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 "validcalculator.h"
  17
  18 class RareFactSharedCommand : public Command {
  19
  20 public:
  21         RareFactSharedCommand(string);
  22         RareFactSharedCommand();
  23         ~RareFactSharedCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "rarefaction.shared";          }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getHelpString();
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33
  34 private:
  35
  36         vector<SharedRAbundVector*> lookup;
  37         InputData* input;
  38         Rarefact* rCurve;
  39         vector<Display*> rDisplays;
  40         int nIters;
  41         string format;
  42         float freq;
  43
  44         bool abort, allLines, jumble;
  45         set<string> labels; //holds labels to be used
  46         string label, calc, groups, outputDir, sharedfile;
  47         vector<string>  Estimators, Groups, outputNames;
  48
  49 };
  50
  51 #endif