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, argv;
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();
81 string getTemplateFile();
88 string getGapextend();
95 void setListFile(string);
96 void setGroupFile(string file);
97 void setPhylipFile(string);
98 void setColumnFile(string);
99 void setNameFile(string);
100 void setRabundFile(string);
101 void setSabundFile(string);
102 void setSharedFile(string);
103 void setFormat(string);
104 void setRandomTree(string);
105 void setGroups(string);
106 void setCalc(string);
107 void setEnds(string);
108 void setProcessors(string);
114 void parseGlobalData(string, string);
116 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
117 //this is required in case user has sequences in the names file that are
118 //not included in the tree.
119 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
124 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
125 string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, templatefile, search, ksize, align, match, size;
126 string mismatch, gapopen, gapextend;
129 static GlobalData* _uniqueInstance;
130 GlobalData( const GlobalData& ); // Disable copy constructor
131 void operator=( const GlobalData& ); // Disable assignment operator
134 void reset(); //clears all non filename parameters
135 void readTreeString(ifstream&);