X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=69dccb5226638a3af2a2bb9936b774f6dc90169e;hb=e189982e0a9b7352ad57cc38ccee675f128be22e;hp=cdf819baa6badc6e89c65bb6c6428e01be41d40d;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index cdf819b..69dccb5 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -27,12 +27,10 @@ string GlobalData::getNameFile()		{	return namefile;		}
 string GlobalData::getGroupFile()		{	return groupfile;		}
 string GlobalData::getOrderFile()		{	return orderfile;		}
 string GlobalData::getTreeFile()		{	return treefile;		}
-string GlobalData::getSharedFile()		{	return sharedfile;		}
-//string GlobalData::getFastaFile()		{	return fastafile;		}	
+string GlobalData::getSharedFile()		{	return sharedfile;		}	
 string GlobalData::getFormat()			{	return format;			}
 
 void GlobalData::setListFile(string file)		{	listfile = file;	inputFileName = file;					}
-//void GlobalData::setFastaFile(string file)		{	fastafile = file;	inputFileName = file;					}
 void GlobalData::setTreeFile(string file)		{	treefile = file;	inputFileName = file;					}
 void GlobalData::setRabundFile(string file)		{	rabundfile = file;	inputFileName = file;					}
 void GlobalData::setSabundFile(string file)		{	sabundfile = file;	inputFileName = file;					}
@@ -49,6 +47,7 @@ void GlobalData::setFormat(string Format)		{	format = Format;		}
 
 /******************************************************/
 GlobalData::GlobalData() {
+	m = MothurOut::getInstance();
 	//option definitions should go here...
 	clear();
 	gListVector = NULL;		
@@ -63,6 +62,7 @@ GlobalData::GlobalData() {
 	gMatrix = NULL;
 	gTreemap = NULL;
 	gSequenceDB = NULL;
+	nameMap = NULL;
 }
 /*******************************************************/
 
@@ -80,6 +80,7 @@ void GlobalData::clear() {
 //	fastafile		=   ""; //do we need this?
 	treefile		=	"";
 	sharedfile		=	"";
+	format = "";
 }
 
 
@@ -93,26 +94,41 @@ void GlobalData::newRead() {
 			
 			//free memory
 			if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
+
 			if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
+
 			if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
+
 			if (ginput != NULL) { delete ginput; ginput = NULL;}
+
 			if (gorder != NULL) { delete gorder; gorder = NULL; }
+
 			if (glist != NULL) { delete glist; glist = NULL;}
+
 			if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
+
 			if (sabund != NULL) { delete sabund; sabund = NULL;}
+
 			if (rabund != NULL) { delete rabund; rabund = NULL; }
+
 			if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
+
 			if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
+
 			if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+			
+			if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
+
 
 			gTree.clear();
 			Treenames.clear();
-			labels.clear(); lines.clear(); Groups.clear();
+			labels.clear(); Groups.clear();
 			allLines = 1;
 			runParse = true;
+			names.clear();
 	}
 	catch(exception& e) {
-		errorOut(e, "GlobalData", "newRead");
+		m->errorOut(e, "GlobalData", "newRead");
 		exit(1);
 	}
 }
@@ -135,9 +151,10 @@ GlobalData::~GlobalData() {
 		if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
 		if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 		if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+		if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 	}
 	catch(exception& e) {
-		errorOut(e, "GlobalData", "~GlobalData");
+		m->errorOut(e, "GlobalData", "~GlobalData");
 		exit(1);
 	}
 }