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