X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=ae1b0e2ebbb463fefc32a2f8ad3fd1816b01109d;hb=3117b1c3109121dff476997d3c5db5b47a77729b;hp=da81879f48fff6fbe87ac67ba950afd84c03a69e;hpb=f20505bcd9f07e0b5f967be0e8d414076d9a5678;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index da81879..ae1b0e2 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"
 
 /*******************************************************/
 
@@ -30,6 +27,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			clear();
 			gGroupmap = NULL;
 			gTree.clear();
+			Treenames.clear();
 			labels.clear(); lines.clear(); groups.clear();
 			allLines = 1;
 		}
@@ -44,6 +42,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			cutoff = "1.0";
 		}
 		
+		//set default value for cutoff
+		if (commandName == "distance") {	cutoff = "1.0";		}
+
 		string key, value;		
 		//reads in parameters and values
 		if((optionText != "") && (commandName != "help")){
@@ -56,7 +57,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				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 == "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;		}
@@ -75,6 +78,15 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				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 == "filter")		{ filter = value;		}
+				if (key == "soft")		    { soft = value;		    }
+				if (key == "scale")			{ scale = value;		}
+				if (key == "ends" )			{ ends = value;			}
+				if (key == "processors" )	{ processors = value;	}
+				
+
 				
 
 				
@@ -112,6 +124,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			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;		}
@@ -130,6 +144,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			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 == "filter")		{ filter = value;		}
+			if (key == "soft")		    { soft = value;		    }
+			if (key == "scale")			{ scale = value;		}
+			if (key == "ends" )			{ ends = value;			}
+			if (key == "processors" )	{ processors = value;	}
+
 
 			if (key == "line") {//stores lines to be used in a vector
 				lines.clear();
@@ -139,6 +161,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				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();
@@ -161,7 +184,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				
 		//input defaults for calculators
 		if (commandName == "collect.single") {
-			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
+
+			if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -171,17 +195,18 @@ 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-sharedkstest-sharedbdiversity"; }
+
+			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-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
+			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-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+			if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
@@ -190,6 +215,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
+		if (commandName == "distance") {
+			if ((calc == "default") || (calc == "")) {  calc = "onegap";  }
+			Estimators.clear();
+			splitAtDash(calc, Estimators); 
+		}
 		if (commandName == "venn") {
 			if ((calc == "default") || (calc == "")) { 
 				if (format == "list") { calc = "sobs"; }
@@ -198,6 +228,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			Estimators.clear();
 			splitAtDash(calc, Estimators); 
 		}
+		if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
+			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")) {
@@ -230,6 +267,8 @@ 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;	}
@@ -244,6 +283,13 @@ string GlobalData::getGroups()			{	return groups;		}
 string GlobalData::getStep()			{	return step;		}
 string GlobalData::getForm()			{	return form;		}
 string GlobalData::getSorted()			{	return sorted;		}
+string GlobalData::getTrump()			{   return trump;       }
+string GlobalData::getSoft()			{   return soft;		}
+string GlobalData::getFilter()			{   return filter;		}
+string GlobalData::getScale()			{	return scale;		}
+string GlobalData::getEnds()			{   return ends;		}
+string GlobalData::getProcessors()		{	return processors;	}
+
 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;}
@@ -254,6 +300,9 @@ 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::setEnds(string e)				{   ends = e;				}
+void GlobalData::setProcessors(string p)		{	processors = p;			}
+
 
 /*******************************************************/
 
@@ -262,6 +311,8 @@ GlobalData::GlobalData() {
 	//option definitions should go here...
 	helpRequest = "";
 	clear();
+	gListVector == NULL;		
+	gSparseMatrix == NULL;	
 }
 /*******************************************************/
 
@@ -277,6 +328,8 @@ void GlobalData::clear() {
 	groupfile		=	""; 
 	orderfile		=	"";
 	fastafile		=   "";
+	nexusfile		=   "";
+	clustalfile		=   "";
 	treefile		=	"";
 	sharedfile		=	"";
 	cutoff			=	"10.00";
@@ -294,7 +347,15 @@ void GlobalData::clear() {
 	abund           =   "10";
 	step			=	"0.01";
 	form			=	"integral";
-	sorted			=	"1";  //0 means don't sort, 1 means sort.
+	sorted			=	"T";  //F means don't sort, T means sort.
+	vertical        =   "";		
+	trump           =   "";		
+	filter          =   "";		
+	soft            =   "";	
+	scale			=	"log10";
+	ends			=   "T";  //yes
+	processors		=	"1";
+
 }
 
 //*******************************************************/
@@ -306,7 +367,7 @@ void GlobalData::reset() {
 	iters			=	"1000"; 
 	groups			=	"";
 	jumble			=	"1";	//0 means don't jumble, 1 means jumble.
-	sorted			=	"1";  //0 means don't sort, 1 means sort.
+	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";
@@ -314,6 +375,8 @@ void GlobalData::reset() {
 	abund			=   "10";
 	step			=	"0.01";
 	form			=	"integral";
+	ends			=   "T";
+	processors		=	"1";
 }
 /*******************************************************/
 
@@ -325,3 +388,144 @@ GlobalData::~GlobalData() {
 	if(gorder != NULL)			{	delete gorder;		}
 }
 /*******************************************************/
+
+/*******************************************************/
+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")) {
+
+				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);
+	}		
+}	
+
+/*******************************************************/
+
+/*******************************************************/
+
+