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         string inputFileName, argv;
  46         bool allLines, runParse, jumble, sim;
  47         vector<string>  Estimators, Groups; //holds estimators to be used
  48         set<string> labels; //holds labels to be used
  49         vector<string> Treenames;
  50         map<string, string> names;
  51         string saveNextLabel;
  52
  53
  54         string getPhylipFile();
  55         string getColumnFile();
  56         string getListFile();
  57         string getRabundFile();
  58         string getSabundFile();
  59         string getNameFile();   //do we need this?
  60         string getGroupFile();  //do we need this?
  61         string getOrderFile();
  62         string getOrderGroupFile();
  63         string getTreeFile();
  64         string getSharedFile();
  65         string getRelAbundFile();
  66         string getFormat();     //do we need this?
  67
  68
  69         void setListFile(string);
  70         void setTreeFile(string);
  71         void setGroupFile(string);              //do we need this?
  72         void setPhylipFile(string);
  73         void setColumnFile(string);
  74         void setNameFile(string);       //do we need this?
  75         void setRabundFile(string);
  76         void setSabundFile(string);
  77         void setSharedFile(string);
  78         void setRelAbundFile(string);
  79         void setOrderFile(string file);
  80         void setOrderGroupFile(string file);
  81         void setFormat(string); //do we need this?
  82
  83         NameAssignment* nameMap;
  84
  85         void clear();
  86         void clearLabels();
  87         void clearAbund();
  88
  89         void newRead();
  90
  91 private:
  92         MothurOut* m;
  93         string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup, relAbundfile;
  94
  95         static GlobalData* _uniqueInstance;
  96         GlobalData( const GlobalData& ); // Disable copy constructor
  97         void operator=( const GlobalData& ); // Disable assignment operator
  98         GlobalData();
  99         ~GlobalData();
 100
 101
 102 };
 103
 104 #endif