7 #include "rabundvector.hpp"
8 #include "sabundvector.hpp"
9 #include "listvector.hpp"
11 #include "sparsematrix.hpp"
12 #include "sequencedb.h"
13 #include "nameassignment.hpp"
17 class SharedListVector;
31 static GlobalData* getInstance();
32 ListVector* gListVector;
33 SparseMatrix* gSparseMatrix;
38 SharedListVector* gSharedList;
44 SequenceDB* gSequenceDB;
45 string inputFileName, argv;
46 bool allLines, runParse, jumble, sim;
47 vector<string> Estimators, Groups; //holds estimators to be used
48 set<string> labels; //holds labels to be used
49 vector<string> Treenames;
50 map<string, string> names;
54 string getPhylipFile();
55 string getColumnFile();
57 string getRabundFile();
58 string getSabundFile();
59 string getNameFile(); //do we need this?
60 string getGroupFile(); //do we need this?
61 string getOrderFile();
62 string getOrderGroupFile();
64 string getSharedFile();
65 string getRelAbundFile();
66 string getFormat(); //do we need this?
69 void setListFile(string);
70 void setTreeFile(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 setRelAbundFile(string);
79 void setOrderFile(string file);
80 void setOrderGroupFile(string file);
81 void setFormat(string); //do we need this?
83 NameAssignment* nameMap;
93 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, treefile, sharedfile, format, distfile, ordergroup, relAbundfile;
95 static GlobalData* _uniqueInstance;
96 GlobalData( const GlobalData& ); // Disable copy constructor
97 void operator=( const GlobalData& ); // Disable assignment operator