[BioRuby-cvs] bioruby/lib/bio/db/embl common.rb,1.12.2.2,1.12.2.3

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv12842/lib/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb 
Log Message:
Part of changes made between 1.12 and 1.12.2.1 is incorporated with
modifications.


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.12.2.2
retrieving revision 1.12.2.3
diff -C2 -d -r1.12.2.2 -r1.12.2.3
*** common.rb	23 Apr 2008 17:34:15 -0000	1.12.2.2
--- common.rb	23 Apr 2008 18:04:51 -0000	1.12.2.3
***************
*** 74,77 ****
--- 74,78 ----
  require 'bio/db'
  require 'bio/reference'
+ require 'bio/compat/references'
  
  module Bio
***************
*** 274,279 ****
          ent.each {|key, value|
            case key
            when 'RA'
!             hash['authors'] = value.split(/, /)
            when 'RT'
              hash['title'] = value
--- 275,288 ----
          ent.each {|key, value|
            case key
+           when 'RN'
+             if /\[(\d+)\]/ =~ value.to_s
+               hash['embl_gb_record_number'] = $1.to_i
+             end
+           when 'RC'
+             hash['comment'] = value
+           when 'RP'
+             hash['sequence_position'] = value
            when 'RA'
!             hash['authors'] = value.split(/\, /)
            when 'RT'
              hash['title'] = value
***************
*** 288,292 ****
                hash['journal'] = value
              end
!           when 'RX'  # PUBMED, MEDLINE
              value.split(/\. /).each {|item|
                tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') }
--- 297,301 ----
                hash['journal'] = value
              end
!           when 'RX'  # PUBMED, DOI, (AGRICOLA)
              value.split(/\. /).each {|item|
                tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') }
***************
*** 297,301 ****
          Reference.new(hash)
        }
!       @data['references'] = References.new(ary)
      end
      @data['references']
--- 306,310 ----
          Reference.new(hash)
        }
!       @data['references'] = ary.extend(Bio::References::BackwardCompatibility)
      end
      @data['references']