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#ifndef Mothur_getcoremicrobiomcommand_h
#define Mothur_getcoremicrobiomcommand_h
//
// GetCoreMicroBiomeCommand.h
// Mothur
//
// Created by Sarah Westcott on 5/8/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "inputdata.h"
/**************************************************************************************************/
class GetCoreMicroBiomeCommand : public Command {
public:
GetCoreMicroBiomeCommand(string);
~GetCoreMicroBiomeCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.coremicrobiome"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.coremicrobiome"; }
string getDescription() { return "determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string relabundfile, sharedfile, inputFileName, format, output;
bool allLines;
vector<string> Groups;
set<string> labels;
bool abort;
vector<string> outputNames;
float abund;
int samples, factor;
int createTable(SharedRAbundFloatVectors*&);
};
/**************************************************************************************************/
#endif
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