8 #include "rabundvector.hpp"
9 #include "sabundvector.hpp"
10 #include "listvector.hpp"
16 class SharedListVector;
30 static GlobalData* getInstance();
31 ListVector* gListVector;
32 SparseMatrix* gSparseMatrix;
37 SharedListVector* gSharedList;
43 SequenceDB* gSequenceDB;
44 string inputFileName, helpRequest, commandName, vertical;
46 vector<string> Estimators, Groups; //holds estimators to be used
47 set<int> lines; //hold lines to be used
48 set<string> labels; //holds labels to be used
49 vector<string> Treenames;
51 string getPhylipFile();
52 string getColumnFile();
54 string getRabundFile();
55 string getSabundFile();
57 string getGroupFile();
58 string getOrderFile();
59 string getFastaFile();
60 string getNexusFile();
61 string getClustalFile();
63 string getSharedFile();
66 string getPrecision();
73 string getRandomTree();
87 void setListFile(string);
88 void setPhylipFile(string);
89 void setColumnFile(string);
90 void setNameFile(string);
91 void setRabundFile(string);
92 void setSabundFile(string);
93 void setFormat(string);
94 void setRandomTree(string);
95 void setGroups(string);
102 void parseGlobalData(string, string);
104 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
105 //this is required in case user has sequences in the names file that are
106 //not included in the tree.
107 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
112 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
113 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale;
116 static GlobalData* _uniqueInstance;
117 GlobalData( const GlobalData& ); // Disable copy constructor
118 void operator=( const GlobalData& ); // Disable assignment operator
121 void reset(); //clears all non filename parameters
122 void readTreeString(ifstream&);