X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=35415c70c874039c99c758c24a77b7b43eeb6079;hb=7837a9bfdfccdc26360987a44c389832fdb82651;hp=e125e6f3d7032d78d2b1330dece6cf909a6bf320;hpb=f37a59b81c339f574d97042ff6e364146feb457a;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index e125e6f..35415c7 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -10,6 +10,7 @@
 #include "tree.h"
 #include "sparsematrix.hpp"
 #include "sequencedb.h"
+#include "nameassignment.hpp"
 
 
 class ListVector;
@@ -42,10 +43,11 @@ public:
 	TreeMap* gTreemap;
 	SequenceDB* gSequenceDB;
 	string inputFileName, argv;
-	bool allLines, runParse, jumble;
+	bool allLines, runParse, jumble, sim;
 	vector<string>  Estimators, Groups; //holds estimators to be used
 	set<string> labels; //holds labels to be used
 	vector<string> Treenames;
+	map<string, string> names;
 	
 	
 	string getPhylipFile();
@@ -73,6 +75,8 @@ public:
 	void setOrderFile(string file);
 	void setFormat(string);	//do we need this?
 	
+	NameAssignment* nameMap;
+	
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
@@ -80,8 +84,8 @@ public:
 	void newRead();
 	
 private:
-
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
+	MothurOut* m;
+	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor