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         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32         string accnosfile, groupfile, listfile, outputDir, groups, label;
  33         bool abort;
  34         vector<string> outputNames, Groups;
  35         map<string, vector<string> > outputTypes;
  36         GroupMap* groupMap;
  37
  38         void readAccnos();
  39         int readListGroup();
  40         int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
  41
  42 };
  43
  44 #endif
  45
  46
  47
  48