getotuscommand.h

   1 #ifndef GETOTUSCOMMAND_H
   2 #define GETOTUSCOMMAND_H
   3
   4 /*
   5  *  getotuscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/10/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14
  15 #include "command.hpp"
  16 #include "groupmap.h"
  17 #include "listvector.hpp"
  18
  19 class GetOtusCommand : public Command {
  20
  21 public:
  22
  23         GetOtusCommand(string);
  24         GetOtusCommand();
  25         ~GetOtusCommand(){}
  26
  27         vector<string> setParameters();
  28         string getCommandName()                 { return "get.otus";                            }
  29         string getCommandCategory()             { return "OTU-Based Approaches";        }
  30         string getHelpString();
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35
  36 private:
  37         string accnosfile, groupfile, listfile, outputDir, groups, label;
  38         bool abort;
  39         vector<string> outputNames, Groups;
  40         GroupMap* groupMap;
  41
  42         void readAccnos();
  43         int readListGroup();
  44         int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
  45
  46 };
  47
  48 #endif
  49
  50
  51