[BioRuby-cvs] bioruby/lib/bio/db/kegg kgml.rb,1.5,1.6

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv10653/db/kegg

Modified Files:
	kgml.rb 
Log Message:
some methods are renamed to avoid confusion
* :type -> :entry_type
* :type -> :category
* :map -> :pathway


Index: kgml.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/kgml.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** kgml.rb	19 Sep 2006 05:55:38 -0000	1.5
--- kgml.rb	24 Dec 2006 09:18:43 -0000	1.6
***************
*** 22,26 ****
  # <entry>
  #  :id -> :entry_id
! #  :type -> :entry_type
  #  names()
  #  <graphics>
--- 22,27 ----
  # <entry>
  #  :id -> :entry_id
! #  :type -> :category
! #  :map -> :pathway
  #  names()
  #  <graphics>
***************
*** 39,43 ****
  # === Examples
  #
! #  file = ARGF.read("kgml/hsa/hsa00010.xml")
  #  kgml = Bio::KEGG::KGML.new(file)
  #
--- 40,44 ----
  # === Examples
  #
! #  file = File.read("kgml/hsa/hsa00010.xml")
  #  kgml = Bio::KEGG::KGML.new(file)
  #
***************
*** 54,61 ****
  #    puts entry.entry_id
  #    puts entry.name
! #    puts entry.entry_type
  #    puts entry.link
  #    puts entry.reaction
! #    puts entry.map
  #    # <graphics> attributes
  #    puts entry.label	      # name
--- 55,62 ----
  #    puts entry.entry_id
  #    puts entry.name
! #    puts entry.category
  #    puts entry.link
  #    puts entry.reaction
! #    puts entry.pathway
  #    # <graphics> attributes
  #    puts entry.label	      # name
***************
*** 122,126 ****
  
    class Entry
!     attr_accessor :entry_id, :name, :entry_type, :link, :reaction, :map
      attr_accessor :label, :shape, :x, :y, :width, :height, :fgcolor, :bgcolor
      attr_accessor :components
--- 123,127 ----
  
    class Entry
!     attr_accessor :entry_id, :name, :category, :link, :reaction, :pathway
      attr_accessor :label, :shape, :x, :y, :width, :height, :fgcolor, :bgcolor
      attr_accessor :components
***************
*** 162,172 ****
        attr = node.attributes
        entry = Entry.new
!       entry.entry_id   = attr["id"].to_i
!       entry.name       = attr["name"]
!       entry.entry_type = attr["type"]
        # implied
!       entry.link       = attr["link"]
!       entry.reaction   = attr["reaction"]
!       entry.map        = attr["map"]
  
        node.elements.each("graphics") { |graphics|
--- 163,173 ----
        attr = node.attributes
        entry = Entry.new
!       entry.entry_id = attr["id"].to_i
!       entry.name     = attr["name"]
!       entry.category = attr["type"]
        # implied
!       entry.link     = attr["link"]
!       entry.reaction = attr["reaction"]
!       entry.pathway  = attr["map"]
  
        node.elements.each("graphics") { |graphics|