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
40 vector<string> Treenames;
42 string getPhylipFile();
43 string getColumnFile();
45 string getRabundFile();
46 string getSabundFile();
48 string getGroupFile();
49 string getOrderFile();
50 string getFastaFile();
52 string getSharedFile();
55 string getPrecision();
62 string getRandomTree();
68 void setListFile(string);
69 void setPhylipFile(string);
70 void setColumnFile(string);
71 void setNameFile(string);
72 void setRabundFile(string);
73 void setSabundFile(string);
74 void setFormat(string);
75 void setRandomTree(string);
76 void setGroups(string);
83 void parseGlobalData(string, string);
85 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
86 //this is required in case user has sequences in the names file that are
87 //not included in the tree.
88 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
92 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
93 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted;
95 static GlobalData* _uniqueInstance;
96 GlobalData( const GlobalData& ); // Disable copy constructor
97 void operator=( const GlobalData& ); // Disable assignment operator
100 void reset(); //clears all non filename parameters
101 void readTreeString(ifstream&);