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#
# bio/util/restriction_enzyme/range/vertical_cut_range.rb -
#
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License:: The Ruby License
#
module Bio
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
class RestrictionEnzyme
class Range
# FIXME docs are kind of out of date. Change this to VerticalAndHorizontalCutRange
class VerticalCutRange < CutRange
attr_reader :p_cut_left, :p_cut_right
attr_reader :c_cut_left, :c_cut_right
attr_reader :min, :max
attr_reader :range
# 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
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
# 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+
def include?(i)
return false if @range == nil
@range.include?(i)
end
end # VerticalCutRange
end # Range
end # RestrictionEnzyme
end # Bio
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