rarefactsharedcommand.h

   1 #ifndef RAREFACTSHAREDCOMMAND_H
   2 #define RAREFACTSHAREDCOMMAND_H
   3 /*
   4  *  rarefactsharedcommand.h
   5  *  Dotur
   6  *
   7  *  Created by Sarah Westcott on 1/6/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "inputdata.h"
  14 #include "rarefact.h"
  15 #include "display.h"
  16 #include "readotu.h"
  17 #include "validcalculator.h"
  18
  19 class GlobalData;
  20
  21 class RareFactSharedCommand : public Command {
  22
  23 public:
  24         RareFactSharedCommand(string);
  25         ~RareFactSharedCommand();
  26         int execute();
  27         void help();
  28
  29 private:
  30         GlobalData* globaldata;
  31         ReadOTUFile* read;
  32         vector<SharedRAbundVector*> lookup;
  33         InputData* input;
  34         ValidCalculators* validCalculator;
  35         Rarefact* rCurve;
  36         vector<Display*> rDisplays;
  37         int freq, nIters;
  38         string format;
  39
  40         bool abort, allLines, jumble;
  41         set<string> labels; //holds labels to be used
  42         string label, calc, groups, outputDir;
  43         vector<string>  Estimators, Groups;
  44
  45
  46 };
  47
  48 #endif