lib/bio/db/embl/common.rb in bio-1.2.1 vs lib/bio/db/embl/common.rb in bio-1.3.0

@@ -3,11 +3,11 @@
 #
 # Copyright::   Copyright (C) 2001-2006
 #               Mitsuteru C. Nakao <[e-mail]>
 # License::     The Ruby License
 #
-# $Id: common.rb,v 1.12 2007/04/05 23:35:40 trevor Exp $
+# $Id: common.rb,v 1.12.2.5 2008/05/07 12:22:10 ngoto Exp $
 #
 # == Description
 #
 # EMBL style databases class
 #
@@ -71,10 +71,11 @@
 #   http://www.expasy.org/sprot/userman.html
 #
 
 require 'bio/db'
 require 'bio/reference'
+require 'bio/compat/references'
 
 module Bio
 class EMBLDB
 module Common
 
@@ -268,36 +269,51 @@
   # returns Bio::Reference object from Bio::EMBLDB::Common#ref.
   # * Bio::EMBLDB::Common#ref -> Bio::References
   def references
     unless @data['references']
       ary = self.ref.map {|ent|
-        hash = Hash.new('')
+        hash = Hash.new
         ent.each {|key, value|
           case key
+          when 'RN'
+            if /\[(\d+)\]/ =~ value.to_s
+              hash['embl_gb_record_number'] = $1.to_i
+            end
+          when 'RC'
+            unless value.to_s.strip.empty?
+              hash['comments'] ||= []
+              hash['comments'].push value
+            end
+          when 'RP'
+            hash['sequence_position'] = value
           when 'RA'
-            hash['authors'] = value.split(/, /)
+            a = value.split(/\, /)
+            a.each do |x|
+              x.sub!(/( [^ ]+)\z/, ",\\1")
+            end
+            hash['authors'] = a
           when 'RT'
             hash['title'] = value
           when 'RL'
-            if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
-              hash['journal'] = $1
+            if /(.*) (\d+) *(\(([^\)]+)\))?(\, |\:)([a-zA-Z\d]+\-[a-zA-Z\d]+) *\((\d+)\)\.?\z/ =~ value.to_s
+              hash['journal'] = $1.rstrip
               hash['volume']  = $2
-              hash['issue']   = $3
-              hash['pages']   = $4
-              hash['year']    = $5
+              hash['issue']   = $4
+              hash['pages']   = $6
+              hash['year']    = $7
             else
               hash['journal'] = value
             end
-          when 'RX'  # PUBMED, MEDLINE
-            value.split('.').each {|item|
-              tag, xref = item.split(/; /).map {|i| i.strip }
+          when 'RX'  # PUBMED, DOI, (AGRICOLA)
+            value.split(/\. /).each {|item|
+              tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') }
               hash[ tag.downcase ]  = xref
             }
           end
         }
         Reference.new(hash)
       }
-      @data['references'] = References.new(ary)
+      @data['references'] = ary.extend(Bio::References::BackwardCompatibility)
     end
     @data['references']
   end