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 "sharedrabundvector.h"
  16
  17 class MetaStatsCommand : public Command {
  18
  19 public:
  20         MetaStatsCommand(string);
  21         MetaStatsCommand();
  22         ~MetaStatsCommand() {}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "metastats";                           }
  26         string getCommandCategory()             { return "OTU-Based Approaches";        }
  27         string getHelpString();
  28
  29         int execute();
  30         void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33         struct linePair {
  34                 int start;
  35                 int num;
  36                 linePair(int i, int j) : start(i), num(j) {}
  37         };
  38         vector<linePair> lines;
  39
  40         GroupMap* designMap;
  41         InputData* input;
  42         vector<SharedRAbundVector*> lookup;
  43
  44         bool abort, allLines, pickedGroups;
  45         set<string> labels; //holds labels to be used
  46         string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
  47         vector<string> Groups, outputNames, Sets;
  48         vector< vector<string> > namesOfGroupCombos;
  49         int iters, processors;
  50         float threshold;
  51
  52         int process(vector<SharedRAbundVector*>&);
  53         int driver(int, int, vector<SharedRAbundVector*>&);
  54 };
  55
  56 #endif
  57