11 class SharedListVector;
23 static GlobalData* getInstance();
24 ListVector* gListVector;
25 SparseMatrix* gSparseMatrix;
30 SharedListVector* gSharedList;
35 string inputFileName, helpRequest, commandName;
37 vector<string> Estimators, Groups; //holds estimators to be used
38 set<int> lines; //hold lines to be used
39 set<string> labels; //holds labels to be used
41 string getPhylipFile();
42 string getColumnFile();
44 string getRabundFile();
45 string getSabundFile();
47 string getGroupFile();
48 string getOrderFile();
49 string getFastaFile();
51 string getSharedFile();
54 string getPrecision();
61 string getRandomTree();
67 void setListFile(string);
68 void setPhylipFile(string);
69 void setColumnFile(string);
70 void setNameFile(string);
71 void setRabundFile(string);
72 void setSabundFile(string);
73 void setFormat(string);
74 void setRandomTree(string);
75 void setGroups(string);
82 void parseGlobalData(string, string);
85 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
86 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted;
88 static GlobalData* _uniqueInstance;
89 GlobalData( const GlobalData& ); // Disable copy constructor
90 void operator=( const GlobalData& ); // Disable assignment operator
93 void reset(); //clears all non filename parameters