getgroupscommand.h

   1 #ifndef GETGROUPSCOMMAND_H
   2 #define GETGROUPSCOMMAND_H
   3
   4 /*
   5  *  getgroupscommand.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 #include "command.hpp"
  15 #include "groupmap.h"
  16
  17 class GetGroupsCommand : public Command {
  18
  19 public:
  20
  21         GetGroupsCommand(string);
  22         GetGroupsCommand();
  23         ~GetGroupsCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "get.groups";                          }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34
  35 private:
  36         set<string> names;
  37         string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
  38         bool abort;
  39         vector<string> outputNames, Groups;
  40         GroupMap* groupMap;
  41
  42         int readFasta();
  43         int readName();
  44         int readGroup();
  45         void readAccnos();
  46         int readList();
  47         int readTax();
  48         int fillNames();
  49
  50 };
  51
  52 #endif
  53
  54
  55