7 #include "rabundvector.hpp"
8 #include "sabundvector.hpp"
9 #include "listvector.hpp"
11 #include "sparsematrix.hpp"
14 class SharedListVector;
28 static GlobalData* getInstance();
29 ListVector* gListVector;
30 SparseMatrix* gSparseMatrix;
35 SharedListVector* gSharedList;
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;
49 string getPhylipFile();
50 string getColumnFile();
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();
59 string getSharedFile();
60 string getFormat(); //do we need this?
61 // string getCandidateFile();
62 // string getTemplateFile();
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?
87 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
89 static GlobalData* _uniqueInstance;
90 GlobalData( const GlobalData& ); // Disable copy constructor
91 void operator=( const GlobalData& ); // Disable assignment operator