*/
#include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
-class GlobalData;
+//class GlobalData;
+class GroupMap;
class AmovaCommand : public Command {
bool abort;
- GlobalData* globaldata;
map<string, vector<string> > outputTypes;
vector<string> outputNames;
vector< vector<double> > distanceMatrix;
int iters;
double experimentwiseAlpha;
-
-// 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