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 "readotu.h"
  16 #include "sharedrabundvector.h"
  17
  18 class GlobalData;
  19
  20 class NormalizeSharedCommand : public Command {
  21
  22 public:
  23         NormalizeSharedCommand(string);
  24         ~NormalizeSharedCommand();
  25         int execute();
  26         void help();
  27
  28 private:
  29         GlobalData* globaldata;
  30         ReadOTUFile* read;
  31         InputData* input;
  32         vector<SharedRAbundVector*> lookup;
  33
  34         bool abort, allLines, pickedGroups;
  35         set<string> labels; //holds labels to be used
  36         string groups, label, outputDir, method;
  37         int norm;
  38         vector<string> Groups;
  39
  40         int normalize(vector<SharedRAbundVector*>&, ofstream&);
  41         int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
  42
  43 };
  44
  45 #endif
  46