[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.13, 1.14 analysis_basic.rb, 1.6, 1.7

[Trevor Wennblom]

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

Modified Files:
	analysis.rb analysis_basic.rb 
Log Message:


Index: analysis_basic.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** analysis_basic.rb	5 Jan 2007 06:03:22 -0000	1.6
--- analysis_basic.rb	5 Jan 2007 06:11:15 -0000	1.7
***************
*** 90,94 ****
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Analysis::Fragments object populated with Bio::RestrictionEnzyme::Analysis::Fragment objects. (Note: unrelated to SequenceRange::Fragments)
    def cut_without_permutations( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
--- 90,94 ----
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to SequenceRange::Fragments)
    def cut_without_permutations( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
***************
*** 119,161 ****
    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
    
    #########
--- 119,123 ----
    end
  
! 
    
    #########
***************
*** 177,181 ****
      hsh.each do |permutation_id, sequence_range|
        sequence_range.fragments.for_display.each do |fragment|
!         ary << Fragment.new(fragment.primary, fragment.complement)
        end
      end
--- 139,143 ----
      hsh.each do |permutation_id, sequence_range|
        sequence_range.fragments.for_display.each do |fragment|
!         ary << Bio::RestrictionEnzyme::Fragment.new(fragment.primary, fragment.complement)
        end
      end

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** analysis.rb	5 Jan 2007 06:03:22 -0000	1.13
--- analysis.rb	5 Jan 2007 06:11:15 -0000	1.14
***************
*** 51,55 ****
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Analysis::Fragments object populated with Bio::RestrictionEnzyme::Analysis::Fragment objects.   (Note: unrelated to SequenceRange::Fragments)
    def cut( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?
--- 51,55 ----
    # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence.
    # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects.
!   # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects.   (Note: unrelated to SequenceRange::Fragments)
    def cut( sequence, *args )
      return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty?