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         struct linePair {
  30                 int start;
  31                 int num;
  32                 linePair(int i, int j) : start(i), num(j) {}
  33         };
  34         vector<linePair> lines;
  35
  36         GlobalData* globaldata;
  37         GroupMap* designMap;
  38         ReadOTUFile* read;
  39         InputData* input;
  40         vector<SharedRAbundVector*> lookup;
  41
  42         bool abort, allLines, pickedGroups;
  43         set<string> labels; //holds labels to be used
  44         string groups, label, outputDir, inputDir, designfile, sets;
  45         vector<string> Groups, outputNames, Sets;
  46         vector< vector<string> > namesOfGroupCombos;
  47         int iters, processors;
  48         float threshold;
  49
  50         int process(vector<SharedRAbundVector*>&);
  51         int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
  52         int driver(int, int, vector<SharedRAbundVector*>&);
  53 };
  54
  55 #endif
  56