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 "validcalculator.h"
  18
  19 class RareFactCommand : public Command {
  20
  21 public:
  22         RareFactCommand(string);
  23         RareFactCommand();
  24         ~RareFactCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "rarefaction.single";          }
  28         string getCommandCategory()             { return "OTU-Based Approaches";        }
  29         string getHelpString();
  30         string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
  31         string getDescription()         { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37
  38         vector<Display*> rDisplays;
  39         OrderVector* order;
  40         InputData* input;
  41         Rarefact* rCurve;
  42         int nIters, abund, processors;
  43         float freq;
  44
  45         bool abort, allLines, groupMode;
  46         set<string> labels; //holds labels to be used
  47         string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
  48         vector<string>  Estimators;
  49         vector<string> inputFileNames, outputNames;
  50         vector<string> groups;
  51         string outputDir;
  52
  53         vector<string> parseSharedFile(string, map<string, set<int> >&);
  54         vector<string> createGroupFile(vector<string>&, map<int, string>);
  55 };
  56
  57 #endif