void help();
private:
- struct linePair {
- int start;
- int num;
- linePair(int i, int j) : start(i), num(j) {}
- };
- vector<linePair> lines;
+ 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;
GlobalData* globaldata;
- GroupMap* designMap;
map<string, vector<string> > outputTypes;
+ vector<string> outputNames;
+
+ string outputDir, inputDir, designFileName, phylipFileName;
+ GroupMap* designMap;
+ vector< vector<double> > distanceMatrix;
+ int iters;
+ double experimentwiseAlpha;
- 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 calcAmova(ofstream&, int, vector<string>);
- double calcWithin(vector< vector<double> >&, int, vector<string>);
- double calcTotal(int);
+// struct linePair {
+// int start;
+// int num;
+// linePair(int i, int j) : start(i), num(j) {}
+// };
+// vector<linePair> lines;
+//
+// vector< vector<string> > namesOfGroupCombos;
+// vector<string> Groups, outputNames, Sets;
+// int processors;
+// string groups, sets, calc, sharedfile, label, allLines, pickedGroups;
+// vector<Calculator*> calculators;
+// set<string> labels; //holds labels to be used
+// int driver(int, int, vector<SharedRAbundVector*>, string);
+// int driver(int, int, vector<string>, string, vector< vector<double> >&);
+// int process(vector<SharedRAbundVector*>);
};
#endif