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//
// getmetacommunitycommand.h
// Mothur
//
// Created by SarahsWork on 4/9/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_getmetacommunitycommand_h
#define Mothur_getmetacommunitycommand_h
#include "command.hpp"
#include "inputdata.h"
#include "qFinderDMM.h"
#include "pam.h"
#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorclass.h"
#include "sharedjest.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
#include "sharedkstest.h"
#include "whittaker.h"
#include "sharedochiai.h"
#include "sharedanderbergs.h"
#include "sharedkulczynski.h"
#include "sharedkulczynskicody.h"
#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
//#include "sharedjackknife.h"
#include "whittaker.h"
#include "odum.h"
#include "canberra.h"
#include "structeuclidean.h"
#include "structchord.h"
#include "hellinger.h"
#include "manhattan.h"
#include "structpearson.h"
#include "soergel.h"
#include "spearman.h"
#include "structkulczynski.h"
#include "structchi2.h"
#include "speciesprofile.h"
#include "hamming.h"
#include "gower.h"
#include "memchi2.h"
#include "memchord.h"
#include "memeuclidean.h"
#include "mempearson.h"
#include "sharedjsd.h"
#include "sharedrjsd.h"
/**************************************************************************************************/
class GetMetaCommunityCommand : public Command {
public:
GetMetaCommunityCommand(string);
~GetMetaCommunityCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.communitytype"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getOutputPattern(string);
string getHelpString();
string getCitation() { return "Holmes I, Harris K, Quince C (2012) Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE 7(2): e30126. doi:10.1371/journal.pone.0030126 http://www.mothur.org/wiki/get.communitytype"; }
string getDescription() { return "Assigns samples to bins using a Dirichlet multinomial mixture model"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines, subsample, withReplacement;
vector<string> outputNames;
string sharedfile, method, calc;
int minpartitions, maxpartitions, optimizegap, iters, subsampleSize;
vector<string> Groups, Estimators;
set<string> labels;
vector<vector<double> > generateDistanceMatrix(SharedRAbundVectors*& lookup);
int driver(SharedRAbundVectors*& thisLookup, vector< vector<seqDist> >& calcDists, Calculator*);
int processDriver(SharedRAbundVectors*&, vector<int>&, string, vector<string>, vector<string>, vector<string>, int);
int createProcesses(SharedRAbundVectors*&);
vector<double> generateDesignFile(int, map<string,string>);
int generateSummaryFile(int, map<string,string>, vector<double>);
};
/**************************************************************************************************/
struct summaryData {
string name;
double refMean, difference;
vector<double> partMean, partLCI, partUCI;
};
/**************************************************************************************************/
#endif
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