globaldata.hpp

   1 #ifndef GLOBALDATA_HPP
   2 #define GLOBALDATA_HPP
   3 /*
   4 #include "mothur.h"
   5 #include "groupmap.h"
   6 #include "treemap.h"
   7 #include "rabundvector.hpp"
   8 #include "sabundvector.hpp"
   9 #include "listvector.hpp"
  10 #include "tree.h"
  11 #include "sparsematrix.hpp"
  12 #include "sequencedb.h"
  13 #include "nameassignment.hpp"
  14
  15
  16 class ListVector;
  17 class SharedListVector;
  18 class SparseMatrix;
  19 class FullMatrix;
  20 class Tree;
  21 class OrderVector;
  22 class InputData;
  23 class GroupMap;
  24 class TreeMap;
  25 class SAbundVector;
  26 class RAbundVector;
  27 class SequenceDB;
  28
  29 class GlobalData {
  30 public:
  31         static GlobalData* getInstance();
  32         /*ListVector* gListVector;
  33         //SparseMatrix* gSparseMatrix;
  34         InputData* ginput;
  35         OrderVector* gorder;
  36         ListVector* glist;
  37         vector<Tree*> gTree;
  38         SharedListVector* gSharedList;
  39         SAbundVector* sabund;
  40         RAbundVector* rabund;
  41         //GroupMap* gGroupmap;
  42         FullMatrix* gMatrix;
  43         TreeMap* gTreemap;
  44         SequenceDB* gSequenceDB;
  45         NameAssignment* nameMap;
  46         string argv; //inputFileName,
  47         bool runParse, jumble, sim; //allLines,
  48         vector<string>  Estimators;//, Groups; //holds estimators to be used
  49         //set<string> labels; //holds labels to be used
  50         vector<string> Treenames;
  51         map<string, string> names;
  52         string saveNextLabel;
  53
  54
  55         /*string getPhylipFile();
  56         string getColumnFile();
  57         string getListFile();
  58         string getRabundFile();
  59         string getSabundFile();
  60         string getNameFile();   //do we need this?
  61         string getGroupFile();  //do we need this?
  62         string getOrderFile();
  63         string getOrderGroupFile();
  64         string getTreeFile();
  65         string getSharedFile();
  66         string getRelAbundFile();
  67         string getFormat();     //do we need this?
  68
  69
  70         void setListFile(string);
  71         void setTreeFile(string);
  72         void setGroupFile(string);              //do we need this?
  73         void setPhylipFile(string);
  74         void setColumnFile(string);
  75         void setNameFile(string);       //do we need this?
  76         void setRabundFile(string);
  77         void setSabundFile(string);
  78         void setSharedFile(string);
  79         void setRelAbundFile(string);
  80         void setOrderFile(string file);
  81         void setOrderGroupFile(string file);
  82         void setFormat(string); //do we need this?*/
  83
  84
  85
  86         //void clear();
  87         //void clearLabels();
  88         //void clearAbund();
  89
  90         //void newRead();
  91         /*
  92 private:
  93         MothurOut* m;
  94         //string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup, relAbundfile;
  95
  96         static GlobalData* _uniqueInstance;
  97         GlobalData( const GlobalData& ); // Disable copy constructor
  98         void operator=( const GlobalData& ); // Disable assignment operator
  99         GlobalData();
 100         ~GlobalData();
 101
 102
 103 };*/
 104
 105 #endif