working on testing

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index b4b8e0d33912acdd9790a49bc276dc8deef4d6d8..b5e8c7cfc7cb246b9fbf9ca24097b1f3d190366c 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -43,11 +43,12 @@ 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;
        map<string, string> names;
+       string saveNextLabel;
        
        
        string getPhylipFile();
@@ -58,8 +59,10 @@ public:
        string getNameFile();   //do we need this?
        string getGroupFile();  //do we need this?
        string getOrderFile();
+       string getOrderGroupFile();
        string getTreeFile();
        string getSharedFile();
+       string getRelAbundFile();
        string getFormat();     //do we need this?
 
 
@@ -72,7 +75,9 @@ 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;
@@ -85,7 +90,7 @@ public:
        
 private:
        MothurOut* m;
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup, relAbundfile;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor