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();
79 string getProcessors();
89 void setListFile(string);
90 void setGroupFile(string file);
91 void setPhylipFile(string);
92 void setColumnFile(string);
93 void setNameFile(string);
94 void setRabundFile(string);
95 void setSabundFile(string);
96 void setSharedFile(string);
97 void setFormat(string);
98 void setRandomTree(string);
99 void setGroups(string);
100 void setCalc(string);
101 void setEnds(string);
102 void setProcessors(string);
108 void parseGlobalData(string, string);
110 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
111 //this is required in case user has sequences in the names file that are
112 //not included in the tree.
113 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
118 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
119 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors;
122 static GlobalData* _uniqueInstance;
123 GlobalData( const GlobalData& ); // Disable copy constructor
124 void operator=( const GlobalData& ); // Disable assignment operator
127 void reset(); //clears all non filename parameters
128 void readTreeString(ifstream&);