fixed bug with creation of .tree.sum file

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index f3b9b9ac148131b186ed1f94da55706714cd6c6d..301527a3f9b1e07d7f82ecbd4a04778ec0f39c37 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -43,7 +43,7 @@ public:
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
        string inputFileName, argv;
-       bool allLines, runParse, jumble;
+       bool allLines, runParse, jumble, sim;
        vector<string>  Estimators, Groups; //holds estimators to be used
        set<string> labels; //holds labels to be used
        vector<string> Treenames;
@@ -58,6 +58,7 @@ public:
        string getNameFile();   //do we need this?
        string getGroupFile();  //do we need this?
        string getOrderFile();
+       string getOrderGroupFile();
        string getTreeFile();
        string getSharedFile();
        string getFormat();     //do we need this?
@@ -73,6 +74,7 @@ public:
        void setSabundFile(string);
        void setSharedFile(string);
        void setOrderFile(string file);
+       void setOrderGroupFile(string file);
        void setFormat(string); //do we need this?
        
        NameAssignment* nameMap;
@@ -84,8 +86,8 @@ public:
        void newRead();
        
 private:
-
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
+       MothurOut* m;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor