[BioRuby-cvs] bioruby/lib/bio/db gff.rb,1.3,1.4

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv17970/lib/bio/db

Modified Files:
	gff.rb 
Log Message:
* Converted to RDoc.


Index: gff.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/gff.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** gff.rb	26 Sep 2005 13:00:06 -0000	1.3
--- gff.rb	7 Nov 2005 13:19:17 -0000	1.4
***************
*** 1,6 ****
  #
! # bio/db/gff.rb - GFF format class
  #
! #   Copyright (C) 2003 KATAYAMA Toshiaki <k at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,18 ----
  #
! # = bio/db/gff.rb - GFF format class
  #
! # Copyright::  Copyright (C) 2003 KATAYAMA Toshiaki <k at bioruby.org>
! # Licence::    LGPL
! #
! #  $Id$
! #
! # == Description
! #
! #
! # == Example
! # == References
! # * http://www.sanger.ac.uk/Software/formats/GFF/
! #
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 18,27 ****
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
  module Bio
  
    class GFF
      def initialize(str = '')
        @records = Array.new
--- 30,45 ----
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
  
  module Bio
  
+   # = GFF
    class GFF
+ 
+     # Returns
+     attr_accessor :records
+ 
+     #
      def initialize(str = '')
        @records = Array.new
***************
*** 30,36 ****
        end
      end
-     attr_accessor :records
  
      class Record
        def initialize(str)
          @comments = str.chomp[/#.*/]
--- 48,86 ----
        end
      end
  
+     # = GFF::Record
      class Record
+ 
+       # Returns
+       attr_accessor :seqname
+ 
+       # Returns
+       attr_accessor :source
+ 
+       # Returns
+       attr_accessor :feature
+ 
+       # Returns
+       attr_accessor :start
+ 
+       # Returns
+       attr_accessor :end
+ 
+       # Returns
+       attr_accessor :score
+ 
+       # Returns
+       attr_accessor :strand
+ 
+       # Returns
+       attr_accessor :frame
+ 
+       # Returns
+       attr_accessor :attributes
+ 
+       # Returns
+       attr_accessor :comments
+ 
+       #
        def initialize(str)
          @comments = str.chomp[/#.*/]
***************
*** 40,45 ****
          @attributes = parse_attributes(attributes) if attributes
        end
-       attr_accessor :seqname, :source, :feature, :start, :end, :score,
-         :strand, :frame, :attributes, :comments
  
        private
--- 90,93 ----
***************
*** 56,64 ****
--- 104,118 ----
    end
  
+   # = GFF2
    class GFF2 < GFF
+ 
+     #
      VERSION = 2
    end
  
+   # = GFF3
    class GFF3 < GFF
+ 
+     #
      VERSION = 3
    end
***************
*** 76,82 ****
    p Bio::GFF.new(ARGF.read)
  end
- 
- 
- =begin
-   http://www.sanger.ac.uk/Software/formats/GFF/
- =end
--- 130,131 ----