class Bio::RestrictionEnzyme::Range::VerticalCutRange

VerticalCutRange provides an extremely raw, yet precise, method of defining the location of cuts on primary and complementary sequences.

Many VerticalCutRange objects are used with HorizontalCutRange objects to be contained in CutRanges to define the cut pattern that a specific enzyme may make.

VerticalCutRange takes up to four possible cuts, two on the primary strand and two on the complementary strand. In typical usage you will want to make a single cut on the primary strand and a single cut on the complementary strand.

However, you can construct it with whatever cuts you desire to accomadate the most eccentric of imaginary restriction enzymes.

Arguments

• p_cut_left: (optional) Left-most cut on the primary strand. nil to skip

• p_cut_right: (optional) Right-most cut on the primary strand. nil to skip

• c_cut_left: (optional) Left-most cut on the complementary strand. nil to skip

• c_cut_right: (optional) Right-most cut on the complementary strand. nil to skip

Returns

nothing

   # File lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
45 def initialize( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil )
46   @p_cut_left = p_cut_left
47   @p_cut_right = p_cut_right
48   @c_cut_left = c_cut_left
49   @c_cut_right = c_cut_right
50 
51   a = [@p_cut_left, @c_cut_left, @p_cut_right, @c_cut_right]
52   a.delete(nil)
53   a.sort!
54   @min = a.first
55   @max = a.last
56 
57   @range = nil
58   @range = (@min..@max) unless @min == nil or @max == nil
59   return
60 end

Check if a location falls within the minimum or maximum values of this range.

Arguments

• i: Location to check if it is included in the range

Returns

true or false

   # File lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
69 def include?(i)
70   return false if @range == nil
71   @range.include?(i)
72 end