X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=35415c70c874039c99c758c24a77b7b43eeb6079;hb=291eaab661778e1fd02c5c22bc388daa97bb1d54;hp=6515521768bfe2291775965e80eb94eac4d7a760;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 6515521..35415c7 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -9,6 +9,9 @@
 #include "listvector.hpp"
 #include "tree.h"
 #include "sparsematrix.hpp"
+#include "sequencedb.h"
+#include "nameassignment.hpp"
+
 
 class ListVector;
 class SharedListVector;
@@ -40,11 +43,12 @@ public:
 	TreeMap* gTreemap;
 	SequenceDB* gSequenceDB;
 	string inputFileName, argv;
-	bool allLines, runParse;
+	bool allLines, runParse, jumble, sim;
 	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();
 	string getColumnFile();
@@ -54,18 +58,13 @@ public:
 	string getNameFile();	//do we need this?
 	string getGroupFile();	//do we need this?
 	string getOrderFile();
-//	string getFastaFile();
 	string getTreeFile();
 	string getSharedFile();
 	string getFormat();	//do we need this?
-//	string getCandidateFile();
-//	string getTemplateFile();
+
 
 	void setListFile(string);
-//	void setFastaFile(string);
 	void setTreeFile(string);
-//	void setCandidateFile(string);
-//	void setTemplateFile(string);
 	void setGroupFile(string);		//do we need this?
 	void setPhylipFile(string);
 	void setColumnFile(string);
@@ -76,6 +75,8 @@ public:
 	void setOrderFile(string file);
 	void setFormat(string);	//do we need this?
 	
+	NameAssignment* nameMap;
+	
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
@@ -83,8 +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