#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
+#include "counttable.h"
class ClassifyOtuCommand : public Command {
void help() { m->mothurOut(getHelpString()); }
private:
-
+ GroupMap* groupMap;
+ CountTable* ct;
ListVector* list;
InputData* input;
- string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
+ string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis, countfile;
bool abort, allLines, probs;
int cutoff;
set<string> labels; //holds labels to be used