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#
# = bio/compat/references.rb - Obsoleted References class
#
# Copyright:: Copyright (C) 2008
# Toshiaki Katayama <k@bioruby.org>,
# Ryan Raaum <ryan@raaum.org>,
# Jan Aerts <jandot@bioruby.org>,
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# $Id: references.rb,v 1.1.2.1 2008/03/04 10:07:49 ngoto Exp $
#
# == Description
#
# The Bio::References class was obsoleted after BioRuby 1.2.1.
# To keep compatibility, some wrapper methods are provided in this file.
# As the compatibility methods (and Bio::References) will soon be removed,
# Please change your code not to use Bio::References.
#
# Note that Bio::Reference is different from Bio::References.
# Bio::Reference still exists for storing a reference information
# in sequence entries.
module Bio
# = DESCRIPTION
#
# This class is OBSOLETED, and will soon be removed.
# Instead of this class, an array is to be used.
#
#
# A container class for Bio::Reference objects.
#
# = USAGE
#
# This class should NOT be used.
#
# refs = Bio::References.new
# refs.append(Bio::Reference.new(hash))
# refs.each do |reference|
# ...
# end
#
class References
# module to keep backward compatibility with obsoleted Bio::References
module BackwardCompatibility #:nodoc:
# Backward compatibility with Bio::References#references.
# Now, references are stored in an array, and
# you should change your code not to use this method.
def references
warn 'Bio::References is obsoleted. Now, references are stored in an array.'
self
end
# Backward compatibility with Bio::References#append.
# Now, references are stored in an array, and
# you should change your code not to use this method.
def append(reference)
warn 'Bio::References is obsoleted. Now, references are stored in an array.'
self.push(reference) if reference.is_a? Reference
self
end
end #module BackwardCompatibility
# This method should not be used.
# Only for backward compatibility of existing code.
#
# Since Bio::References is obsoleted,
# Bio::References.new not returns Bio::References object,
# but modifies given _ary_ and returns the _ary_.
#
# *Arguments*:
# * (optional) __: Array of Bio::Reference objects
# *Returns*:: the given array
def self.new(ary = [])
warn 'Bio::References is obsoleted. Some methods are added to given array to keep backward compatibility.'
ary.extend(BackwardCompatibility)
ary
end
# Array of Bio::Reference objects
attr_accessor :references
# Normally, users can not call this method.
#
# Create a new Bio::References object
#
# refs = Bio::References.new
# ---
# *Arguments*:
# * (optional) __: Array of Bio::Reference objects
# *Returns*:: Bio::References object
def initialize(ary = [])
@references = ary
end
# Add a Bio::Reference object to the container.
#
# refs.append(reference)
# ---
# *Arguments*:
# * (required) _reference_: Bio::Reference object
# *Returns*:: current Bio::References object
def append(reference)
@references.push(reference) if reference.is_a? Reference
return self
end
# Iterate through Bio::Reference objects.
#
# refs.each do |reference|
# ...
# end
# ---
# *Block*:: yields each Bio::Reference object
def each
@references.each do |reference|
yield reference
end
end
end #class References
end #module Bio
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