[BioRuby-cvs] bioruby/lib/bio/util restriction_enzyme.rb, 1.10, 1.11

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory dev.open-bio.org:/tmp/cvs-serv16002

Modified Files:
	restriction_enzyme.rb 
Log Message:


Index: restriction_enzyme.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** restriction_enzyme.rb	5 Jan 2007 06:11:15 -0000	1.10
--- restriction_enzyme.rb	5 Jan 2007 06:33:01 -0000	1.11
***************
*** 233,265 ****
      end
  
!     # A Fragment is a sequence fragment composed of a primary and 
!     # complementary that would be found floating in solution after a full
!     # sequence is digested by a RestrictionEnzyme.
      #
      # You will notice that either the primary or complement strand will be
      # padded with spaces to make them line up according to the original DNA
!     # configuration before being cut.
      #
      # Example:
      #
!     #   primary =    "gattaca"
!     #   complement = "   atga"
      # 
!     # View these with the 'primary' and 'complement' methods.
      # 
!     # Bio::RestrictionEnzyme::Analysis::Fragment is a simple +Struct+ object.
      # 
!     # *Note: unrelated to SequenceRange::Fragment*
      Fragment = Struct.new(:primary, :complement)
  
!     # Fragments inherits from +Array+.
      #
!     # Fragments is a container for Fragment objects.  It adds the
      # methods +primary+ and +complement+ which returns an +Array+ of all
!     # respective strands from it's Fragment members.  Note that it will
!     # not return duplicate items and does not return the spacing that you would
      # find by accessing the members directly.
      #
!     # *Note: unrelated to SequenceRange::Fragments*
      class Fragments < Array
        def primary; strip_and_sort(:primary); end
--- 233,277 ----
      end
  
!     # A Bio::RestrictionEnzyme::Fragment is a DNA fragment composed of fused primary and 
!     # complementary strands that would be found floating in solution after a full
!     # sequence is digested by one or more RestrictionEnzymes.
      #
      # You will notice that either the primary or complement strand will be
      # padded with spaces to make them line up according to the original DNA
!     # configuration before they were cut.
      #
      # Example:
      #
!     # Fragment 1:
!     #   primary =    "attaca"
!     #   complement = "  atga"
      # 
!     # Fragment 2:
!     #   primary =    "g  "
!     #   complement = "cta"
      # 
!     # View these with the +primary+ and +complement+ methods.
      # 
!     # Bio::RestrictionEnzyme::Fragment is a simple +Struct+ object.
!     # 
!     # Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
      Fragment = Struct.new(:primary, :complement)
  
!     # Bio::RestrictionEnzyme::Fragments inherits from +Array+.
      #
!     # Bio::RestrictionEnzyme::Fragments is a container for Fragment objects.  It adds the
      # methods +primary+ and +complement+ which returns an +Array+ of all
!     # respective strands from it's Fragment members in alphabetically sorted 
!     # order.  Note that it will
!     # not return duplicate items and does not return the spacing/padding 
!     # that you would
      # find by accessing the members directly.
+     # 
+     # Example:
      #
!     #   primary = ['attaca', 'g']
!     #   complement = ['atga', 'cta']
!     #
!     # Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
      class Fragments < Array
        def primary; strip_and_sort(:primary); end