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                 int execute();
  22                 void help();
  23
  24         private:
  25                 set<string> names;
  26                 vector<string> outputNames;
  27                 string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
  28                 bool abort;
  29
  30                 void readFasta();
  31                 void readName();
  32                 void readGroup();
  33                 void readAlign();
  34                 void readAccnos();
  35                 void readList();
  36
  37 };
  38
  39 #endif
  40