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         ~MetaStatsCommand();
  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         struct linePair {
  35                 int start;
  36                 int num;
  37                 linePair(int i, int j) : start(i), num(j) {}
  38         };
  39         vector<linePair> lines;
  40
  41         GlobalData* globaldata;
  42         GroupMap* designMap;
  43         ReadOTUFile* read;
  44         InputData* input;
  45         vector<SharedRAbundVector*> lookup;
  46         map<string, vector<string> > outputTypes;
  47
  48         bool abort, allLines, pickedGroups;
  49         set<string> labels; //holds labels to be used
  50         string groups, label, outputDir, inputDir, designfile, sets;
  51         vector<string> Groups, outputNames, Sets;
  52         vector< vector<string> > namesOfGroupCombos;
  53         int iters, processors;
  54         float threshold;
  55
  56         int process(vector<SharedRAbundVector*>&);
  57         int driver(int, int, vector<SharedRAbundVector*>&);
  58 };
  59
  60 #endif
  61