[BioRuby-cvs] bioruby/lib/bio/db transfac.rb,1.9,1.10

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv9041/lib/bio/db

Modified Files:
	transfac.rb 
Log Message:
* Bio::TF* is renamed to Bio::TRANSFAC::*


Index: transfac.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/transfac.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** transfac.rb	8 Sep 2005 01:22:11 -0000	1.9
--- transfac.rb	28 Nov 2005 04:57:33 -0000	1.10
***************
*** 26,104 ****
  module Bio
  
!   class TRANSFAC < EMBLDB
! 
!     DELIMITER	= RS = "\n//\n"
!     TAGSIZE	= 4
  
!     def initialize(entry)
!       super(entry, TAGSIZE)
!     end
  
!     # AC  Accession number                   (1 per entry)
!     #
!     #  AC  T00001   in the case of FACTOR
!     #  AC  M00001   in the case of MATRIX
!     #  AC  R00001   in the case of SITE
!     #  AC  G000001  in the case of GENE
!     #  AC  C00001   in the case of CLASS
!     #  AC  00001    in the case of CELL 
!     #
!     def ac
!       unless @data['AC']
!         @data['AC'] = fetch('AC')
!       end
!       @data['AC']
!     end
!     alias entry_id ac
  
!     # DT  Date                               (1 per entry)
!     #
!     #  DT  DD.MM.YYYY (created); ewi.
!     #  DT  DD.MM.YYYY (updated); mpr.
!     #
!     def dt
!       field_fetch('DT')
      end
!     alias date dt
  
!     def cc
!       field_fetch('CC')
!     end
!     alias comment cc
  
!     def os
!       field_fetch('OS')
!     end
!     alias org_species os
  
!     def oc
!       field_fetch('OC')
!     end
!     alias org_class oc
  
!     def rn
!       field_fetch('RN')
!     end
!     alias ref_no rn
  
!     def ra
!       field_fetch('RA')
!     end
!     alias ref_authors ra
  
!     def rt
!       field_fetch('RT')
!     end
!     alias ref_title rt
  
!     def rl
!       field_fetch('RL')
!     end
!     alias ref_data rl
  
    end
  
  
!   class TFMATRIX < TRANSFAC
  
      def initialize(entry)
--- 26,102 ----
  module Bio
  
! class TRANSFAC < EMBLDB
  
!   DELIMITER	= RS = "\n//\n"
!   TAGSIZE	= 4
  
!   def initialize(entry)
!     super(entry, TAGSIZE)
!   end
  
!   # AC  Accession number                   (1 per entry)
!   #
!   #  AC  T00001   in the case of FACTOR
!   #  AC  M00001   in the case of MATRIX
!   #  AC  R00001   in the case of SITE
!   #  AC  G000001  in the case of GENE
!   #  AC  C00001   in the case of CLASS
!   #  AC  00001    in the case of CELL 
!   #
!   def ac
!     unless @data['AC']
!       @data['AC'] = fetch('AC')
      end
!     @data['AC']
!   end
!   alias entry_id ac
  
!   # DT  Date                               (1 per entry)
!   #
!   #  DT  DD.MM.YYYY (created); ewi.
!   #  DT  DD.MM.YYYY (updated); mpr.
!   #
!   def dt
!     field_fetch('DT')
!   end
!   alias date dt
  
!   def cc
!     field_fetch('CC')
!   end
!   alias comment cc
  
!   def os
!     field_fetch('OS')
!   end
!   alias org_species os
  
!   def oc
!     field_fetch('OC')
!   end
!   alias org_class oc
  
!   def rn
!     field_fetch('RN')
!   end
!   alias ref_no rn
  
!   def ra
!     field_fetch('RA')
!   end
!   alias ref_authors ra
  
!   def rt
!     field_fetch('RT')
!   end
!   alias ref_title rt
  
+   def rl
+     field_fetch('RL')
    end
+   alias ref_data rl
  
  
!   class MATRIX < TRANSFAC
  
      def initialize(entry)
***************
*** 151,155 ****
  
  
!   class TFSITE < TRANSFAC
  
      def initialize(entry)
--- 149,153 ----
  
  
!   class SITE < TRANSFAC
  
      def initialize(entry)
***************
*** 209,213 ****
  
  
!   class TFFACTOR < TRANSFAC
  
      def initialize(entry)
--- 207,211 ----
  
  
!   class FACTOR < TRANSFAC
  
      def initialize(entry)
***************
*** 303,307 ****
  
  
!   class TFCELL < TRANSFAC
  
      def initialize(entry)
--- 301,305 ----
  
  
!   class CELL < TRANSFAC
  
      def initialize(entry)
***************
*** 317,321 ****
  
  
!   class TFCLASS < TRANSFAC
  
      def initialize(entry)
--- 315,319 ----
  
  
!   class CLASS < TRANSFAC
  
      def initialize(entry)
***************
*** 346,350 ****
  
  
!   class TFGENE < TRANSFAC
  
      def initialize(entry)
--- 344,348 ----
  
  
!   class GENE < TRANSFAC
  
      def initialize(entry)
***************
*** 384,387 ****
    end
  
! end
  
--- 382,387 ----
    end
  
! end # class TRANSFAC
! 
! end # module Bio