class Bio::FANTOM::MaXML::Sequence

Constants

Data_XPath

(MaXML sequence) fantom2.gsc.riken.go.jp/fantom/2.1/allseq.sep.xml.gz fantom2.gsc.riken.go.jp/fantom/2.1/repseq.sep.xml.gz

Private Class Methods

define_id_method(array) click to toggle source
    # File lib/bio/db/fantom.rb
251 def self.define_id_method(array)
252   array.each do |tagstr|
253     module_eval("
254       def #{tagstr}
255         unless defined?(@#{tagstr})
256           @#{tagstr} = gsub_entities(@elem.text('#{tagstr}'))
257           @#{tagstr} = altid('#{tagstr}') unless @#{tagstr}
258         end
259         @#{tagstr}
260       end
261     ")
262   end
263 end

Public Instance Methods

altid(t = nil) click to toggle source
    # File lib/bio/db/fantom.rb
219 def altid(t = nil)
220   unless defined?(@altid)
221     @altid = {}
222     @elem.each_element('altid') do |e|
223       @altid[e.attributes['type']] = gsub_entities(e.text)
224     end
225   end
226   if t then
227     @altid[t]
228   else
229     @altid
230   end
231 end
annotations() click to toggle source
    # File lib/bio/db/fantom.rb
241 def annotations
242   unless defined?(@annotations)
243     @annotations =
244       MaXML::Annotations.new(@elem.elements['annotations'])
245   end
246   @annotations
247 end
id_strings() click to toggle source
    # File lib/bio/db/fantom.rb
233 def id_strings
234   altid.values.sort.uniq
235 end
library_id() click to toggle source
    # File lib/bio/db/fantom.rb
237 def library_id
238   entry_id[0,2]
239 end