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
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
  32         string getDescription()         { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37
  38 private:
  39
  40         vector<SharedRAbundVector*> lookup;
  41         int nIters, subsampleSize, iters;
  42         string format;
  43         float freq;
  44
  45      map<int, string> file2Group; //index in outputNames[i] -> group
  46         bool abort, allLines, jumble, groupMode, subsample;
  47         set<string> labels; //holds labels to be used
  48         string label, calc, groups, outputDir, sharedfile, designfile;
  49         vector<string>  Estimators, Groups, outputNames, Sets;
  50
  51     int process(GroupMap&, string);
  52     vector<string> createGroupFile(vector<string>&);
  53     int subsampleLookup(vector<SharedRAbundVector*>&, string);
  54
  55 };
  56
  57 #endif