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
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34         InputData* input;
  35         vector<SharedRAbundVector*> lookup;
  36
  37         bool abort, allLines, pickedGroups;
  38         set<string> labels; //holds labels to be used
  39         string groups, label, outputDir, scale, sharedfile;
  40         vector<string> Groups, outputNames;
  41
  42         int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
  43
  44 };
  45
  46 #endif
  47