venncommand.h

   1 #ifndef VENNCOMMAND_H
   2 #define VENNCOMMAND_H
   3 /*
   4  *  venncommand.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 3/30/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "inputdata.h"
  14 #include "readotu.h"
  15 #include "sharedlistvector.h"
  16 #include "venn.h"
  17 #include "validcalculator.h"
  18
  19
  20 class GlobalData;
  21
  22
  23 class VennCommand : public Command {
  24
  25 public:
  26         VennCommand(string);
  27         VennCommand();
  28         ~VennCommand();
  29         vector<string> getRequiredParameters();
  30         vector<string> getValidParameters();
  31         vector<string> getRequiredFiles();
  32         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  33         int execute();
  34         void help();
  35
  36 private:
  37         GlobalData* globaldata;
  38         ReadOTUFile* read;
  39         InputData* input;
  40         SharedListVector* SharedList;
  41         Venn* venn;
  42         vector<Calculator*> vennCalculators;
  43         ValidCalculators* validCalculator;
  44         vector<SharedRAbundVector*> lookup;
  45         set< set<int> > combosOfFour;
  46         SAbundVector* sabund;
  47         int abund;
  48
  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;
  54
  55         set< set<int> > findCombinations(int);
  56         int getCombos(set<int>, set< set<int> >&);
  57
  58
  59 };
  60
  61
  62
  63 #endif