[BioRuby-cvs] bioruby/lib/bio/util sirna.rb,1.5,1.6

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory pub.open-bio.org:/tmp/cvs-serv27856/lib/bio/util

Modified Files:
	sirna.rb 
Log Message:
* Updated RDoc.


Index: sirna.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/sirna.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** sirna.rb	14 Nov 2005 14:47:59 -0000	1.5
--- sirna.rb	14 Nov 2005 15:44:30 -0000	1.6
***************
*** 2,17 ****
  # = bio/util/sirna.rb - Class for designing small inhibitory RNAs
  #
! # Copyright::    Copyright (C) 2004, 2005
! #        Itoshi NIKAIDO <dritoshi at gmail.com>
! # License::    LGPL
  #
  # $Id$
  #
! # = Bio::SiRNA - Designing siRNA.
  #
  # This class implements the selection rules described by Kumiko Ui-Tei
  # et al. (2004) and Reynolds et al. (2004).
  #
! # = Example
  #
  #  seq = Bio::Sequence::NA.new(ARGF.read)
--- 2,17 ----
  # = bio/util/sirna.rb - Class for designing small inhibitory RNAs
  #
! # Copyright::   Copyright (C) 2004, 2005
! #               Itoshi NIKAIDO <dritoshi at gmail.com>
! # License::     LGPL
  #
  # $Id$
  #
! # == Bio::SiRNA - Designing siRNA.
  #
  # This class implements the selection rules described by Kumiko Ui-Tei
  # et al. (2004) and Reynolds et al. (2004).
  #
! # == Example
  #
  #  seq = Bio::Sequence::NA.new(ARGF.read)
***************
*** 30,34 ****
  #  end
  #
! # = References
  # 
  # * Kumiko Ui-Tei et al.  Guidelines for the selection of highly effective
--- 30,34 ----
  #  end
  #
! # == References
  # 
  # * Kumiko Ui-Tei et al.  Guidelines for the selection of highly effective
***************
*** 39,54 ****
  #   Nature Biotech. 2004 22: 326-330.
  #
! # = ChangeLog
! #
! #   2005/03/21 Itoshi NIKAIDO <itoshi.nikaido at nifty.com>
! #   Bio::SiRNA#ShRNA_designer method was changed design method.
! #
! #   2004/06/25
! #   Bio::ShRNA class was added.
! #
! #   2004/06/17 Itoshi NIKAIDO <itoshi.nikaido at nifty.com>
! #   We can use shRNA loop sequence from piGene document.
! #
! # #--
  #
  #  This library is free software; you can redistribute it and/or
--- 39,43 ----
  #   Nature Biotech. 2004 22: 326-330.
  #
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 75,78 ****
--- 64,70 ----
    # = Bio::SiRNA
    # Designing siRNA.
+   #
+   # This class implements the selection rules described by Kumiko Ui-Tei
+   # et al. (2004) and Reynolds et al. (2004).
    class SiRNA
  
***************
*** 159,163 ****
      end
  
!     # == Bio::SiRNA::Pair
      class Pair
  
--- 151,155 ----
      end
  
!     # = Bio::SiRNA::Pair
      class Pair
  
***************
*** 205,210 ****
      end # class Pair
  
!     # == Bio::SiRNA::ShRNA
!     # Input is a Bio::SiRNA::Pair object (the target sequence).
      class ShRNA
  
--- 197,203 ----
      end # class Pair
  
! 
!     # = Bio::SiRNA::ShRNA
!     # Designing shRNA.
      class ShRNA
  
***************
*** 214,223 ****
        # aBio::Sequence::NA
        attr_accessor :bottom_strand
!     
        def initialize(pair)
          @pair = pair
        end
  
- 
        # only the 'BLOCK-iT' rule is implemented for now.
        def design(method = 'BLOCK-iT')
--- 207,216 ----
        # aBio::Sequence::NA
        attr_accessor :bottom_strand
! 
!       # Input is a Bio::SiRNA::Pair object (the target sequence).    
        def initialize(pair)
          @pair = pair
        end
  
        # only the 'BLOCK-iT' rule is implemented for now.
        def design(method = 'BLOCK-iT')
***************
*** 298,299 ****
--- 291,306 ----
  end  
  
+ =begin
+ 
+ = ChangeLog
+ 
+   2005/03/21 Itoshi NIKAIDO <itoshi.nikaido at nifty.com>
+   Bio::SiRNA#ShRNA_designer method was changed design method.
+ 
+   2004/06/25
+   Bio::ShRNA class was added.
+ 
+   2004/06/17 Itoshi NIKAIDO <itoshi.nikaido at nifty.com>
+   We can use shRNA loop sequence from piGene document.
+ 
+ =end