reversecommand.h

   1 #ifndef REVERSECOMMAND_H
   2 #define REVERSECOMMAND_H
   3
   4 /*
   5  *  reversecommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 6/6/09.
   9  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 class ReverseSeqsCommand : public Command {
  16 public:
  17         ReverseSeqsCommand(string);
  18         ReverseSeqsCommand();
  19         ~ReverseSeqsCommand() {}
  20
  21         vector<string> setParameters();
  22         string getCommandName()                 { return "reverse.seqs";                        }
  23         string getCommandCategory()             { return "Sequence Processing";         }
  24
  25         string getHelpString();
  26     string getOutputPattern(string);
  27         string getCitation() { return "http://www.mothur.org/wiki/Reverse.seqs"; }
  28         string getDescription()         { return "outputs a fasta file containing the reverse-complements"; }
  29
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35
  36         bool abort;
  37         string fastaFileName, qualFileName, outputDir;
  38         vector<string> outputNames;
  39
  40 };
  41
  42 #endif