class Bio::EMBL

    # File lib/bio/db/embl/embl.rb
402 def cc
403   get('CC').to_s.gsub(/^CC   /, '')
404 end

    # File lib/bio/db/embl/embl.rb
130 def data_class
131   id_line('DATA_CLASS')
132 end

    # File lib/bio/db/embl/embl.rb
462 def date_created
463   parse_date(self.dt['created'])
464 end

    # File lib/bio/db/embl/embl.rb
457 def date_modified
458   parse_date(self.dt['updated'])
459 end

    # File lib/bio/db/embl/embl.rb
512 def dblinks
513   get('DR').split(/\n/).collect { |x|
514     Bio::Sequence::DBLink.parse_embl_DR_line(x)
515   }
516 end

    # File lib/bio/db/embl/embl.rb
140 def division
141   id_line('DIVISION')
142 end

    # File lib/bio/db/embl/embl.rb
182 def dt(key=nil)
183   unless @data['DT']
184     tmp = Hash.new
185     dt_line = self.get('DT').split(/\n/)
186     tmp['created'] = dt_line[0].sub(/\w{2}   /,'').strip
187     tmp['updated'] = dt_line[1].sub(/\w{2}   /,'').strip
188     @data['DT'] = tmp
189   end
190   if key
191     @data['DT'][key]
192   else
193     @data['DT']
194   end
195 end

    # File lib/bio/db/embl/embl.rb
381 def each_cds
382   ft.each do |cds_feature|
383     if cds_feature.feature == 'CDS'
384       yield cds_feature
385     end
386   end
387 end

    # File lib/bio/db/embl/embl.rb
390 def each_gene
391   ft.each do |gene_feature|
392     if gene_feature.feature == 'gene'
393       yield gene_feature
394     end
395   end
396 end

    # File lib/bio/db/embl/embl.rb
117 def entry
118   id_line('ENTRY_NAME')
119 end

    # File lib/bio/db/embl/embl.rb
477 def entry_version
478   parse_release_version(self.dt['updated'])[1]
479 end

    # File lib/bio/db/embl/embl.rb
326 def fh
327   fetch('FH')
328 end

    # File lib/bio/db/embl/embl.rb
337 def ft
338   unless @data['FT']
339     ary = Array.new
340     in_quote = false
341     @orig['FT'].each_line do |line|
342       next if line =~ /^FEATURES/
343 
344       #head = line[0,20].strip  # feature key (source, CDS, ...)
345       body = line[20,60].chomp # feature value (position, /qualifier=)
346       if line =~ /^FT {3}(\S+)/
347         ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
348       elsif body =~ /^ \// and not in_quote
349         ary.last.push(body)    # /q="data..., /q=data, /q
350 
351         if body =~ /=" / and body !~ /"$/
352           in_quote = true
353         end
354 
355       else
356         ary.last.last << body # ...data..., ...data..."
357 
358         if body =~ /"$/
359           in_quote = false
360         end
361       end
362     end
363 
364     ary.map! do |subary|
365       parse_qualifiers(subary)
366     end
367 
368     @data['FT'] = ary.extend(Bio::Features::BackwardCompatibility)
369   end
370   if block_given?
371     @data['FT'].each do |feature|
372       yield feature
373     end
374   else
375     @data['FT']
376   end
377 end

    # File lib/bio/db/embl/embl.rb
 89 def id_line(key=nil)
 90   unless @data['ID']
 91     tmp = Hash.new
 92     idline = fetch('ID').split(/; +/)         
 93     tmp['ENTRY_NAME'], tmp['DATA_CLASS'] = idline.shift.split(/ +/)
 94     if idline.first =~ /^SV/
 95       tmp['SEQUENCE_VERSION'] = idline.shift.split(' ').last
 96       tmp['TOPOLOGY'] = idline.shift
 97       tmp['MOLECULE_TYPE'] = idline.shift
 98       tmp['DATA_CLASS'] = idline.shift
 99     else
100       tmp['MOLECULE_TYPE'] = idline.shift
101     end
102     tmp['DIVISION'] = idline.shift
103     tmp['SEQUENCE_LENGTH'] = idline.shift.strip.split(' ').first.to_i
104 
105     @data['ID'] = tmp
106   end
107   
108   if key
109     @data['ID'][key]
110   else
111     @data['ID']
112   end
113 end

    # File lib/bio/db/embl/embl.rb
125 def molecule
126   id_line('MOLECULE_TYPE')
127 end

    # File lib/bio/db/embl/embl.rb
266 def os(num = nil)
267   unless @data['OS']
268     os = Array.new
269     tmp = fetch('OS')
270     if /([A-Z][a-z]* *[\w \:\'\+\-]+\w) *\(([\w ]+)\)\s*\z/ =~ tmp
271       org = $1
272       name = $2
273       os.push({'name' => name, 'os' => org})
274     else
275       os.push({'name' => nil, 'os' => tmp})
276     end
277     @data['OS'] = os
278   end
279   if num
280     # EX. "Trifolium repens (white clover)"
281     "#{@data['OS'][num]['os']} {#data['OS'][num]['name']"
282   end
283   @data['OS']
284 end

    # File lib/bio/db/embl/embl.rb
472 def release_created
473   parse_release_version(self.dt['created'])[0]
474 end

    # File lib/bio/db/embl/embl.rb
467 def release_modified
468   parse_release_version(self.dt['updated'])[0]
469 end

    # File lib/bio/db/embl/embl.rb
446 def seq
447   Bio::Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
448 end

    # File lib/bio/db/embl/embl.rb
146 def sequence_length
147   id_line('SEQUENCE_LENGTH')
148 end

    # File lib/bio/db/embl/embl.rb
519 def species
520   self.fetch('OS')
521 end

    # File lib/bio/db/embl/embl.rb
423 def sq(base = nil)
424   unless @data['SQ']
425     fetch('SQ') =~ \
426            /(\d+) BP\; (\d+) A; (\d+) C; (\d+) G; (\d+) T; (\d+) other;/
427     @data['SQ'] = {'ntlen' => $1.to_i, 'other' => $6.to_i,
428                    'a' => $2.to_i, 'c' => $3.to_i , 'g' => $4.to_i, 't' => $5.to_i}
429   else
430     @data['SQ']
431   end
432 
433   if base
434     @data['SQ'][base.downcase]
435   else
436     @data['SQ']
437   end
438 end

    # File lib/bio/db/embl/embl.rb
162 def sv
163   if (v = field_fetch('SV').sub(/;/,'')) == ""
164     [id_line['ENTRY_NAME'], id_line['SEQUENCE_VERSION']].join('.') 
165   else
166     v
167   end  
168 end

    # File lib/bio/db/embl/embl.rb
531 def to_biosequence
532   Bio::Sequence.adapter(self, Bio::Sequence::Adapter::EMBL)
533 end

    # File lib/bio/db/embl/embl.rb
134 def topology
135   id_line('TOPOLOGY')
136 end

    # File lib/bio/db/embl/embl.rb
169 def version
170   (sv.split(".")[1] || id_line['SEQUENCE_VERSION']).to_i
171 end