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
  14
  15 #include "command.hpp"
  16 #include "groupmap.h"
  17 #include "listvector.hpp"
  18
  19 class RemoveOtusCommand : public Command {
  20
  21 public:
  22
  23         RemoveOtusCommand(string);
  24         RemoveOtusCommand();
  25         ~RemoveOtusCommand(){}
  26         vector<string> getRequiredParameters();
  27         vector<string> getValidParameters();
  28         vector<string> getRequiredFiles();
  29         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  30         int execute();
  31         void help();
  32
  33 private:
  34         string accnosfile, groupfile, listfile, outputDir, groups, label;
  35         bool abort;
  36         vector<string> outputNames, Groups;
  37         map<string, vector<string> > outputTypes;
  38         GroupMap* groupMap;
  39
  40         void readAccnos();
  41         int readListGroup();
  42         int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
  43
  44 };
  45
  46 #endif
  47
  48
  49
  50