From: westcott <westcott>
Date: Mon, 9 Mar 2009 12:18:46 +0000 (+0000)
Subject: fixed memory issue with cluster command
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=1c2f1171eee8879de9dbe03a8a9d9093fc6a1f95

fixed memory issue with cluster command
---

diff --git a/clustercommand.cpp b/clustercommand.cpp
index f0ef51f..307b774 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -15,13 +15,13 @@ ClusterCommand::ClusterCommand(){
 	try{
 		globaldata = GlobalData::getInstance();
 	
-		if(globaldata->getSparseMatrix() != NULL)	{	matrix = new SparseMatrix(*globaldata->getSparseMatrix());		}
+		if(globaldata->gSparseMatrix != NULL)	{	matrix = new SparseMatrix(*globaldata->gSparseMatrix);		}
 	//  Not sure if we want the address or an entire new memory allocation.  Might be nice to have new memory so data
 	//  doesn't need to be re-read, but then again, it could suck up a ton of memory.  Dunno.
 	//	if(globaldata->getSparseMatrix() != NULL)	{	matrix = globaldata->getSparseMatrix();		}
 	
-		if(globaldata->getListVector() != NULL){
-			list = new ListVector(*globaldata->getListVector());
+		if(globaldata->gListVector != NULL){
+			list = new ListVector(*globaldata->gListVector);
 			rabund = new RAbundVector(list->getRAbundVector());
 			//rabund->print(cout);
 		}
@@ -108,11 +108,8 @@ int ClusterCommand::execute(){
 		}
 		
 		//delete globaldata's copy of the sparsematrix and listvector to free up memory
-		SparseMatrix* clearM = NULL;
-		globaldata->setSparseMatrix(clearM);
-		ListVector* clearL = NULL;
-		globaldata->setListVector(clearL);
-
+		delete globaldata->gSparseMatrix;  globaldata->gSparseMatrix = NULL;
+		delete globaldata->gListVector;	 globaldata->gListVector = NULL;
 		
 		//saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
 		if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
diff --git a/errorchecking.cpp b/errorchecking.cpp
index b76542a..d827929 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -367,8 +367,8 @@ bool ErrorCheck::checkInput(string input) {
 		}
 		
 		//are you trying to cluster before you have read something			
-		if (((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL)) ||
-			((commandName == "cluster") && (globaldata->getListVector() == NULL))) {
+		if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
+			((commandName == "cluster") && (globaldata->gListVector == NULL))) {
 				cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
 				errorFree = false;
 		} 
diff --git a/globaldata.cpp b/globaldata.cpp
index b1ac4e8..60a106a 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){
diff --git a/globaldata.hpp b/globaldata.hpp
index 0dc4c34..6070dd7 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -21,8 +21,8 @@ class SAbundVector;
 class GlobalData {
 public:
 	static GlobalData* getInstance();
-	ListVector* getListVector();
-	SparseMatrix* getSparseMatrix();
+	ListVector* gListVector;
+	SparseMatrix* gSparseMatrix;
 	InputData* ginput;
 	OrderVector* gorder;
 	ListVector* glist;
@@ -72,9 +72,6 @@ public:
 	void setGroups(string);
 	void setCalc(string);
 
-	
-	void setListVector(ListVector*);
-	void setSparseMatrix(SparseMatrix*);
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
@@ -90,8 +87,6 @@ private:
 	void operator=( const GlobalData& ); // Disable assignment operator
 	GlobalData();
 	~GlobalData();
-	ListVector* gListVector;
-	SparseMatrix* gSparseMatrix;
 	void reset();	//clears all non filename parameters
 	
 	
diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 116e670..a9d7721 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -72,8 +72,8 @@ int ReadDistCommand::execute(){
 			globaldata->gMatrix = matrix; //save matrix for coverage commands
 		}else {
 			read->read(nameMap);
-			globaldata->setListVector(read->getListVector());
-			globaldata->setSparseMatrix(read->getMatrix());
+			globaldata->gListVector = read->getListVector();
+			globaldata->gSparseMatrix = read->getMatrix();
 		}
 		return 0;
 	}