[BioRuby-cvs] bioruby/lib/bio/sequence compat.rb,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory pub.open-bio.org:/tmp/cvs-serv2032/sequence

Modified Files:
	compat.rb 
Log Message:
* added RDoc header with Ruby's license
* changed to use autoload
* pikachu method is moved from lib/bio/sequence/na.rb
* changed to warn when to_fasta method is used in debug mode


Index: compat.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/compat.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** compat.rb	23 Jan 2006 04:13:36 -0000	1.1
--- compat.rb	6 Feb 2006 14:18:03 -0000	1.2
***************
*** 1,3 ****
! # only for backward compatibility, use Bio::Sequence#output(:fasta) instead
  
  module Bio
--- 1,12 ----
! #
! # = bio/sequence/compat.rb - methods for backward compatibility
! #
! # Copyright::   Copyright (C) 2006
! #               Toshiaki Katayama <k at bioruby.org>
! # License::     Ruby's
! #
! # $Id$
! #
! 
  
  module Bio
***************
*** 5,8 ****
--- 14,21 ----
  class Sequence
  
+   autoload :Common, 'bio/sequence/common'
+   autoload :NA,     'bio/sequence/na'
+   autoload :AA,     'bio/sequence/aa'
+ 
    def to_s
      String.new(@seq)
***************
*** 10,14 ****
    alias to_str to_s
  
!   module Common
  
    # Output the FASTA format string of the sequence.  The 1st argument is
--- 23,28 ----
    alias to_str to_s
  
! 
! module Common
  
    # Output the FASTA format string of the sequence.  The 1st argument is
***************
*** 16,19 ****
--- 30,34 ----
    # sequence will be folded.
    def to_fasta(header = '', width = nil)
+     warn "Bio::Sequence#to_fasta is obsolete. Use Bio::Sequence#output(:fasta) instead" if $DEBUG
      ">#{header}\n" +
      if width
***************
*** 26,29 ****
--- 41,45 ----
  end # Common
  
+ 
  class NA
  
***************
*** 32,37 ****
--- 48,58 ----
    end
  
+   def pikachu
+     self.dna.tr("atgc", "pika") # joke, of course :-)
+   end
+ 
  end # NA
  
+ 
  class AA
  
***************
*** 41,44 ****
--- 62,66 ----
  
  end # AA
+ 
  
  end # Sequence