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Contents
#
# = bio/db/biosql/biosql_to_biosequence.rb - Bio::SQL::Sequence to Bio::Sequence adapter module
#
# Copyright:: Copyright (C) 2008
# Naohisa Goto <ng@bioruby.org>,
# Raoul Jean Pierre Bonnal
# License:: The Ruby License
#
# $Id:$
#
require 'bio/sequence'
require 'bio/sequence/adapter'
# Internal use only. Normal users should not use this module.
#
# Bio::SQL::Sequence to Bio::Sequence adapter module.
# It is internally used in Bio::SQL::Sequence#to_biosequence.
#
module Bio::Sequence::Adapter::BioSQL
extend Bio::Sequence::Adapter
private
def_biosequence_adapter :seq
def_biosequence_adapter :entry_id
def_biosequence_adapter :primary_accession
def_biosequence_adapter :secondary_accessions
def_biosequence_adapter :molecule_type
#--
#TODO: identify where is stored data_class in biosql
#++
def_biosequence_adapter :data_class
def_biosequence_adapter :definition, :description
def_biosequence_adapter :topology
def_biosequence_adapter :date_created
def_biosequence_adapter :date_modified
#do |bs|
# Date.parse(bs.date_modified.to_s).strftime("%d-%b-%Y").upcase
# end
def_biosequence_adapter :division
def_biosequence_adapter :sequence_version
def_biosequence_adapter :keywords
def_biosequence_adapter :species
def_biosequence_adapter :classification, :taxonomy
def_biosequence_adapter :references
def_biosequence_adapter :features
def_biosequence_adapter :comments
def_biosequence_adapter :other_seqids do |orig|
orig.identifier.split(',').collect do |dblink|
database, id = dblink.split(':')
Bio::Sequence::DBLink.new(database,id)
end
end
end #module Bio::Sequence::Adapter::BioSQL
Version data entries
10 entries across 10 versions & 3 rubygems