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#ifndef Mothur_listotucommand_h
#define Mothur_listotucommand_h
//
// listotucommand.h
// Mothur
//
// Created by Sarah Westcott on 5/15/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "listvector.hpp"
#include "sharedrabundvectors.hpp"
#include "sharedrabundfloatvectors.hpp"
/**************************************************************************************************/
class ListOtusCommand : public Command {
public:
ListOtusCommand(string);
~ListOtusCommand(){}
vector<string> setParameters();
string getCommandName() { return "list.otus"; }
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/List.otulabels"; }
string getDescription() { return "lists otu labels from shared or relabund file. Can be used by get.otus with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
string sharedfile, relabundfile, label, inputFileName, format, listfile, constaxonomy;
vector<string> outputNames;
vector<string> Groups;
set<string> labels;
int printList(vector<string> currentLabels, string distance);
int createList(string);
};
/**************************************************************************************************/
#endif
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