X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=b5e8c7cfc7cb246b9fbf9ca24097b1f3d190366c;hb=c6e5f84783b39a558119835963dec3c4facb0154;hp=6f66cbe8bbd09577ff0ce709e7fc882d79eb8874;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index 6f66cbe..b5e8c7c 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;
@@ -42,11 +43,13 @@ 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 saveNextLabel;
+	
 	
 	string getPhylipFile();
 	string getColumnFile();
@@ -56,18 +59,15 @@ public:
 	string getNameFile();	//do we need this?
 	string getGroupFile();	//do we need this?
 	string getOrderFile();
-//	string getFastaFile();
+	string getOrderGroupFile();
 	string getTreeFile();
 	string getSharedFile();
+	string getRelAbundFile();
 	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);
@@ -75,9 +75,13 @@ public:
 	void setRabundFile(string);
 	void setSabundFile(string);
 	void setSharedFile(string);
+	void setRelAbundFile(string);
 	void setOrderFile(string file);
+	void setOrderGroupFile(string file);
 	void setFormat(string);	//do we need this?
 	
+	NameAssignment* nameMap;
+	
 	void clear(); 
 	void clearLabels();
 	void clearAbund();
@@ -85,8 +89,8 @@ 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, ordergroup, relAbundfile;
 
 	static GlobalData* _uniqueInstance;
 	GlobalData( const GlobalData& ); // Disable copy constructor