X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=b18324b8766f9d498295a6e630caaec1b5cc9595;hb=0486bc2eed084ac387d2f59b6d23d13b2382daf7;hp=690a8c3400c802844dc71c49f13f898a0e822e0e;hpb=f37a59b81c339f574d97042ff6e364146feb457a;p=mothur.git

diff --git a/globaldata.cpp b/globaldata.cpp
index 690a8c3..b18324b 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -26,13 +26,13 @@ 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;			}
 
 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;					}
@@ -40,8 +40,10 @@ void GlobalData::setPhylipFile(string file)		{	phylipfile = file;    inputFileNa
 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;		}
 
 
@@ -49,6 +51,7 @@ void GlobalData::setFormat(string Format)		{	format = Format;		}
 
 /******************************************************/
 GlobalData::GlobalData() {
+	m = MothurOut::getInstance();
 	//option definitions should go here...
 	clear();
 	gListVector = NULL;		
@@ -63,6 +66,8 @@ GlobalData::GlobalData() {
 	gMatrix = NULL;
 	gTreemap = NULL;
 	gSequenceDB = NULL;
+	nameMap = NULL;
+	saveNextLabel = "";
 }
 /*******************************************************/
 
@@ -77,9 +82,13 @@ void GlobalData::clear() {
 	namefile		=	""; //do we need this?
 	groupfile		=	""; //do we need this?
 	orderfile		=	"";
+	ordergroup		=	"";
 //	fastafile		=   ""; //do we need this?
 	treefile		=	"";
 	sharedfile		=	"";
+	relAbundfile	=	"";
+	format = "";
+	saveNextLabel = "";
 }
 
 
@@ -115,6 +124,8 @@ void GlobalData::newRead() {
 			if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
 
 			if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+			
+			if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
 
 
 			gTree.clear();
@@ -122,9 +133,10 @@ void GlobalData::newRead() {
 			labels.clear(); Groups.clear();
 			allLines = 1;
 			runParse = true;
+			names.clear();
 	}
 	catch(exception& e) {
-		errorOut(e, "GlobalData", "newRead");
+		m->errorOut(e, "GlobalData", "newRead");
 		exit(1);
 	}
 }
@@ -147,9 +159,10 @@ 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);
 	}
 }