
+		//ifyou 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; 
+	
+				//ifthere 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(c == EOF) { break; }
+					filehandle.putback(c);  //put back first ( of tree.
+					readTreeString(filehandle);	
+					break;
+				}
+			}
+			
+			//use nexus translation rather than parsing tree to save time
+			if((holder == "translate") || (holder == "Translate")) {
+
+				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
 			}
 		}
-		//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";
+		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. 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";
+		cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
-	}
-
+	}		
 }
 /*******************************************************/
 
-/******************************************************/
-//This function parses the line options and puts them in a set
-void GlobalData::splitAtDash(string& estim, set<int>& container) {
+/*******************************************************/
+void GlobalData::readTreeString(ifstream& filehandle)	{
 	try {
-		string individual;
-		int lineNum;
+		int c;
+		string name; //k
 		
-		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);
+		while((c = filehandle.peek()) != ';') { 
+				//ifyou 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);
 			}
-		}
-		//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);
-	}
+			c = filehandle.get();
+			if(c == ';') { break; }
+		//	k = c;
+//cout << k << endl;
 
-}
-/*******************************************************/
-
-/******************************************************/
-
-//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());
 		}
 	}
 	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";
+		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		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";
+		cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
-	}
+	}		
+}	
 
-}
 /*******************************************************/
 
-/******************************************************/
-//This function separates the key value from the option value i.e. dist=96_...
-void GlobalData::splitAtEquals(string& key, string& value){		
-	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;
-		}
-	}
-	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";
-		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);
-	}
-
-}
 /*******************************************************/
 
-/******************************************************/
+