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#ifndef Mothur_getotulabelscommand_h
#define Mothur_getotulabelscommand_h
//
// getotuscommand.h
// Mothur
//
// Created by Sarah Westcott on 5/21/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
/**************************************************************************************************/
class GetOtusCommand : public Command {
public:
GetOtusCommand(string);
~GetOtusCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.otus"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
string getDescription() { return "Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string accnosfile, constaxonomyfile, otucorrfile, corraxesfile, listfile, sharedfile, label;
vector<string> outputNames;
unordered_set<string> labels;
ListVector* list;
int readClassifyOtu();
int readOtuAssociation();
int readCorrAxes();
int readList();
int readShared();
int getListVector();
SharedRAbundVectors* getShared();
};
/**************************************************************************************************/
#endif
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