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         ~RareFactSharedCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35         GlobalData* globaldata;
  36         ReadOTUFile* read;
  37         vector<SharedRAbundVector*> lookup;
  38         InputData* input;
  39         ValidCalculators* validCalculator;
  40         Rarefact* rCurve;
  41         vector<Display*> rDisplays;
  42         int nIters;
  43         string format;
  44         float freq;
  45
  46         bool abort, allLines, jumble;
  47         set<string> labels; //holds labels to be used
  48         string label, calc, groups, outputDir;
  49         vector<string>  Estimators, Groups, outputNames;
  50         map<string, vector<string> > outputTypes;
  51
  52
  53 };
  54
  55 #endif