removerarecommand.h

   1 #ifndef REMOVERARECOMMAND_H
   2 #define REMOVERARECOMMAND_H
   3
   4 /*
   5  *  removerarecommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 1/21/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15 #include "listvector.hpp"
  16
  17
  18 class RemoveRareCommand : public Command {
  19
  20 public:
  21
  22         RemoveRareCommand(string);
  23         RemoveRareCommand();
  24         ~RemoveRareCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "remove.rare";                         }
  28         string getCommandCategory()             { return "OTU-Based Approaches";        }
  29         string getHelpString();
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34 private:
  35         string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
  36         int nseqs, allLines;
  37         bool abort, byGroup;
  38         vector<string> outputNames, Groups;
  39         set<string> labels;
  40
  41         int processSabund();
  42         int processRabund();
  43         int processList();
  44         int processShared();
  45         int processLookup(vector<SharedRAbundVector*>&, ofstream&);
  46
  47 };
  48
  49 #endif
  50
  51
  52
  53