#include "validcalculator.h"
#include "tree.h"
#include "treemap.h"
+#include "readmatrix.hpp"
+#include "readcolumn.h"
+#include "readphylip.h"
+#include "sparsematrix.hpp"
/* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups.
class GlobalData;
+typedef list<PCell>::iterator MatData;
+
class TreeGroupCommand : public Command {
public:
private:
void createTree();
void printSims(ostream&);
+ void makeSimsShared();
+ void makeSimsDist();
GlobalData* globaldata;
ReadOTUFile* read;
+ ReadMatrix* readMatrix;
+ SparseMatrix* matrix;
+ NameAssignment* nameMap;
+ ListVector* list;
TreeMap* tmap;
Tree* t;
vector<Calculator*> treeCalculators;
InputData* input;
ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
- string format, outputFile, groupNames;
+ string format, outputFile, groupNames, filename;
int numGroups;
ofstream out;
+ float precision, cutoff;
};