metastatscommand.h

   1 #ifndef METASTATSCOMMAND_H
   2 #define METASTATSCOMMAND_H
   3
   4 /*
   5  *  metastatscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/16/10.
   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 MetaStatsCommand : public Command {
  21
  22 public:
  23         MetaStatsCommand(string);
  24         ~MetaStatsCommand();
  25         int execute();
  26         void help();
  27
  28 private:
  29         GlobalData* globaldata;
  30         GroupMap* designMap;
  31         ReadOTUFile* read;
  32         InputData* input;
  33         vector<SharedRAbundVector*> lookup;
  34
  35         bool abort, allLines, pickedGroups;
  36         set<string> labels; //holds labels to be used
  37         string groups, label, outputDir, inputDir, designfile;
  38         vector<string> Groups, outputNames;
  39         int iters, g;
  40         float threshold;
  41
  42         int process(vector<SharedRAbundVector*>&);
  43         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  44 };
  45
  46 #endif
  47