FullMatrix* gMatrix;
TreeMap* gTreemap;
SequenceDB* gSequenceDB;
- string inputFileName, helpRequest, commandName, vertical;
+ string inputFileName, helpRequest, commandName, vertical, argv;
bool allLines;
vector<string> Estimators, Groups; //holds estimators to be used
set<int> lines; //hold lines to be used
string getSorted();
string getEnds();
string getProcessors();
-
+ string getSize();
+ string getCandidateFile();
+ string getSearch();
+ string getKSize();
+ string getAlign();
+ string getMatch();
+ string getMismatch();
+ string getGapopen();
+ string getGapextend();
string getTrump();
string getSoft();
string getFilter();
-
-
string getScale();
private:
string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, nexusfile, clustalfile, treefile, sharedfile, line, label, randomtree, groups;
- string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors;
+ string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund, step, form, sorted, trump, soft, filter, scale, ends, processors, candidatefile, search, ksize, align, match, size;
+ string mismatch, gapopen, gapextend;
static GlobalData* _uniqueInstance;