countgroupscommand.h

   1 #ifndef COUNTGROUPSCOMMAND_H
   2 #define COUNTGROUPSCOMMAND_H
   3
   4 /*
   5  *  countgroupscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 8/9/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 class CountGroupsCommand : public Command {
  16
  17 public:
  18
  19         CountGroupsCommand(string);
  20         CountGroupsCommand();
  21         ~CountGroupsCommand(){}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "count.groups";                        }
  25         string getCommandCategory()             { return "Sequence Processing";         }
  26         string getHelpString();
  27         string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
  28         string getDescription()         { return "counts the number of sequences in each group"; }
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33
  34 private:
  35         string sharedfile, groupfile, outputDir, groups, accnosfile;
  36         bool abort;
  37         vector<string> Groups;
  38
  39         void readAccnos();
  40 };
  41
  42 #endif