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         string getHelpString();
  28         string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
  29         string getDescription()         { return "normalize samples in a shared or relabund file"; }
  30
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35
  36 private:
  37         InputData* input;
  38         vector<SharedRAbundVector*> lookup;
  39         vector<SharedRAbundFloatVector*> lookupFloat;
  40
  41         bool abort, allLines, pickedGroups, makeRelabund;
  42         set<string> labels; //holds labels to be used
  43         string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
  44         int norm;
  45         vector<string> Groups, outputNames;
  46
  47         int normalize(vector<SharedRAbundVector*>&);
  48         int normalize(vector<SharedRAbundFloatVector*>&);
  49         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  50         int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
  51
  52 };
  53
  54 #endif
  55