X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=35415c70c874039c99c758c24a77b7b43eeb6079;hb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;hp=1d38d63afc4df198599b77cf725b734c531a33ac;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 1d38d63..35415c7 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -7,6 +7,11 @@
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
+#include "tree.h"
+#include "sparsematrix.hpp"
+#include "sequencedb.h"
+#include "nameassignment.hpp"
+
 
 class ListVector;
 class SharedListVector;
@@ -38,39 +43,39 @@ 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();
 	string getListFile();
 	string getRabundFile();
 	string getSabundFile();
-	string getNameFile();
-	string getGroupFile();
+	string getNameFile();	//do we need this?
+	string getGroupFile();	//do we need this?
 	string getOrderFile();
-	string getFastaFile();
 	string getTreeFile();
 	string getSharedFile();
-	string getFormat();
-	string getCandidateFile();
-		
+	string getFormat();	//do we need this?
+
+
 	void setListFile(string);
-	void setFastaFile(string);
 	void setTreeFile(string);
-	void setCandidateFile(string);
-	void setGroupFile(string);	
+	void setGroupFile(string);		//do we need this?
 	void setPhylipFile(string);
 	void setColumnFile(string);
-	void setNameFile(string);
+	void setNameFile(string);	//do we need this?
 	void setRabundFile(string);
 	void setSabundFile(string);
 	void setSharedFile(string);
 	void setOrderFile(string file);
-	void setFormat(string);
+	void setFormat(string);	//do we need this?
+	
+	NameAssignment* nameMap;
 	
 	void clear(); 
 	void clearLabels();
@@ -79,8 +84,8 @@ public:
 	void newRead();
 	
 private:
-
-	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, format, candidatefile;
+	MothurOut* m;
+	string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor