removeotuscommand.h

   1 #ifndef REMOVEOTUSCOMMAND_H
   2 #define REMOVEOTUSCOMMAND_H
   3
   4 /*
   5  *  removeotuscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/12/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "groupmap.h"
  15 #include "listvector.hpp"
  16
  17 class RemoveOtusCommand : public Command {
  18
  19 public:
  20
  21         RemoveOtusCommand(string);
  22         RemoveOtusCommand();
  23         ~RemoveOtusCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "remove.otus";                         }
  27         string getCommandCategory()             { return "OTU-Based Approaches";        }
  28         string getOutputFileNameTag(string, string);
  29         string getHelpString();
  30         string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
  31         string getDescription()         { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         string accnosfile, groupfile, listfile, outputDir, groups, label;
  38         bool abort;
  39         vector<string> outputNames, Groups;
  40         GroupMap* groupMap;
  41
  42         int readListGroup();
  43         int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
  44
  45 };
  46
  47 #endif
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