getmetacommunitycommand.h

   1 //
   2 //  getmetacommunitycommand.h
   3 //  Mothur
   4 //
   5 //  Created by SarahsWork on 4/9/13.
   6 //  Copyright (c) 2013 Schloss Lab. All rights reserved.
   7 //
   8
   9 #ifndef Mothur_getmetacommunitycommand_h
  10 #define Mothur_getmetacommunitycommand_h
  11
  12 #include "command.hpp"
  13 #include "inputdata.h"
  14
  15 /**************************************************************************************************/
  16
  17 class GetMetaCommunityCommand : public Command {
  18 public:
  19     GetMetaCommunityCommand(string);
  20     GetMetaCommunityCommand();
  21     ~GetMetaCommunityCommand(){}
  22
  23     vector<string> setParameters();
  24     string getCommandName()                     { return "get.metacommunity";           }
  25     string getCommandCategory()         { return "OTU-Based Approaches";         }
  26
  27     string getOutputPattern(string);
  28
  29         string getHelpString();
  30     string getCitation() { return "http://www.mothur.org/wiki/Get.metacommunity"; }
  31     string getDescription()             { return "brief description"; }
  32
  33     int execute();
  34     void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37     bool abort, allLines;
  38     string outputDir;
  39     vector<string> outputNames;
  40     string sharedfile;
  41     int minpartitions, maxpartitions, optimizegap;
  42     vector<string> Groups;
  43     set<string> labels;
  44
  45     int process(vector<SharedRAbundVector*>&);
  46     vector<double> generateDesignFile(int, string);
  47     int generateSummaryFile(int, string, string, string, string);
  48
  49 };
  50
  51 /**************************************************************************************************/
  52 struct summaryData {
  53
  54     string name;
  55     double refMean, difference;
  56     vector<double> partMean, partLCI, partUCI;
  57
  58 };
  59 /**************************************************************************************************/
  60
  61
  62
  63
  64 #endif