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 "sharedlistvector.h"
  15 #include "venn.h"
  16 #include "validcalculator.h"
  17
  18 class VennCommand : public Command {
  19
  20 public:
  21         VennCommand(string);
  22         VennCommand();
  23         ~VennCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "venn";                                        }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28
  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"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38         InputData* input;
  39         SharedListVector* SharedList;
  40         Venn* venn;
  41         vector<Calculator*> vennCalculators;
  42         vector<SharedRAbundVector*> lookup;
  43         set< set<int> > combosOfFour;
  44         SAbundVector* sabund;
  45         int abund, fontsize;
  46
  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;
  51
  52         set< set<int> > findCombinations(int);
  53         int getCombos(set<int>, set< set<int> >&);
  54
  55
  56 };
  57
  58
  59
  60 #endif