#include "groupmap.h"
#include "validcalculator.h"
#include "tree.h"
-#include "treemap.h"
+#include "counttable.h"
#include "readmatrix.hpp"
#include "readcolumn.h"
#include "readphylip.h"
-#include "sparsematrix.hpp"
#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
They can also use as many or as few calculators as they wish. */
-typedef list<PCell>::iterator MatData;
-
class TreeGroupCommand : public Command {
public:
NameAssignment* nameMap;
ListVector* list;
- TreeMap* tmap;
+ CountTable* ct;
Tree* t;
InputData* input;
vector<Calculator*> treeCalculators;
vector<SharedRAbundVector*> lookup;
string lastLabel;
- string format, groupNames, filename, sharedfile, inputfile;
+ string format, groupNames, filename, sharedfile, countfile, inputfile;
int numGroups, subsampleSize, iters, processors;
ofstream out;
float precision, cutoff;