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;
42 string inputFileName, helpRequest, commandName;
44 vector<string> Estimators, Groups; //holds estimators to be used
45 set<int> lines; //hold lines to be used
46 set<string> labels; //holds labels to be used
47 vector<string> Treenames;
49 string getPhylipFile();
50 string getColumnFile();
52 string getRabundFile();
53 string getSabundFile();
55 string getGroupFile();
56 string getOrderFile();
57 string getFastaFile();
59 string getSharedFile();
62 string getPrecision();
69 string getRandomTree();
76 void setListFile(string);
77 void setPhylipFile(string);
78 void setColumnFile(string);
79 void setNameFile(string);
80 void setRabundFile(string);
81 void setSabundFile(string);
82 void setFormat(string);
83 void setRandomTree(string);
84 void setGroups(string);
91 void parseGlobalData(string, string);
93 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
94 //this is required in case user has sequences in the names file that are
95 //not included in the tree.
96 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
100 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
101 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, scale;
103 static GlobalData* _uniqueInstance;
104 GlobalData( const GlobalData& ); // Disable copy constructor
105 void operator=( const GlobalData& ); // Disable assignment operator
108 void reset(); //clears all non filename parameters
109 void readTreeString(ifstream&);