rarefactcommand.h

   1 #ifndef RAREFACTCOMMAND_H
   2 #define RAREFACTCOMMAND_H
   3 /*
   4  *  rarefactcommand.h
   5  *  Dotur
   6  *
   7  *  Created by Sarah Westcott on 1/2/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "ordervector.hpp"
  14 #include "inputdata.h"
  15 #include "rarefact.h"
  16 #include "display.h"
  17 #include "readotu.h"
  18 #include "validcalculator.h"
  19
  20
  21 class GlobalData;
  22
  23 class RareFactCommand : public Command {
  24
  25 public:
  26         RareFactCommand(string);
  27         ~RareFactCommand();
  28         int execute();
  29         void help();
  30
  31 private:
  32         GlobalData* globaldata;
  33         vector<Display*> rDisplays;
  34         ReadOTUFile* read;
  35         OrderVector* order;
  36         InputData* input;
  37         ValidCalculators* validCalculator;
  38         Rarefact* rCurve;
  39         int nIters, abund;
  40         float freq;
  41
  42         bool abort, allLines;
  43         set<string> labels; //holds labels to be used
  44         string label, calc;
  45         vector<string>  Estimators;
  46         vector<string> inputFileNames;
  47         vector<string> groups;
  48         string outputDir;
  49
  50         vector<string> parseSharedFile(string);
  51
  52
  53 };
  54
  55 #endif