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#ifndef VENNCOMMAND_H
#define VENNCOMMAND_H
/*
* venncommand.h
* Mothur
*
* Created by Sarah Westcott on 3/30/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "sharedlistvector.h"
#include "venn.h"
#include "validcalculator.h"
class VennCommand : public Command {
public:
VennCommand(string);
~VennCommand() = default;
vector<string> setParameters();
string getCommandName() { return "venn"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
string getDescription() { return "generates a Venn diagram from data provided in a shared file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
SharedListVector* SharedList;
Venn* venn;
vector<Calculator*> vennCalculators;
set< set<int> > combos;
SAbundVector* sabund;
int abund, fontsize, perm;
bool abort, allLines, nseqs, sharedOtus;
set<string> labels; //holds labels to be used
string format, groups, calc, label, sharedfile, listfile, inputfile;
vector<string> Estimators, Groups, outputNames;
set< set<int> > findCombinations(int);
int getCombos(set<int>, set< set<int> >&);
};
#endif
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