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