7 * Created by Sarah Westcott on 3/30/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "inputdata.h"
14 #include "sharedlistvector.h"
16 #include "validcalculator.h"
18 class VennCommand : public Command {
25 vector<string> setParameters();
26 string getCommandName() { return "venn"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
32 void help() { m->mothurOut(getHelpString()); }
36 SharedListVector* SharedList;
38 vector<Calculator*> vennCalculators;
39 vector<SharedRAbundVector*> lookup;
40 set< set<int> > combosOfFour;
44 bool abort, allLines, nseqs, perm;
45 set<string> labels; //holds labels to be used
46 string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
47 vector<string> Estimators, Groups, outputNames;
49 set< set<int> > findCombinations(int);
50 int getCombos(set<int>, set< set<int> >&);