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"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
32 string getDescription() { return "generates a Venn diagram from data provided in a shared file"; }
35 void help() { m->mothurOut(getHelpString()); }
39 SharedListVector* SharedList;
41 vector<Calculator*> vennCalculators;
42 vector<SharedRAbundVector*> lookup;
43 set< set<int> > combosOfFour;
47 bool abort, allLines, nseqs, perm, sharedOtus;
48 set<string> labels; //holds labels to be used
49 string format, groups, calc, label, outputDir, sharedfile, listfile, inputfile;
50 vector<string> Estimators, Groups, outputNames;
52 set< set<int> > findCombinations(int);
53 int getCombos(set<int>, set< set<int> >&);