removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index e125e6f3d7032d78d2b1330dece6cf909a6bf320..59bbac5dc3c0bf0a4d99d6e671b083f9ed2dd954 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,6 +1,6 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
-
+/*
 #include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
@@ -10,6 +10,7 @@
 #include "tree.h"
 #include "sparsematrix.hpp"
 #include "sequencedb.h"
+#include "nameassignment.hpp"
 
 
 class ListVector;
@@ -28,8 +29,8 @@ class SequenceDB;
 class GlobalData {
 public:
        static GlobalData* getInstance();
-       ListVector* gListVector;
-       SparseMatrix* gSparseMatrix;
+       /*ListVector* gListVector;
+       //SparseMatrix* gSparseMatrix;
        InputData* ginput;
        OrderVector* gorder;
        ListVector* glist;
@@ -37,18 +38,21 @@ public:
        SharedListVector* gSharedList;
        SAbundVector* sabund;
        RAbundVector* rabund;
-       GroupMap* gGroupmap;
+       //GroupMap* gGroupmap;
        FullMatrix* gMatrix;
        TreeMap* gTreemap;
        SequenceDB* gSequenceDB;
-       string inputFileName, argv;
-       bool allLines, runParse, jumble;
-       vector<string>  Estimators, Groups; //holds estimators to be used
-       set<string> labels; //holds labels to be used
+       NameAssignment* nameMap;
+       string argv; //inputFileName,
+       bool runParse, jumble, sim; //allLines, 
+       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();
+       /*string getPhylipFile();
        string getColumnFile();
        string getListFile();
        string getRabundFile();
@@ -56,8 +60,10 @@ 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?
 
 
@@ -70,18 +76,22 @@ public:
        void setRabundFile(string);
        void setSabundFile(string);
        void setSharedFile(string);
+       void setRelAbundFile(string);
        void setOrderFile(string file);
-       void setFormat(string); //do we need this?
+       void setOrderGroupFile(string file);
+       void setFormat(string); //do we need this?*/
+       
        
-       void clear(); 
-       void clearLabels();
-       void clearAbund();
        
-       void newRead();
+       //void clear(); 
+       //void clearLabels();
+       //void clearAbund();
        
+       //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, relAbundfile;
 
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
@@ -90,6 +100,6 @@ private:
        ~GlobalData();
        
        
-};
+};*/
 
 #endif