#include "groupmap.h"
#include "validcalculator.h"
#include "tree.h"
-#include "treemap.h"
+#include "counttable.h"
#include "readmatrix.hpp"
#include "readcolumn.h"
#include "readphylip.h"
vector<string> setParameters();
string getCommandName() { return "tree.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
string getDescription() { return "generate a tree file that describes the dissimilarity among groups"; }
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;