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"
15 #include "sharedlistvector.h"
17 #include "validcalculator.h"
23 class VennCommand : public Command {
29 vector<string> getRequiredParameters();
30 vector<string> getValidParameters();
31 vector<string> getRequiredFiles();
32 map<string, vector<string> > getOutputFiles() { return outputTypes; }
37 GlobalData* globaldata;
40 SharedListVector* SharedList;
42 vector<Calculator*> vennCalculators;
43 ValidCalculators* validCalculator;
44 vector<SharedRAbundVector*> lookup;
45 set< set<int> > combosOfFour;
49 bool abort, allLines, nseqs, perm;
50 set<string> labels; //holds labels to be used
51 string format, groups, calc, label, outputDir;
52 vector<string> Estimators, Groups, outputNames;
53 map<string, vector<string> > outputTypes;
55 set< set<int> > findCombinations(int);
56 int getCombos(set<int>, set< set<int> >&);