8 #include "rabundvector.hpp"
9 #include "sabundvector.hpp"
10 #include "listvector.hpp"
16 class SharedListVector;
29 static GlobalData* getInstance();
30 ListVector* gListVector;
31 SparseMatrix* gSparseMatrix;
36 SharedListVector* gSharedList;
41 string inputFileName, helpRequest, commandName;
43 vector<string> Estimators, Groups; //holds estimators to be used
44 set<int> lines; //hold lines to be used
45 set<string> labels; //holds labels to be used
46 vector<string> Treenames;
48 string getPhylipFile();
49 string getColumnFile();
51 string getRabundFile();
52 string getSabundFile();
54 string getGroupFile();
55 string getOrderFile();
56 string getFastaFile();
58 string getSharedFile();
61 string getPrecision();
68 string getRandomTree();
75 void setListFile(string);
76 void setPhylipFile(string);
77 void setColumnFile(string);
78 void setNameFile(string);
79 void setRabundFile(string);
80 void setSabundFile(string);
81 void setFormat(string);
82 void setRandomTree(string);
83 void setGroups(string);
90 void parseGlobalData(string, string);
92 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
93 //this is required in case user has sequences in the names file that are
94 //not included in the tree.
95 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
99 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
100 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, scale;
102 static GlobalData* _uniqueInstance;
103 GlobalData( const GlobalData& ); // Disable copy constructor
104 void operator=( const GlobalData& ); // Disable assignment operator
107 void reset(); //clears all non filename parameters
108 void readTreeString(ifstream&);