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
  14
  15 class ListVector;
  16 class SharedListVector;
  17 class SparseMatrix;
  18 class FullMatrix;
  19 class Tree;
  20 class OrderVector;
  21 class InputData;
  22 class GroupMap;
  23 class TreeMap;
  24 class SAbundVector;
  25 class RAbundVector;
  26 class SequenceDB;
  27
  28 class GlobalData {
  29 public:
  30         static GlobalData* getInstance();
  31         ListVector* gListVector;
  32         SparseMatrix* gSparseMatrix;
  33         InputData* ginput;
  34         OrderVector* gorder;
  35         ListVector* glist;
  36         vector<Tree*> gTree;
  37         SharedListVector* gSharedList;
  38         SAbundVector* sabund;
  39         RAbundVector* rabund;
  40         GroupMap* gGroupmap;
  41         FullMatrix* gMatrix;
  42         TreeMap* gTreemap;
  43         SequenceDB* gSequenceDB;
  44         string inputFileName, argv;
  45         bool allLines, runParse;
  46         vector<string>  Estimators, Groups; //holds estimators to be used
  47         set<int> lines; //hold lines to be used
  48         set<string> labels; //holds labels to be used
  49         vector<string> Treenames;
  50
  51         string getPhylipFile();
  52         string getColumnFile();
  53         string getListFile();
  54         string getRabundFile();
  55         string getSabundFile();
  56         string getNameFile();   //do we need this?
  57         string getGroupFile();  //do we need this?
  58         string getOrderFile();
  59 //      string getFastaFile();
  60         string getTreeFile();
  61         string getSharedFile();
  62         string getFormat();     //do we need this?
  63 //      string getCandidateFile();
  64 //      string getTemplateFile();
  65
  66         void setListFile(string);
  67 //      void setFastaFile(string);
  68         void setTreeFile(string);
  69 //      void setCandidateFile(string);
  70 //      void setTemplateFile(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 setOrderFile(string file);
  79         void setFormat(string); //do we need this?
  80
  81         void clear();
  82         void clearLabels();
  83         void clearAbund();
  84
  85         void newRead();
  86
  87 private:
  88
  89         string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
  90
  91         static GlobalData* _uniqueInstance;
  92         GlobalData( const GlobalData& ); // Disable copy constructor
  93         void operator=( const GlobalData& ); // Disable assignment operator
  94         GlobalData();
  95         ~GlobalData();
  96
  97
  98 };
  99
 100 #endif