*/
#include "command.hpp"
-#include "treemap.h"
+#include "counttable.h"
#include "sharedutilities.h"
#include "tree.h"
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- TreeMap* tmap;
+ CountTable* ct;
float freq;
int iters, processors, numUniquesInName;
bool abort, rarefy, summary, collect, scale;
- string groups, outputDir, treefile, groupfile, namefile;
+ string groups, outputDir, treefile, groupfile, namefile, countfile;
vector<string> Groups, outputNames; //holds groups to be used, and outputFile names
map<string, int> getRootForGroups(Tree* t);