#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:
Tree* createTree(vector< vector<double> >&);
void printSims(ostream&, vector< vector<double> >&);
int makeSimsShared();
- vector< vector<double> > makeSimsDist();
+ vector< vector<double> > makeSimsDist(SparseDistanceMatrix*);
int writeTree(string, Tree*);
int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
- ReadMatrix* readMatrix;
- SparseMatrix* matrix;
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;