getrelabundcommand.h

   1 #ifndef GETRELABUNDCOMMAND_H
   2 #define GETRELABUNDCOMMAND_H
   3
   4 /*
   5  *  getrelabundcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 6/21/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "sharedrabundvector.h"
  16
  17
  18 class GetRelAbundCommand : public Command {
  19
  20 public:
  21         GetRelAbundCommand(string);
  22         GetRelAbundCommand();
  23         ~GetRelAbundCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "get.relabund";                        }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35         InputData* input;
  36         vector<SharedRAbundVector*> lookup;
  37
  38         bool abort, allLines, pickedGroups;
  39         set<string> labels; //holds labels to be used
  40         string groups, label, outputDir, scale, sharedfile;
  41         vector<string> Groups, outputNames;
  42
  43         int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
  44
  45 };
  46
  47 #endif
  48