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
  30         string getHelpString();
  31     string getOutputPattern(string);
  32         string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
  33         string getDescription()         { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
  34
  35
  36         int execute();
  37         void help() { m->mothurOut(getHelpString()); }
  38
  39 private:
  40         string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
  41         int nseqs, allLines;
  42         bool abort, byGroup;
  43         vector<string> outputNames, Groups;
  44         set<string> labels;
  45
  46         int processSabund();
  47         int processRabund();
  48         int processList();
  49         int processShared();
  50         int processLookup(vector<SharedRAbundVector*>&);
  51
  52 };
  53
  54 #endif
  55
  56
  57
  58