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         ~RareFactCommand();
  29         vector<string> getRequiredParameters();
  30         vector<string> getValidParameters();
  31         vector<string> getRequiredFiles();
  32         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  33         int execute();
  34         void help();
  35
  36 private:
  37         GlobalData* globaldata;
  38         vector<Display*> rDisplays;
  39         ReadOTUFile* read;
  40         OrderVector* order;
  41         InputData* input;
  42         ValidCalculators* validCalculator;
  43         Rarefact* rCurve;
  44         int nIters, abund, processors;
  45         float freq;
  46
  47         bool abort, allLines;
  48         set<string> labels; //holds labels to be used
  49         string label, calc;
  50         vector<string>  Estimators;
  51         vector<string> inputFileNames, outputNames;
  52         vector<string> groups;
  53         map<string, vector<string> > outputTypes;
  54         string outputDir;
  55
  56         vector<string> parseSharedFile(string);
  57
  58
  59 };
  60
  61 #endif