pat's ../ bug fix

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index ff09a36c31727bb6d04e3b2dbe50b50574a2a19f..f3b9b9ac148131b186ed1f94da55706714cd6c6d 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;
+       bool allLines, runParse, jumble;
        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();
@@ -57,18 +58,13 @@ public:
        string getNameFile();   //do we need this?
        string getGroupFile();  //do we need this?
        string getOrderFile();
-//     string getFastaFile();
        string getTreeFile();
        string getSharedFile();
        string getFormat();     //do we need this?
-//     string getCandidateFile();
-//     string getTemplateFile();
+
 
        void setListFile(string);
-//     void setFastaFile(string);
        void setTreeFile(string);
-//     void setCandidateFile(string);
-//     void setTemplateFile(string);
        void setGroupFile(string);              //do we need this?
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -79,6 +75,8 @@ public:
        void setOrderFile(string file);
        void setFormat(string); //do we need this?
        
+       NameAssignment* nameMap;
+       
        void clear(); 
        void clearLabels();
        void clearAbund();
@@ -87,7 +85,7 @@ public:
        
 private:
 
-       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
+       string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor