module Bio::EMBLDB::Common

   # File lib/bio/db/embl/common.rb
87 def initialize(entry)
88   super(entry, TAGSIZE)
89 end

    # File lib/bio/db/embl/common.rb
100 def ac
101   unless @data['AC']
102     tmp = Array.new
103     field_fetch('AC').split(/ /).each do |e|
104       tmp.push(e.sub(/;/,''))
105     end
106     @data['AC'] = tmp
107   end
108   @data['AC']
109 end

    # File lib/bio/db/embl/common.rb
114 def accession
115   ac[0]
116 end

    # File lib/bio/db/embl/common.rb
122 def de
123   unless @data['DE']
124     @data['DE'] = fetch('DE')
125   end
126   @data['DE']
127 end

    # File lib/bio/db/embl/common.rb
332 def dr
333   unless @data['DR']
334     tmp = Hash.new
335     self.get('DR').split(/\n/).each do |db|
336       a = db.sub(/^DR   /,'').sub(/.$/,'').strip.split(/;[ ]/)
337       dbname = a.shift
338       tmp[dbname] = Array.new unless tmp[dbname]
339       tmp[dbname].push(a)
340     end
341     @data['DR'] = tmp
342   end
343   if block_given?
344     @data['DR'].each do |k,v|
345       yield(k, v)
346     end
347   else
348     @data['DR']
349   end
350 end

    # File lib/bio/db/embl/common.rb
221 def kw
222   unless @data['KW']
223     if get('KW').size > 0
224       tmp = fetch('KW').sub(/.$/,'')
225       @data['KW'] = tmp.split(/;/).map {|e| e.strip }
226     else
227       @data['KW'] = []
228     end
229   end
230   @data['KW']
231 end

    # File lib/bio/db/embl/common.rb
204 def oc
205   unless @data['OC']
206     begin
207       @data['OC'] = fetch('OC').sub(/.$/,'').split(/;/).map {|e|
208         e.strip 
209       }
210     rescue NameError
211       nil
212     end
213   end
214   @data['OC']
215 end

    # File lib/bio/db/embl/common.rb
181 def og
182   unless @data['OG']
183     og = Array.new
184     if get('OG').size > 0
185       ogstr = fetch('OG')
186       ogstr.sub!(/\.$/,'')
187       ogstr.sub!(/ and/,'')
188       ogstr.sub!(/;/, ',')
189       ogstr.split(',').each do |tmp|
190         og.push(tmp.strip)
191       end
192     end
193     @data['OG'] = og
194   end
195   @data['OG']
196 end

    # File lib/bio/db/embl/common.rb
149 def os(num = nil)
150   unless @data['OS']
151     os = Array.new
152     fetch('OS').split(/, and|, /).each do |tmp|
153       if tmp =~ /([A-Z][a-z]* *[\w \:\'\+\-]+\w)/
154         org = $1
155         tmp =~ /(\(.+\))/ 
156         os.push({'name' => $1, 'os' => org})
157       else
158         raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n"
159       end
160     end
161     @data['OS'] = os
162   end
163   if num
164     # EX. "Trifolium repens (white clover)"
165     "#{@data['OS'][num]['os']} {#data['OS'][num]['name']"
166   end
167   @data['OS']
168 end

    # File lib/bio/db/embl/common.rb
243 def ref
244   unless @data['R']
245     ary = Array.new
246     get('R').split(/\nRN   /).each do |str|
247       raw = {'RN' => String.new, 'RC' => String.new,
248              'RP' => String.new, 'RX' => String.new,
249              'RA' => String.new, 'RT' => String.new,
250              'RL' => String.new, 'RG' => String.new}
251       str = 'RN   ' + str unless /^RN   / =~ str
252       str.split("\n").each do |line|
253         if /^(R[NPXARLCTG])   (.+)/ =~ line
254           raw[$1] += $2 + ' '
255         else
256           raise "Invalid format in R lines, \n[#{line}]\n"
257         end
258       end
259       raw.each_value {|v| 
260         v.strip! 
261         v.sub!(/^"/,'')
262         v.sub!(/;$/,'')
263         v.sub!(/"$/,'')
264       }
265       ary.push(raw)
266     end
267     @data['R'] = ary
268   end
269   @data['R']
270 end

    # File lib/bio/db/embl/common.rb
274 def references
275   unless @data['references']
276     ary = self.ref.map {|ent|
277       hash = Hash.new
278       ent.each {|key, value|
279         case key
280         when 'RN'
281           if /\[(\d+)\]/ =~ value.to_s
282             hash['embl_gb_record_number'] = $1.to_i
283           end
284         when 'RC'
285           unless value.to_s.strip.empty?
286             hash['comments'] ||= []
287             hash['comments'].push value
288           end
289         when 'RP'
290           hash['sequence_position'] = value
291         when 'RA'
292           a = value.split(/\, /)
293           a.each do |x|
294             x.sub!(/( [^ ]+)\z/, ",\\1")
295           end
296           hash['authors'] = a
297         when 'RT'
298           hash['title'] = value
299         when 'RL'
300           if /(.*) (\d+) *(\(([^\)]+)\))?(\, |\:)([a-zA-Z\d]+\-[a-zA-Z\d]+) *\((\d+)\)\.?\z/ =~ value.to_s
301             hash['journal'] = $1.rstrip
302             hash['volume']  = $2
303             hash['issue']   = $4
304             hash['pages']   = $6
305             hash['year']    = $7
306           else
307             hash['journal'] = value
308           end
309         when 'RX'  # PUBMED, DOI, (AGRICOLA)
310           value.split(/\. /).each {|item|
311             tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') }
312             hash[ tag.downcase ]  = xref
313           }
314         end
315       }
316       Reference.new(hash)
317     }
318     @data['references'] = ary.extend(Bio::References::BackwardCompatibility)
319   end
320   @data['references']
321 end