fixed bug with creation of .tree.sum file

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 759bcae6fd7631988bf15407e7234330c2c9f659..301527a3f9b1e07d7f82ecbd4a04778ec0f39c37 100644 (file)
--- 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 +43,11 @@ 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<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
        vector<string> Treenames;
+       map<string, string> names;
        
        
        string getPhylipFile();
@@ -57,6 +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?
@@ -72,8 +74,11 @@ public:
        void setSabundFile(string);
        void setSharedFile(string);
        void setOrderFile(string file);
+       void setOrderGroupFile(string file);
        void setFormat(string); //do we need this?
        
+       NameAssignment* nameMap;
+       
        void clear(); 
        void clearLabels();
        void clearAbund();
@@ -81,8 +86,8 @@ 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;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor