fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index b36545effa90467bbfeddab77c56351ebeea934a..0dc4c348584989f101567c229c8246158f5ca70c 100644 (file)
--- 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