chopseqscommand.h

   1 #ifndef CHOPSEQSCOMMAND_H
   2 #define CHOPSEQSCOMMAND_H
   3
   4 /*
   5  *  chopseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 5/10/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "sequence.hpp"
  16
  17 class ChopSeqsCommand : public Command {
  18
  19         public:
  20
  21                 ChopSeqsCommand(string);
  22                 ChopSeqsCommand();
  23                 ~ChopSeqsCommand(){};
  24
  25                 vector<string> setParameters();
  26                 string getCommandName()                 { return "chop.seqs";           }
  27                 string getCommandCategory()             { return "Sequence Processing"; }
  28                 string getOutputFileNameTag(string, string);
  29         string getHelpString();
  30                 string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
  31                 string getDescription()         { return "trim sequence length"; }
  32
  33                 int execute();
  34                 void help() { m->mothurOut(getHelpString()); }
  35
  36         private:
  37                 string fastafile, outputDir, keep;
  38                 bool abort, countGaps, Short;
  39                 int numbases;
  40                 vector<string> outputNames;
  41
  42                 string getChopped(Sequence);
  43 };
  44
  45 #endif
  46
  47