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