class Bio::PROSITE

   # File lib/bio/db/prosite.rb
27 def initialize(entry)
28   super(entry, TAGSIZE)
29 end

    # File lib/bio/db/prosite.rb
468 def self.pa2re(pattern)
469   pattern = pattern.dup
470   pattern.gsub!(/\s/, '')     # remove white spaces
471   pattern.sub!(/\.$/, '')     # (1) remove trailing '.'
472   pattern.sub!(/^</, '^')     # (2) restricted to the N-terminal : `<'
473   pattern.sub!(/>$/, '$')     # (2) restricted to the C-terminal : `>'
474   pattern.gsub!(/\{(\w+)\}/) { |m|
475     '[^' + $1 + ']'           # (3) not accepted at a given position : '{}'
476   }
477   pattern.gsub!(/\(([\d,]+)\)/) { |m|
478     '{' + $1 + '}'            # (4) repetition of an element : (n), (n,m)
479   }
480   pattern.tr!('x', '.')       # (5) any amino acid is accepted : 'x'
481   pattern.tr!('-', '')        # (6) each element is separated by a '-'
482   Regexp.new(pattern, Regexp::IGNORECASE)
483 end

   # File lib/bio/db/prosite.rb
58 def ac
59   unless @data['AC']
60     @data['AC'] = fetch('AC').chomp(';')
61   end
62   @data['AC']
63 end

    # File lib/bio/db/prosite.rb
274 def cc
275   unless @data['CC']
276     hash = {}                 # temporal hash
277     fetch('CC').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
278       hash[k] = v
279     end
280     @data['CC'] = hash
281   end
282   @data['CC']
283 end

   # File lib/bio/db/prosite.rb
85 def de
86   field_fetch('DE')
87 end

   # File lib/bio/db/prosite.rb
45 def division
46   unless @data['TYPE']
47     name
48   end
49   @data['TYPE']
50 end

    # File lib/bio/db/prosite.rb
350 def dr
351   unless @data['DR']
352     hash = {}                 # temporal hash
353     if fetch('DR')
354       fetch('DR').scan(/(\w+)\s*, (\w+)\s*, (.);/).each do |a, e, c|
355         hash[a] = [e, c]      # SWISS-PROT : accession, entry, true/false
356       end
357     end
358     @data['DR'] = hash
359   end
360   @data['DR']
361 end

   # File lib/bio/db/prosite.rb
73 def dt
74   field_fetch('DT')
75 end

    # File lib/bio/db/prosite.rb
251 def false_neg
252   statistics['FALSE_NEG']
253 end

    # File lib/bio/db/prosite.rb
236 def false_pos
237   statistics['FALSE_POS']
238 end

    # File lib/bio/db/prosite.rb
241 def false_positive_hits
242   false_pos.first
243 end

    # File lib/bio/db/prosite.rb
246 def false_positive_sequences
247   false_pos.last
248 end

    # File lib/bio/db/prosite.rb
387 def list_falsenegative(by_name = nil)
388   list_xref('F', by_name)
389 end

    # File lib/bio/db/prosite.rb
392 def list_falsepositive(by_name = nil)
393   list_xref('P', by_name)
394 end

    # File lib/bio/db/prosite.rb
397 def list_potentialhit(by_name = nil)
398   list_xref('P', by_name)
399 end

    # File lib/bio/db/prosite.rb
382 def list_truepositive(by_name = nil)
383   list_xref('T', by_name)
384 end

    # File lib/bio/db/prosite.rb
402 def list_unknown(by_name = nil)
403   list_xref('?', by_name)
404 end

    # File lib/bio/db/prosite.rb
366 def list_xref(flag, by_name = nil)
367   ary = []
368   sp_xref.each do |sp_acc, value|
369     if value[1] == flag
370       if by_name
371         sp_name = value[0]
372         ary.push(sp_name)
373       else
374         ary.push(sp_acc)
375       end
376     end
377   end
378   return ary
379 end

    # File lib/bio/db/prosite.rb
112 def ma
113   field_fetch('MA')
114 end

    # File lib/bio/db/prosite.rb
499 def ma2re(matrix)
500   raise NotImplementedError
501 end

    # File lib/bio/db/prosite.rb
307 def max_repeat
308   comment['MAX-REPEAT'].to_i
309 end

   # File lib/bio/db/prosite.rb
37 def name
38   unless @data['ID']
39     @data['ID'], @data['TYPE'] = fetch('ID').chomp('.').split('; ')
40   end
41   @data['ID']
42 end

    # File lib/bio/db/prosite.rb
151 def nr
152   unless @data['NR']
153     hash = {}                 # temporal hash
154     fetch('NR').scan(%r{/(\S+)=([^;]+);}).each do |k, v|
155       if v =~ /^(\d+)\((\d+)\)$/
156         hits = $1.to_i                # the number of hits
157         seqs = $2.to_i                # the number of sequences
158         v = [hits, seqs]
159       elsif v =~ /([\d\.]+),(\d+)/
160         sprel = $1                    # the number of SWISS-PROT release
161         spseq = $2.to_i               # the number of SWISS-PROT sequences
162         v = [sprel, spseq]
163       else
164         v = v.to_i
165       end
166       hash[k] = v
167     end
168     @data['NR'] = hash
169   end
170   @data['NR']
171 end

    # File lib/bio/db/prosite.rb
 97 def pa
 98   field_fetch('PA')
 99   @data['PA'] = fetch('PA') unless @data['PA']
100   @data['PA'].gsub!(/\s+/, '') if @data['PA']
101   @data['PA']
102 end

    # File lib/bio/db/prosite.rb
485 def pa2re(pattern)
486   self.class.pa2re(pattern)
487 end

    # File lib/bio/db/prosite.rb
257 def partial
258   statistics['PARTIAL']
259 end

    # File lib/bio/db/prosite.rb
412 def pdb_xref
413   unless @data['3D']
414     @data['3D'] = fetch('3D').split(/; */)
415   end
416   @data['3D']
417 end

    # File lib/bio/db/prosite.rb
425 def pdoc_xref
426   @data['DO'] = fetch('DO').chomp(';')
427 end

    # File lib/bio/db/prosite.rb
206 def positive
207   statistics['POSITIVE']
208 end

    # File lib/bio/db/prosite.rb
211 def positive_hits
212   positive.first
213 end

    # File lib/bio/db/prosite.rb
216 def positive_sequences
217   positive.last
218 end

    # File lib/bio/db/prosite.rb
489 def re
490   self.class.pa2re(self.pa)
491 end

    # File lib/bio/db/prosite.rb
176 def release
177   statistics['RELEASE']
178 end

    # File lib/bio/db/prosite.rb
126 def ru
127   field_fetch('RU')
128 end

    # File lib/bio/db/prosite.rb
312 def site
313   if comment['SITE']
314     num, desc = comment['SITE'].split(',')
315   end
316   return [num.to_i, desc]
317 end

    # File lib/bio/db/prosite.rb
320 def skip_flag
321   if comment['SKIP-FLAG'] == 'TRUE'
322     return true
323   end
324 end

    # File lib/bio/db/prosite.rb
181 def swissprot_release_number
182   release.first
183 end

    # File lib/bio/db/prosite.rb
186 def swissprot_release_sequences
187   release.last
188 end

    # File lib/bio/db/prosite.rb
288 def taxon_range(expand = nil)
289   range = comment['TAXO-RANGE']
290   if range and expand
291     expand = []
292     range.scan(/./) do |x|
293       case x
294       when 'A'; expand.push('archaebacteria')
295       when 'B'; expand.push('bacteriophages')
296       when 'E'; expand.push('eukaryotes')
297       when 'P'; expand.push('prokaryotes')
298       when 'V'; expand.push('eukaryotic viruses')
299       end
300     end
301     range = expand
302   end
303   return range
304 end

    # File lib/bio/db/prosite.rb
191 def total
192   statistics['TOTAL']
193 end

    # File lib/bio/db/prosite.rb
196 def total_hits
197   total.first
198 end

    # File lib/bio/db/prosite.rb
201 def total_sequences
202   total.last
203 end

    # File lib/bio/db/prosite.rb
221 def unknown
222   statistics['UNKNOWN']
223 end

    # File lib/bio/db/prosite.rb
226 def unknown_hits
227   unknown.first
228 end

    # File lib/bio/db/prosite.rb
231 def unknown_sequences
232   unknown.last
233 end