#include "command.hpp"
#include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "sharedlistvector.h"
#include "venn.h"
#include "validcalculator.h"
class VennCommand : public Command {
public:
- VennCommand();
+ VennCommand(string);
~VennCommand();
int execute();
+ void help();
private:
GlobalData* globaldata;
- ReadMatrix* read;
+ ReadOTUFile* read;
InputData* input;
SharedListVector* SharedList;
- SharedOrderVector* order;
- OrderVector* ordersingle;
Venn* venn;
- string format;
vector<Calculator*> vennCalculators;
ValidCalculators* validCalculator;
+ vector<SharedRAbundVector*> lookup;
+ SAbundVector* sabund;
int abund;
- void setGroups();
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string format, groups, calc, label, outputDir;
+ vector<string> Estimators, Groups;
+
};
-#endif
\ No newline at end of file
+#endif