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#
# = bio/appl/muscle.rb - MUSCLE application wrapper class
#
# Copyright:: Copyright (C) 2006-2007
# Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# $Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
#
#
# Bio::Muscle is a wrapper class to execute MUSCLE.
#
# == References
#
# * http://www.drive5.com/muscle/
# * Edgar R.C.
# MUSCLE: multiple sequence alignment with high accuracy and
# high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.
# * Edgar, R.C.
# MUSCLE: a multiple sequence alignment method with reduced time
# and space complexity. BMC Bioinformatics 5: 113, 2004.
#
module Bio
# Bio::Muscle is a wrapper class to execute MUSCLE.
#
# Please refer documents in bio/apple/muscle.rb for references.
class Muscle < Bio::Alignment::FactoryTemplate::StdinInFileOut
# default program name
DEFAULT_PROGRAM = 'muscle'.freeze
# default report parser
DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat
private
# generates options specifying input filename.
# returns an array of string
def _option_input_file(fn)
[ '-in', fn ]
end
# generates options specifying output filename.
# returns an array of string
def _option_output_file(fn)
[ '-out', fn ]
end
end #class Muscle
end #module Bio
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