X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=f3b9b9ac148131b186ed1f94da55706714cd6c6d;hb=5f44783e6d74a9c207492ac244210c915cadc272;hp=759bcae6fd7631988bf15407e7234330c2c9f659;hpb=861f46b74c17adec8c6ad6d89f232ae7485797bf;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 759bcae..f3b9b9a 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;
@@ -44,9 +45,9 @@ public:
 	string inputFileName, argv;
 	bool allLines, runParse, jumble;
 	vector<string>  Estimators, Groups; //holds estimators to be used
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
 	vector<string> Treenames;
+	map<string, string> names;
 	
 	
 	string getPhylipFile();
@@ -74,6 +75,8 @@ public:
 	void setOrderFile(string file);
 	void setFormat(string);	//do we need this?
 	
+	NameAssignment* nameMap;
+	
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
@@ -82,7 +85,7 @@ public:
 	
 private:
 
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
+	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor