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Versions: 12
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Contents
#
# = bio/sequence/dblink.rb - sequence ID with database name
#
# Copyright:: Copyright (C) 2008
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
module Bio
require 'bio/sequence' unless const_defined?(:Sequence)
# Bio::Sequence::DBLink stores IDs with the database name.
# Its main purpose is to store database cross-reference information
# for a sequence entry.
class Sequence::DBLink
# creates a new DBLink object
def initialize(database, primary_id, *secondary_ids)
@database = database
@id = primary_id
@secondary_ids = secondary_ids
end
# Database name, or namespace identifier (String).
attr_reader :database
# Primary identifier (String)
attr_reader :id
# Secondary identifiers (Array of String)
attr_reader :secondary_ids
#--
# class methods
#++
# Parses DR line in EMBL entry, and returns a DBLink object.
def self.parse_embl_DR_line(str)
str = str.sub(/\.\s*\z/, '')
str.sub!(/\ADR /, '')
self.new(*(str.split(/\s*\;\s*/, 3)))
end
# Parses DR line in UniProt entry, and returns a DBLink object.
def self.parse_uniprot_DR_line(str)
str = str.sub(/\.\s*\z/, '')
str.sub!(/\ADR /, '')
self.new(*(str.split(/\s*\;\s*/)))
end
end #class Sequence::DBLink
end #module Bio
Version data entries
12 entries across 12 versions & 1 rubygems