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 getOutputFileNameTag(string, string);
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
  30         string getDescription()         { return "normalize samples in a shared or relabund file"; }
  31
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36
  37 private:
  38         InputData* input;
  39         vector<SharedRAbundVector*> lookup;
  40         vector<SharedRAbundFloatVector*> lookupFloat;
  41
  42         bool abort, allLines, pickedGroups, makeRelabund;
  43         set<string> labels; //holds labels to be used
  44         string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
  45         int norm;
  46         vector<string> Groups, outputNames;
  47
  48         int normalize(vector<SharedRAbundVector*>&);
  49         int normalize(vector<SharedRAbundFloatVector*>&);
  50         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  51         int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
  52
  53 };
  54
  55 #endif
  56