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         string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
  30         string getDescription()         { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35
  36 private:
  37
  38         vector<SharedRAbundVector*> lookup;
  39         int nIters;
  40         string format;
  41         float freq;
  42
  43         bool abort, allLines, jumble;
  44         set<string> labels; //holds labels to be used
  45         string label, calc, groups, outputDir, sharedfile, designfile;
  46         vector<string>  Estimators, Groups, outputNames, Sets;
  47
  48     int process(GroupMap&, string);
  49
  50 };
  51
  52 #endif