#include "command.hpp"
#include "readtree.h"
-#include "treemap.h"
+#include "counttable.h"
#include "sharedrabundvector.h"
#include "sharedrabundfloatvector.h"
#include "inputdata.h"
private:
ReadTree* read;
- TreeMap* treeMap;
+ CountTable* ct;
GroupMap* designMap;
string treefile, sharedfile, relabundfile, groups, label, inputFileName, outputDir, designfile;
bool abort;