[BioRuby-cvs] bioruby/lib/bio/util restriction_enzyme.rb,1.9,1.10

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory dev.open-bio.org:/tmp/cvs-serv15916

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 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** restriction_enzyme.rb	5 Jan 2007 06:03:22 -0000	1.9
--- restriction_enzyme.rb	5 Jan 2007 06:11:15 -0000	1.10
***************
*** 233,236 ****
--- 233,275 ----
      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
+       def complement; strip_and_sort(:complement); end
+ 
+       protected
+ 
+       def strip_and_sort( sym_strand )
+         self.map {|uf| uf.send( sym_strand ).tr(' ', '') }.sort
+       end
+     end
  end # RestrictionEnzyme
  end # Bio