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#
# = bio/compat/features.rb - Obsoleted Features class
#
# Copyright:: Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org>
# 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
# 2008 Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# $Id: features.rb,v 1.1.2.2 2008/03/10 13:42:26 ngoto Exp $
#
# == Description
#
# The Bio::Features 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::Features) will soon be removed,
# Please change your code not to use Bio::Features.
#
# Note that Bio::Feature is different from the Bio::Features.
# Bio::Feature still exists to store DDBJ/GenBank/EMBL feature information.
require 'bio/location'
module Bio
# = DESCRIPTION
#
# This class is OBSOLETED, and will soon be removed.
# Instead of this class, an array is to be used.
#
#
# Container for a list of Feature objects.
#
# = USAGE
# # First, create some Bio::Feature objects
# feature1 = Bio::Feature.new('intron','3627..4059')
# feature2 = Bio::Feature.new('exon','4060..4236')
# feature3 = Bio::Feature.new('intron','4237..4426')
# feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',
# [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
# Bio::Feature::Qualifier.new('translation','MGXXTVMHLL...')
# ])
#
# # And create a container for them
# feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
#
# # Iterate over all features and print
# feature_container.each do |feature|
# puts feature.feature + "\t" + feature.position
# feature.each do |qualifier|
# puts "- " + qualifier.qualifier + ": " + qualifier.value
# end
# end
#
# # Iterate only over CDS features and extract translated amino acid sequences
# features.each("CDS") do |feature|
# hash = feature.to_hash
# name = hash["gene"] || hash["product"] || hash["note"]
# aaseq = hash["translation"]
# pos = feature.position
# if name and seq
# puts ">#{gene} #{feature.position}"
# puts aaseq
# end
# end
class Features
# module to keep backward compatibility with obsoleted Bio::Features
module BackwardCompatibility #:nodoc:
# Backward compatibility with Bio::Features#features.
# Now, features are stored in an array, and
# you should change your code not to use this method.
def features
warn 'Bio::Features is obsoleted. Now, features are stored in an array.'
self
end
# Backward compatibility with Bio::Features#append.
# Now, references are stored in an array, and
# you should change your code not to use this method.
def append(feature)
warn 'Bio::Features is obsoleted. Now, features are stored in an array.'
self.push(feature) if feature.is_a? Feature
self
end
end #module BackwardCompatibility
# This method should not be used.
# Only for backward compatibility of existing code.
#
# Since Bio::Features is obsoleted,
# Bio::Features.new not returns Bio::Features object,
# but modifies given _ary_ and returns the _ary_.
#
# *Arguments*:
# * (optional) __: Array of Bio::Feature objects
# *Returns*:: the given array
def self.new(ary = [])
warn 'Bio::Features is obsoleted. Some methods are added to given array to keep backward compatibility.'
ary.extend(BackwardCompatibility)
ary
end
# Normally, users can not call this method.
#
# Create a new Bio::Features object.
#
# *Arguments*:
# * (optional) _list of features_: list of Bio::Feature objects
# *Returns*:: Bio::Features object
def initialize(ary = [])
@features = ary
end
# Returns an Array of Feature objects.
attr_accessor :features
# Appends a Feature object to Features.
#
# *Arguments*:
# * (required) _feature_: Bio::Feature object
# *Returns*:: Bio::Features object
def append(a)
@features.push(a) if a.is_a? Feature
return self
end
# Iterates on each feature object.
#
# *Arguments*:
# * (optional) _key_: if specified, only iterates over features with this key
def each(arg = nil)
@features.each do |x|
next if arg and x.feature != arg
yield x
end
end
# Short cut for the Features#features[n]
def [](*arg)
@features[*arg]
end
# Short cut for the Features#features.first
def first
@features.first
end
# Short cut for the Features#features.last
def last
@features.last
end
end # Features
end # Bio
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