7 #include "rabundvector.hpp"
8 #include "sabundvector.hpp"
9 #include "listvector.hpp"
11 #include "sparsematrix.hpp"
12 #include "sequencedb.h"
16 class SharedListVector;
30 static GlobalData* getInstance();
31 ListVector* gListVector;
32 SparseMatrix* gSparseMatrix;
37 SharedListVector* gSharedList;
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;
52 string getPhylipFile();
53 string getColumnFile();
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();
62 string getSharedFile();
63 string getFormat(); //do we need this?
64 // string getCandidateFile();
65 // string getTemplateFile();
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?
90 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format;
92 static GlobalData* _uniqueInstance;
93 GlobalData( const GlobalData& ); // Disable copy constructor
94 void operator=( const GlobalData& ); // Disable assignment operator