filtersharedcommand.h

   1 //
   2 //  filtersharedcommand.h
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 1/4/13.
   6 //  Copyright (c) 2013 Schloss Lab. All rights reserved.
   7 //
   8
   9 #ifndef Mothur_filtersharedcommand_h
  10 #define Mothur_filtersharedcommand_h
  11
  12 #include "command.hpp"
  13 #include "sharedrabundvector.h"
  14 #include "inputdata.h"
  15
  16
  17 class FilterSharedCommand : public Command {
  18
  19 public:
  20         FilterSharedCommand(string);
  21         FilterSharedCommand();
  22         ~FilterSharedCommand() {}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "filter.shared";       }
  26         string getCommandCategory()             { return "OTU-Based Approaches";                }
  27
  28         string getHelpString();
  29     string getOutputPattern(string);
  30         string getCitation() { return "http://www.mothur.org/wiki/Filter.shared"; }
  31         string getDescription()         { return "remove OTUs based on various criteria"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         bool abort, pickedGroups, allLines, makeRare, keepties;
  38         set<string> labels; //holds labels to be used
  39         string groups, label, outputDir, sharedfile;
  40         vector<string> Groups, outputNames;
  41         int minAbund, minTotal, minSamples;
  42     float minPercent, minPercentSamples, rarePercent;
  43
  44     int processShared(vector<SharedRAbundVector*>&);
  45
  46 };
  47
  48
  49
  50 #endif