- int driver(int, int, vector<SharedRAbundVector*>, string);
- int driver(int, int, vector<string>, string, vector< vector<double> >&);
- int process(vector<SharedRAbundVector*>);
- int calcAmova(ofstream&, int, vector<string>);
- double calcWithin(vector< vector<double> >&, int, vector<string>);
- double calcTotal(int);
+private:
+ double runAMOVA(ofstream&, map<string, vector<int> >, double);
+ double calcSSWithin(map<string, vector<int> >&);
+ double calcSSTotal(map<string, vector<int> >&);
+ map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
+ bool abort;
+ vector<string> outputNames, Sets;
+
+ string outputDir, inputDir, designFileName, phylipFileName;
+ GroupMap* designMap;
+ vector< vector<double> > distanceMatrix;
+ int iters;
+ double experimentwiseAlpha;