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                 vector<string> getRequiredParameters();
  23                 vector<string> getValidParameters();
  24                 vector<string> getRequiredFiles();
  25                 map<string, vector<string> > getOutputFiles() { return outputTypes; }
  26                 int execute();
  27                 void help();
  28
  29         private:
  30                 set<string> names;
  31                 vector<string> outputNames;
  32                 string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
  33                 bool abort, dups;
  34                 map<string, vector<string> > outputTypes;
  35
  36                 int readFasta();
  37                 int readName();
  38                 int readGroup();
  39                 int readAlign();
  40                 int readAccnos();
  41                 int readList();
  42                 int readTax();
  43                 int readQual();
  44                 int compareAccnos();
  45
  46 };
  47
  48 #endif
  49