[BioRuby-cvs] bioruby/lib/bio/db/embl embl.rb,1.29.2.2,1.29.2.3

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv7563/lib/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	embl.rb 
Log Message:
In Bio::EMBL#ft(), added "extend Bio::Features::BackwardCompatibility"
to keep backward compatibility.


Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.29.2.2
retrieving revision 1.29.2.3
diff -C2 -d -r1.29.2.2 -r1.29.2.3
*** embl.rb	20 Feb 2008 09:56:22 -0000	1.29.2.2
--- embl.rb	4 Mar 2008 10:56:42 -0000	1.29.2.3
***************
*** 257,261 ****
    def ft
      unless @data['FT']
!       @data['FT'] = Array.new
        in_quote = false
        @orig['FT'].each_line do |line|
--- 257,261 ----
    def ft
      unless @data['FT']
!       ary = Array.new
        in_quote = false
        @orig['FT'].each_line do |line|
***************
*** 265,271 ****
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           @data['FT'].push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           @data['FT'].last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
--- 265,271 ----
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           ary.last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
***************
*** 274,278 ****
  
          else
!           @data['FT'].last.last << body # ...data..., ...data..."
  
            if body =~ /"$/
--- 274,278 ----
  
          else
!           ary.last.last << body # ...data..., ...data..."
  
            if body =~ /"$/
***************
*** 282,289 ****
        end
  
!       @data['FT'].map! do |subary|
          parse_qualifiers(subary)
        end
  
      end
      if block_given?
--- 282,290 ----
        end
  
!       ary.map! do |subary|
          parse_qualifiers(subary)
        end
  
+       @data['FT'] = ary.extend(Bio::Features::BackwardCompatibility)
      end
      if block_given?
***************
*** 445,447 ****
      puts entry.to_biosequence.output(:embl)
    end
! end
\ No newline at end of file
--- 446,448 ----
      puts entry.to_biosequence.output(:embl)
    end
! end