getseqscommand.h

   1 #ifndef GETSEQSCOMMAND_H
   2 #define GETSEQSCOMMAND_H
   3
   4 /*
   5  *  getseqscommand.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 GetSeqsCommand : public Command {
  16
  17         public:
  18
  19                 GetSeqsCommand(string);
  20                 GetSeqsCommand();
  21                 ~GetSeqsCommand(){}
  22
  23                 vector<string> setParameters();
  24                 string getCommandName()                 { return "get.seqs";                            }
  25                 string getCommandCategory()             { return "Sequence Processing";         }
  26                 string getHelpString();
  27                 string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
  28                 string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
  29
  30                 int execute();
  31                 void help() { m->mothurOut(getHelpString()); }
  32
  33
  34         private:
  35                 set<string> names;
  36                 vector<string> outputNames;
  37                 string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
  38                 bool abort, dups;
  39
  40                 int readFasta();
  41                 int readName();
  42                 int readGroup();
  43                 int readAlign();
  44                 int readAccnos();
  45                 int readList();
  46                 int readTax();
  47                 int readQual();
  48                 int compareAccnos();
  49
  50 };
  51
  52 #endif
  53