degapseqscommand.h

   1 #ifndef DEGAPSEQSCOMMAND_H
   2 #define DEGAPSEQSCOMMAND_H
   3
   4 /*
   5  *  degapseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 6/21/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class DegapSeqsCommand : public Command {
  17 public:
  18         DegapSeqsCommand(string);
  19         DegapSeqsCommand();
  20         ~DegapSeqsCommand(){}
  21
  22         vector<string> setParameters();
  23         string getCommandName()                 { return "degap.seqs";          }
  24         string getCommandCategory()             { return "Sequence Processing";         }
  25         string getOutputFileNameTag(string, string);
  26         string getHelpString();
  27         string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
  28         string getDescription()         { return "removes gap characters from sequences"; }
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34
  35         bool abort;
  36         string fastafile, outputDir;
  37         vector<string> outputNames;
  38         vector<string> fastaFileNames;
  39
  40 };
  41
  42 #endif
  43