X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=6ab20f3ced51bc003f6beb0760753023e2cdc76f;hb=3329385a816a97bdde934d98a615865c29eaacad;hp=9b740a68c1a6b945d4f12789a5ee125e308f2c8c;hpb=1b2517db06f3c6cd5f5c67198261361ce8dad611;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 9b740a6..6ab20f3 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,9 +1,6 @@
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
+#include "sparsematrix.hpp"
 
 /*******************************************************/
 
@@ -16,65 +13,23 @@ GlobalData* GlobalData::getInstance() {
 }
 /*******************************************************/
 
-/******************************************************/
-
-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 values
+		//set all non filename paramters to default
 		reset();
 		
 		//clears out data from previous read
-		if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree") || (commandName == "read.shared")) { 
+		if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { 
 			clear();
 			gGroupmap = NULL;
 			gTree.clear();
+			Treenames.clear();
+			labels.clear(); lines.clear(); groups.clear();
+			allLines = 1;
 		}
 		
 		//saves help request
@@ -82,6 +37,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			helpRequest = optionText;
 		}
 		
+		if (commandName == "libshuff") {
+			iters = "10000";
+			cutoff = "1.0";
+		}
+		
 		string key, value;		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
@@ -107,12 +67,19 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				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 == "calc")			{ calc = 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 == "scaler")		{ scaler = value;		}
+				
+
 				
 				if (key == "line") {//stores lines to be used in a set
 					lines.clear();
+					labels.clear();
 					line = value;
 					label = "";
 					splitAtDash(value, lines);
@@ -120,16 +87,19 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				}
 				if (key == "label") {//stores labels to be used in a set
 					labels.clear();
+					lines.clear();
 					label = value;
 					line = "";
 					splitAtDash(value, labels);
 					allLines = 0;
 				}
+
 				if (key == "groups") {//stores groups to be used in a vector
 					Groups.clear();
 					groups = value;
 					splitAtDash(value, Groups);
 				}
+
 			}
 			
 			//saves the last parameter
@@ -153,25 +123,33 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			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 == "calc")			{ calc = 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 == "scaler")		{ scaler = 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 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
 					Groups.clear();
 					groups = value;
@@ -181,10 +159,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		
 		//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-bootstrap-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -194,17 +173,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "collect.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
+			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
 		if (commandName == "summary.shared") {
-			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; }
+			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -213,6 +192,21 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			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.groups") {
+			if (calc != "") { 
+				Estimators.clear();
+				splitAtDash(calc, Estimators);			
+			}else { cout << "You have not specified any calculators." << endl; }
+		}
+
 
 		//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")) {
@@ -253,7 +247,13 @@ 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::getScaler()			{	return scaler;		}
 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;}
@@ -262,7 +262,8 @@ void GlobalData::setColumnFile(string file)	{	columnfile = file;    inputFileNam
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
 void GlobalData::setRandomTree(string Random)	{	randomtree = Random;	}
-void GlobalData::setCalc(string Calc)			{	calc = Calc;	}
+void GlobalData::setGroups(string g)			{	groups = g;				}
+void GlobalData::setCalc(string Calc)			{	calc = Calc;			}
 
 /*******************************************************/
 
@@ -296,27 +297,34 @@ 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		=	"";
-	calc			=	"";
+	abund           =   "10";
+	step			=	"0.01";
+	form			=	"integral";
+	sorted			=	"1";  //0 means don't sort, 1 means sort.
+	scaler			=	"log10";
 }
-/*******************************************************/
+
+//*******************************************************/
 
 /******************************************************/
 void GlobalData::reset() {
 	cutoff			=	"10.00";
 	precision		=	"100";
 	iters			=	"1000"; 
-	line			=   "";
-	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.
+	sorted			=	"1";  //0 means don't sort, 1 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";
 }
 /*******************************************************/
 
@@ -329,5 +337,143 @@ GlobalData::~GlobalData() {
 }
 /*******************************************************/
 
-/******************************************************/
+/*******************************************************/
+void GlobalData::parseTreeFile() {
+	//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();
+				}
+
+				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 (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")) {
+cout << "there is a translate " << endl;
+				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
+			}
+		}
+		
+	}
+	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";
+		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;
+
+		}
+	}
+	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";
+		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);
+	}		
+}	
+
+/*******************************************************/
+
+/*******************************************************/
+