X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=globaldata.cpp;h=17b4908515179211b792a6d06801d2dc878a7bca;hb=3659285c05daa94306a7b61dd97ec945b23d472b;hp=9b740a68c1a6b945d4f12789a5ee125e308f2c8c;hpb=1b2517db06f3c6cd5f5c67198261361ce8dad611;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 9b740a6..17b4908 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -16,65 +16,22 @@ 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();
+			labels.clear(); lines.clear(); groups.clear();
+			allLines = 1;
 		}
 		
 		//saves help request
@@ -107,9 +64,10 @@ 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 == "abund" )        { abund = value;        }
+				if (key == "random" )		{ randomtree = value;	}
 				if (key == "calc")			{ calc = value;		}
+
 				
 				if (key == "line") {//stores lines to be used in a set
 					lines.clear();
@@ -125,11 +83,13 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 					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
@@ -153,8 +113,8 @@ 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 == "abund" )        { abund = value;        }
+			if (key == "random" )		{ randomtree = value;	}
 			if (key == "calc")			{ calc = value;		}
 
 
@@ -162,16 +122,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				lines.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();
 				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;
@@ -181,6 +142,7 @@ 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") {
@@ -253,7 +215,9 @@ 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;		}
 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 +226,8 @@ 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 +261,27 @@ 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";
 }
-/*******************************************************/
+
+//*******************************************************/
 
 /******************************************************/
 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.
+	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";
 }
 /*******************************************************/
 
@@ -328,6 +293,3 @@ GlobalData::~GlobalData() {
 	if(gorder != NULL)			{	delete gorder;		}
 }
 /*******************************************************/
-
-/******************************************************/
-