X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=74daaa2cc87cea237619fec03afdf28a8095f65f;hb=7ae40733a270f73ec8a331540cc7f28fd60b24fc;hp=68f7fc389bb70948c1a22255af0cec275ba0ca5a;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 68f7fc3..74daaa2 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,6 +1,9 @@
+
+
 #include "globaldata.hpp"
-#include "tree.h"
-#include "sparsematrix.hpp"
+#include "sharedlistvector.h"
+#include "inputdata.h"
+#include "fullmatrix.h"
 
 /*******************************************************/
 
@@ -23,25 +26,24 @@ string GlobalData::getSabundFile()		{	return sabundfile;		}
 string GlobalData::getNameFile()		{	return namefile;		}
 string GlobalData::getGroupFile()		{	return groupfile;		}
 string GlobalData::getOrderFile()		{	return orderfile;		}
+string GlobalData::getOrderGroupFile()	{	return ordergroup;		}
 string GlobalData::getTreeFile()		{	return treefile;		}
-string GlobalData::getSharedFile()		{	return sharedfile;		}
-string GlobalData::getFastaFile()		{	return fastafile;		}	
+string GlobalData::getSharedFile()		{	return sharedfile;		}	
+string GlobalData::getRelAbundFile()	{	return relAbundfile;	}	
 string GlobalData::getFormat()			{	return format;			}
-string GlobalData::getCandidateFile()	{	return candidatefile;	}
-
 
 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::setCandidateFile(string file)	{	candidatefile = file;										}
 void GlobalData::setRabundFile(string file)		{	rabundfile = file;	inputFileName = file;					}
 void GlobalData::setSabundFile(string file)		{	sabundfile = file;	inputFileName = file;					}
 void GlobalData::setPhylipFile(string file)		{	phylipfile = file;    inputFileName = file;					}
 void GlobalData::setColumnFile(string file)		{	columnfile = file;    inputFileName = file;					}
 void GlobalData::setGroupFile(string file)		{	groupfile = file;											}
 void GlobalData::setSharedFile(string file)		{	sharedfile = file;	inputFileName = file;					}
+void GlobalData::setRelAbundFile(string file)	{	relAbundfile = file;	inputFileName = file;				}
 void GlobalData::setNameFile(string file)		{	namefile = file;		}
 void GlobalData::setOrderFile(string file)		{	orderfile = file;		}
+void GlobalData::setOrderGroupFile(string file)	{	ordergroup = file;		}
 void GlobalData::setFormat(string Format)		{	format = Format;		}
 
 
@@ -49,50 +51,90 @@ void GlobalData::setFormat(string Format)		{	format = Format;		}
 
 /******************************************************/
 GlobalData::GlobalData() {
+	m = MothurOut::getInstance();
 	//option definitions should go here...
 	clear();
 	gListVector = NULL;		
 	gSparseMatrix = NULL;	
+	ginput = NULL;
+	gorder = NULL;
+	glist = NULL;
+	gSharedList = NULL;
+	sabund = NULL;
+	rabund = NULL;
+	gGroupmap = NULL;
+	gMatrix = NULL;
+	gTreemap = NULL;
+	gSequenceDB = NULL;
+	nameMap = NULL;
 }
 /*******************************************************/
 
 /******************************************************/
 void GlobalData::clear() {
 	//option definitions should go here...
-	phylipfile		=	"";
-	columnfile		=	"";
+	phylipfile		=	""; //do we need this?
+	columnfile		=	""; //do we need this?
 	listfile		=	"";
 	rabundfile		=	"";
 	sabundfile		=	"";
-	namefile		=	"";
-	groupfile		=	""; 
+	namefile		=	""; //do we need this?
+	groupfile		=	""; //do we need this?
 	orderfile		=	"";
-	fastafile		=   "";
+	ordergroup		=	"";
+//	fastafile		=   ""; //do we need this?
 	treefile		=	"";
 	sharedfile		=	"";
-	candidatefile	=	"";
+	relAbundfile	=	"";
+	format = "";
 }
+
+
 /*******************************************************/
 
 /******************************************************/
 void GlobalData::newRead() {
-	try{
+	try{	
+			//remove old file names
 			clear();
-			gGroupmap = NULL;
-			gListVector = NULL;
-			gSparseMatrix = NULL;
+			
+			//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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the GlobalData class function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "GlobalData", "newRead");
 		exit(1);
 	}
 }
@@ -102,9 +144,25 @@ void GlobalData::newRead() {
 /******************************************************/
 GlobalData::~GlobalData() {
 	_uniqueInstance = 0;
-	if(gListVector != NULL)		{	delete gListVector;		}
-	if(gSparseMatrix != NULL)	{	delete gSparseMatrix;	}
-	if(gorder != NULL)			{	delete gorder;		}
+	try {
+		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; }
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GlobalData", "~GlobalData");
+		exit(1);
+	}
 }
 /*******************************************************/