[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.51,0.52

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv1865

Modified Files:
	sequence.rb 
Log Message:
* changed to use autoload
* send to @seq when method_missing
* format_* methods are moved under the module Bio::Sequence::Format
* added skelton for output(:gff) to call Bio::Sequence::Format#format_gff


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.51
retrieving revision 0.52
diff -C2 -d -r0.51 -r0.52
*** sequence.rb	23 Jan 2006 04:13:36 -0000	0.51
--- sequence.rb	6 Feb 2006 14:10:01 -0000	0.52
***************
*** 29,60 ****
  #
  
- require 'bio/data/na'
- require 'bio/data/aa'
- require 'bio/data/codontable'
- require 'bio/location'
- 
- require 'bio/sequence/common'
- require 'bio/sequence/na'
- require 'bio/sequence/aa'
- require 'bio/sequence/format'
  require 'bio/sequence/compat'
  
  module Bio
  
- # Nucleic/Amino Acid sequence
- 
  class Sequence
  
    attr_accessor :entry_id, :definition, :features, :references, :comments,
      :date, :keywords, :dblinks, :taxonomy, :moltype, :seq
  
! #  def method_missing(*arg)
! #    @seq.send(*arg)
! #  end
  
    def output(style)
      case style
      when :fasta
        format_fasta
      when :genbank
        format_genbank
--- 29,62 ----
  #
  
  require 'bio/sequence/compat'
  
  module Bio
  
  class Sequence
  
+   def initialize(str)
+     @seq = str
+   end
+ 
+   def method_missing(*arg)
+     @seq.send(*arg)
+   end
+ 
    attr_accessor :entry_id, :definition, :features, :references, :comments,
      :date, :keywords, :dblinks, :taxonomy, :moltype, :seq
  
!   autoload :Common,  'bio/sequence/common'
!   autoload :NA,      'bio/sequence/na'
!   autoload :AA,      'bio/sequence/aa'
!   autoload :Generic, 'bio/sequence/generic'
!   autoload :Format,  'bio/sequence/format'
  
    def output(style)
+     extend Bio::Sequence::Format
      case style
      when :fasta
        format_fasta
+     when :gff
+       format_gff
      when :genbank
        format_genbank
***************
*** 62,69 ****
        format_embl
      end
-   end
- 
-   def initialize(str)
-     @seq = str
    end
  
--- 64,67 ----