normalizesharedcommand.h

   1 #ifndef NORMALIZESHAREDCOMMAND_H
   2 #define NORMALIZESHAREDCOMMAND_H
   3
   4 /*
   5  *  normalizesharedcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/15/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "sharedrabundvector.h"
  16
  17 class NormalizeSharedCommand : public Command {
  18
  19 public:
  20         NormalizeSharedCommand(string);
  21         NormalizeSharedCommand();
  22         ~NormalizeSharedCommand() {}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "normalize.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/Normalize.shared"; }
  31         string getDescription()         { return "normalize samples in a shared or relabund file"; }
  32
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37
  38 private:
  39         InputData* input;
  40         vector<SharedRAbundVector*> lookup;
  41         vector<SharedRAbundFloatVector*> lookupFloat;
  42
  43         bool abort, allLines, pickedGroups, makeRelabund;
  44         set<string> labels; //holds labels to be used
  45         string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
  46         int norm;
  47         vector<string> Groups, outputNames;
  48
  49         int normalize(vector<SharedRAbundVector*>&);
  50         int normalize(vector<SharedRAbundFloatVector*>&);
  51         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  52         int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
  53
  54 };
  55
  56 #endif
  57