X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.hpp;h=0dc4c348584989f101567c229c8246158f5ca70c;hb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;hp=b36545effa90467bbfeddab77c56351ebeea934a;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/globaldata.hpp b/globaldata.hpp
index b36545e..0dc4c34 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,16 +1,7 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <iomanip>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <exception>
-
+#include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
 
@@ -19,6 +10,7 @@ using namespace std;
 class ListVector;
 class SharedListVector;
 class SparseMatrix;
+class FullMatrix;
 class Tree;
 class OrderVector;
 class InputData;
@@ -38,6 +30,7 @@ public:
 	SharedListVector* gSharedList;
 	SAbundVector* sabund;
 	GroupMap* gGroupmap;
+	FullMatrix* gMatrix;
 	TreeMap* gTreemap;
 	string inputFileName, helpRequest, commandName;
 	bool allLines;
@@ -66,6 +59,7 @@ public:
 	string getFreq();
 	string getAbund();
 	string getRandomTree();
+	string getGroups();
 
 	void setListFile(string);
 	void setPhylipFile(string);
@@ -75,6 +69,7 @@ public:
 	void setSabundFile(string);
 	void setFormat(string);
 	void setRandomTree(string);
+	void setGroups(string);
 	void setCalc(string);
 
 	
@@ -97,7 +92,6 @@ private:
 	~GlobalData();
 	ListVector* gListVector;
 	SparseMatrix* gSparseMatrix;
-	void clear();  //clears all parameters
 	void reset();	//clears all non filename parameters