- map<string, vector<string> > outputTypes;
-
- vector< vector<double> > matrix;
- bool abort, allLines, pickedGroups;
- set<string> labels; //holds labels to be used
- string format, groups, label, outputDir, inputDir, designfile, sets, phylipfile, calc, sharedfile;
- vector<string> Groups, outputNames, Sets;
- vector< vector<string> > namesOfGroupCombos;
- int iters, processors;
- vector<Calculator*> calculators;
-
- int driver(int, int, vector<SharedRAbundVector*>, string);
- int driver(int, int, vector<string>, string, vector< vector<double> >&);
- int process(vector<SharedRAbundVector*>);
- int calcHomova(ofstream&, int, vector<string>);
- map<string, double> calcWithin(vector< vector<double> >&, int, vector<string>, map<string, int>&);
- double calcTotal(int);