7 #include "rabundvector.hpp"
8 #include "sabundvector.hpp"
9 #include "listvector.hpp"
12 class SharedListVector;
26 static GlobalData* getInstance();
27 ListVector* gListVector;
28 SparseMatrix* gSparseMatrix;
33 SharedListVector* gSharedList;
39 SequenceDB* gSequenceDB;
40 string inputFileName, helpRequest, commandName, vertical, argv;
42 vector<string> Estimators, Groups; //holds estimators to be used
43 set<int> lines; //hold lines to be used
44 set<string> labels; //holds labels to be used
45 vector<string> Treenames;
47 string getPhylipFile();
48 string getColumnFile();
50 string getRabundFile();
51 string getSabundFile();
53 string getGroupFile();
54 string getOrderFile();
55 string getFastaFile();
56 string getNexusFile();
57 string getClustalFile();
59 string getSharedFile();
62 string getPrecision();
69 string getRandomTree();
74 string getCountEnds();
75 string getProcessors();
77 string getCandidateFile();
84 string getGapextend();
93 string getMaxHomoPolymer();
94 string getMinLength();
95 string getMaxLength();
97 void setListFile(string);
98 void setGroupFile(string file);
99 void setPhylipFile(string);
100 void setColumnFile(string);
101 void setNameFile(string);
102 void setRabundFile(string);
103 void setSabundFile(string);
104 void setSharedFile(string);
105 void setFormat(string);
106 void setRandomTree(string);
107 void setGroups(string);
108 void setCalc(string);
109 void setCountEnds(string);
110 void setProcessors(string);
116 void parseGlobalData(string, string);
118 void parseTreeFile(); //parses through tree file to find names of nodes and number of them
119 //this is required in case user has sequences in the names file that are
120 //not included in the tree.
121 //only takes names from the first tree in the tree file and assumes that all trees use the same names.
126 string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups, 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, mismatch, gapopen, gapextend, minLength, maxLength, startPos, endPos, maxAmbig, maxHomoPolymer;
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&);