2 // getmetacommunitycommand.h
5 // Created by SarahsWork on 4/9/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_getmetacommunitycommand_h
10 #define Mothur_getmetacommunitycommand_h
12 #include "command.hpp"
13 #include "inputdata.h"
15 /**************************************************************************************************/
17 class GetMetaCommunityCommand : public Command {
19 GetMetaCommunityCommand(string);
20 GetMetaCommunityCommand();
21 ~GetMetaCommunityCommand(){}
23 vector<string> setParameters();
24 string getCommandName() { return "get.metacommunity"; }
25 string getCommandCategory() { return "OTU-Based Approaches"; }
27 string getOutputPattern(string);
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Get.metacommunity"; }
31 string getDescription() { return "brief description"; }
34 void help() { m->mothurOut(getHelpString()); }
39 vector<string> outputNames;
41 int minpartitions, maxpartitions, optimizegap;
42 vector<string> Groups;
45 int process(vector<SharedRAbundVector*>&);
46 vector<double> generateDesignFile(int, string);
47 int generateSummaryFile(int, string, string, string, string);
51 /**************************************************************************************************/
55 double refMean, difference;
56 vector<double> partMean, partLCI, partUCI;
59 /**************************************************************************************************/