class Bio::RestrictionEnzyme::Range::VerticalCutRange

FIXME docs are kind of out of date. Change this to VerticalAndHorizontalCutRange

Attributes

c_cut_left[R]
c_cut_right[R]
max[R]
min[R]
p_cut_left[R]
p_cut_right[R]
range[R]

Public Class Methods

new( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil ) click to toggle source

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, line 45
def initialize( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil )
  @p_cut_left = p_cut_left
  @p_cut_right = p_cut_right
  @c_cut_left = c_cut_left
  @c_cut_right = c_cut_right

  a = [@p_cut_left, @c_cut_left, @p_cut_right, @c_cut_right]
  a.delete(nil)
  a.sort!
  @min = a.first
  @max = a.last

  @range = nil
  @range = (@min..@max) unless @min == nil or @max == nil
  return
end

Public Instance Methods

include?(i) click to toggle source

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, line 69
def include?(i)
  return false if @range == nil
  @range.include?(i)
end