X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=3ddd02e5c24dc03cd8ff7549b6b03a32982562e9;hb=39ef0543b73cb12dfc64529522b66ad3df7527d0;hp=66a44f25b7246af237194e634eeeeb9514623899;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 66a44f2..3ddd02e 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -16,50 +16,6 @@ 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){
@@ -71,7 +27,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 		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();
@@ -110,7 +66,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 				if (key == "fileroot" )		{ fileroot = value;		}
 				if (key == "abund" )        { abund = value;        }
 				if (key == "random" )		{ randomtree = value;	}
-				if (key == "groups" )		{ groups = value;	}
 				if (key == "calc")			{ calc = value;		}
 
 				
@@ -160,7 +115,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
 			if (key == "fileroot" )		{ fileroot = value;		}
 			if (key == "abund" )        { abund = value;        }
 			if (key == "random" )		{ randomtree = value;	}
-			if (key == "groups" )		{ groups = value;	}
 			if (key == "calc")			{ calc = value;		}
 
 
@@ -187,6 +141,7 @@ 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") {
@@ -261,6 +216,7 @@ 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;}
@@ -269,7 +225,8 @@ 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;			}
 
 /*******************************************************/