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 GlobalData;
  18
  19 class NormalizeSharedCommand : public Command {
  20
  21 public:
  22         NormalizeSharedCommand(string);
  23         NormalizeSharedCommand();
  24         ~NormalizeSharedCommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         GlobalData* globaldata;
  34         InputData* input;
  35         vector<SharedRAbundVector*> lookup;
  36         vector<SharedRAbundFloatVector*> lookupFloat;
  37
  38         bool abort, allLines, pickedGroups, makeRelabund;
  39         set<string> labels; //holds labels to be used
  40         string groups, label, outputDir, method;
  41         int norm;
  42         vector<string> Groups, outputNames;
  43         map<string, vector<string> > outputTypes;
  44
  45         int normalize(vector<SharedRAbundVector*>&, ofstream&);
  46         int normalize(vector<SharedRAbundFloatVector*>&, ofstream&);
  47         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  48         int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
  49
  50 };
  51
  52 #endif
  53