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
  13 class ListVector;
  14 class SharedListVector;
  15 class SparseMatrix;
  16 class FullMatrix;
  17 class Tree;
  18 class OrderVector;
  19 class InputData;
  20 class GroupMap;
  21 class TreeMap;
  22 class SAbundVector;
  23 class RAbundVector;
  24 class SequenceDB;
  25
  26 class GlobalData {
  27 public:
  28         static GlobalData* getInstance();
  29         ListVector* gListVector;
  30         SparseMatrix* gSparseMatrix;
  31         InputData* ginput;
  32         OrderVector* gorder;
  33         ListVector* glist;
  34         vector<Tree*> gTree;
  35         SharedListVector* gSharedList;
  36         SAbundVector* sabund;
  37         RAbundVector* rabund;
  38         GroupMap* gGroupmap;
  39         FullMatrix* gMatrix;
  40         TreeMap* gTreemap;
  41         SequenceDB* gSequenceDB;
  42         string inputFileName, argv;
  43         bool allLines, runParse;
  44         vector<string>  Estimators, Groups; //holds estimators to be used
  45         set<int> lines; //hold lines to be used
  46         set<string> labels; //holds labels to be used
  47         vector<string> Treenames;
  48
  49         string getPhylipFile();
  50         string getColumnFile();
  51         string getListFile();
  52         string getRabundFile();
  53         string getSabundFile();
  54         string getNameFile();   //do we need this?
  55         string getGroupFile();  //do we need this?
  56         string getOrderFile();
  57 //      string getFastaFile();
  58         string getTreeFile();
  59         string getSharedFile();
  60         string getFormat();     //do we need this?
  61 //      string getCandidateFile();
  62 //      string getTemplateFile();
  63
  64         void setListFile(string);
  65 //      void setFastaFile(string);
  66         void setTreeFile(string);
  67 //      void setCandidateFile(string);
  68 //      void setTemplateFile(string);
  69         void setGroupFile(string);              //do we need this?
  70         void setPhylipFile(string);
  71         void setColumnFile(string);
  72         void setNameFile(string);       //do we need this?
  73         void setRabundFile(string);
  74         void setSabundFile(string);
  75         void setSharedFile(string);
  76         void setOrderFile(string file);
  77         void setFormat(string); //do we need this?
  78
  79         void clear();
  80         void clearLabels();
  81         void clearAbund();
  82
  83         void newRead();
  84
  85 private:
  86
  87         string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
  88
  89         static GlobalData* _uniqueInstance;
  90         GlobalData( const GlobalData& ); // Disable copy constructor
  91         void operator=( const GlobalData& ); // Disable assignment operator
  92         GlobalData();
  93         ~GlobalData();
  94
  95
  96 };
  97
  98 #endif