removeseqscommand.h

   1 #ifndef REMOVESEQSCOMMAND_H
   2 #define REMOVESEQSCOMMAND_H
   3
   4 /*
   5  *  removeseqscommand.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 RemoveSeqsCommand : public Command {
  16
  17         public:
  18
  19                 RemoveSeqsCommand(string);
  20                 RemoveSeqsCommand();
  21                 ~RemoveSeqsCommand(){}
  22
  23                 vector<string> setParameters();
  24                 string getCommandName()                 { return "remove.seqs";                         }
  25                 string getCommandCategory()             { return "Sequence Processing";         }
  26
  27         string getHelpString();
  28     string getOutputPattern(string);
  29                 string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
  30                 string getDescription()         { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
  31
  32                 int execute();
  33                 void help() { m->mothurOut(getHelpString()); }
  34
  35
  36         private:
  37                 set<string> names;
  38                 string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
  39                 bool abort, dups;
  40                 vector<string> outputNames;
  41         map<string, string> uniqueMap;
  42
  43                 int readFasta();
  44         int readFastq();
  45                 int readName();
  46                 int readGroup();
  47         int readCount();
  48                 int readAlign();
  49                 int readList();
  50                 int readTax();
  51                 int readQual();
  52
  53 };
  54
  55 #endif
  56