listseqscommand.h

   1 #ifndef LISTSEQSCOMMAND_H
   2 #define LISTSEQSCOMMAND_H
   3
   4 /*
   5  *  listseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 7/8/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15 class ListSeqsCommand : public Command {
  16
  17         public:
  18
  19                 ListSeqsCommand(string);
  20                 ListSeqsCommand();
  21                 ~ListSeqsCommand(){}
  22
  23                 vector<string> setParameters();
  24                 string getCommandName()                 { return "list.seqs";                           }
  25                 string getCommandCategory()             { return "Sequence Processing";         }
  26
  27         string getHelpString();
  28     string getOutputPattern(string);
  29                 string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
  30                 string getDescription()         { return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
  31
  32                 int execute();
  33                 void help() { m->mothurOut(getHelpString()); }
  34
  35
  36         private:
  37                 vector<string> names, outputNames;
  38                 string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
  39                 bool abort;
  40
  41                 int readFasta();
  42                 int readName();
  43                 int readGroup();
  44                 int readAlign();
  45                 int readList();
  46                 int readTax();
  47         int readCount();
  48
  49 };
  50
  51 #endif
  52