[BioRuby-cvs] bioruby/lib/bio/db/kegg orthology.rb,1.8,1.9

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv16350/bio/db/kegg

Modified Files:
	orthology.rb 
Log Message:
* The official name of the KEGG KO database is determined to KEGG ORTHOLOGY,
  so the module is renamed. I made CVS trick that mv the file in the repository
  so that we can track the history.


Index: orthology.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/orthology.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** orthology.rb	5 Apr 2007 15:37:50 -0000	1.8
--- orthology.rb	5 Apr 2007 15:42:59 -0000	1.9
***************
*** 1,7 ****
  #
! # = bio/db/kegg/ortholog.rb - KEGG ORTHOLOG database class
  #
  # Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
  #
  # $Id$
--- 1,8 ----
  #
! # = bio/db/kegg/orthology.rb - KEGG ORTHOLOGY database class
  #
  # Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
+ # License::    The Ruby License
  #
  # $Id$
***************
*** 20,26 ****
  #
  # * http://www.genome.jp/dbget-bin/get_htext?KO
! # * ftp://ftp.genome.jp/pub/kegg/tarfiles/ko
  #
! class ORTHOLOG < KEGGDB
    
    DELIMITER	= RS = "\n///\n"
--- 21,27 ----
  #
  # * http://www.genome.jp/dbget-bin/get_htext?KO
! # * ftp://ftp.genome.jp/pub/kegg/genes/ko
  #
! class ORTHOLOGY < KEGGDB
    
    DELIMITER	= RS = "\n///\n"
***************
*** 83,87 ****
    end
    
! end # KO
      
  end # KEGG
--- 84,88 ----
    end
    
! end # ORTHOLOGY
      
  end # KEGG
***************
*** 95,99 ****
  
    flat = Bio::Fetch.query('ko', 'K00001')
!   entry = Bio::KEGG::KO.new(flat)
  
    p entry.entry_id
--- 96,100 ----
  
    flat = Bio::Fetch.query('ko', 'K00001')
!   entry = Bio::KEGG::ORTHOLOGY.new(flat)
  
    p entry.entry_id