class Bio::RestrictionEnzyme::Range::HorizontalCutRange

   # File lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
22 def initialize( left, right=left )
23   raise "left > right" if left > right
24 
25   # The 'range' here is actually off by one on the left
26   # side in relation to a normal CutRange, so using the normal
27   # variables from CutRange would result in bad behavior.
28   #
29   # See below - the first horizontal cut is the primary cut plus one.
30   #
31   #    1 2 3 4 5 6 7
32   #    G A|T T A C A
33   #       +-----+
34   #    C T A A T|G T
35   #    1 2 3 4 5 6 7
36   #
37   # Primary cut = 2
38   # Complement cut = 5
39   # Horizontal cuts = 3, 4, 5
40 
41   @p_cut_left = nil
42   @p_cut_right = nil
43   @c_cut_left = nil
44   @c_cut_right = nil
45   @min = left  # NOTE this used to be 'nil', make sure all tests work
46   @max = right # NOTE this used to be 'nil', make sure all tests work
47   @range = (@min..@max) unless @min == nil or @max == nil # NOTE this used to be 'nil', make sure all tests work
48   
49 
50   @hcuts = (left..right)
51 end

   # File lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
60 def include?(i)
61   @range.include?(i)
62 end