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//
// alignmusclecommand.hpp
// Mothur
//
// Created by Sarah Westcott on 2/16/22.
// Copyright © 2022 Schloss Lab. All rights reserved.
//
#ifndef alignmusclecommand_hpp
#define alignmusclecommand_hpp
#include "command.hpp"
/***********************************************************/
class AlignMuscleCommand : public Command {
public:
AlignMuscleCommand(string);
~AlignMuscleCommand() {}
vector<string> setParameters();
string getCommandName() { return "align.muscle"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCommonQuestions();
string getOutputPattern(string);
string getCitation() { return "R.C. Edgar (2021) MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping. (https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf)\nhttp://www.mothur.org/wiki/align.muscle\n"; }
string getDescription() { return "align protein sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, usePerturb, stratified, diversified, useReplicates, useConsiters, useRefineiters, usePerm;
string fastafile, perturb, method, perm, replicates, consiters, refineiters, muscleLocation;
int processors;
vector<string> outputNames;
void wrapperFunction();
};
/**************************************************************************************************/
#endif /* alignmusclecommand_hpp */
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