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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         
52         string getPhylipFile();
53         string getColumnFile();
54         string getListFile();
55         string getRabundFile();
56         string getSabundFile();
57         string getNameFile();   //do we need this?
58         string getGroupFile();  //do we need this?
59         string getOrderFile();
60 //      string getFastaFile();
61         string getTreeFile();
62         string getSharedFile();
63         string getFormat();     //do we need this?
64 //      string getCandidateFile();
65 //      string getTemplateFile();
66
67         void setListFile(string);
68 //      void setFastaFile(string);
69         void setTreeFile(string);
70 //      void setCandidateFile(string);
71 //      void setTemplateFile(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 setOrderFile(string file);
80         void setFormat(string); //do we need this?
81         
82         void clear(); 
83         void clearLabels();
84         void clearAbund();
85         
86         void newRead();
87         
88 private:
89
90         string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
91
92         static GlobalData* _uniqueInstance;
93         GlobalData( const GlobalData& ); // Disable copy constructor
94         void operator=( const GlobalData& ); // Disable assignment operator
95         GlobalData();
96         ~GlobalData();
97         
98         
99 };
100
101 #endif