class Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair

Stores a single cut location pair in 0-based index notation for use with DoubleStranded enzyme sequences.

Attributes

complement[R]

Location of the cut on the complementary strand. Corresponds - or 'pairs' - to the primary cut. A value of nil is an explicit representation of 'no cut'.

primary[R]

Location of the cut on the primary strand. Corresponds - or 'pairs' - to the complement cut. A value of nil is an explicit representation of 'no cut'.

Public Class Methods

new( *pair ) click to toggle source

CutLocationPair constructor.

Stores a single cut location pair in 0-based index notation for use with DoubleStranded enzyme sequences.

Example:

clp = CutLocationPair.new(3,2)
clp.primary                    # 3
clp.complement                 # 2

Arguments

  • pair: May be two values represented as an Array, a Range, or a combination of Integer and nil values. The first value represents a cut on the primary strand, the second represents a cut on the complement strand.

Returns

nothing

Calls superclass method
# File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 47
def initialize( *pair )
  a = b = nil

  if pair[0].kind_of? Array
    a,b = init_with_array( pair[0] )

  # no idea why this barfs without the second half during test/runner.rb
  # are there two Range objects running around?
  elsif pair[0].kind_of? Range or (pair[0].class.to_s == 'Range')
  #elsif pair[0].kind_of? Range
    a,b = init_with_array( [pair[0].first, pair[0].last] )

  elsif pair[0].kind_of? Integer or pair[0].kind_of? NilClass
    a,b = init_with_array( [pair[0], pair[1]] )

  else
    raise ArgumentError, "#{pair[0].class} is an invalid class type to initalize CutLocationPair."
  end

  super( [a,b] )
  @primary = a
  @complement = b
  return
end

Protected Instance Methods

init_with_array( ary ) click to toggle source
# File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 76
def init_with_array( ary )
  validate_1(ary)
  a = ary.shift
  ary.empty? ? b = nil : b = ary.shift
  validate_2(a,b)
  [a,b]
end
validate_1( ary ) click to toggle source
# File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 84
def validate_1( ary )
  unless ary.size == 1 or ary.size == 2
    raise ArgumentError, "Must be one or two elements."
  end
end
validate_2( a, b ) click to toggle source
# File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 90
def validate_2( a, b )
  if (a != nil and a < 0) or (b != nil and b < 0)
    raise ArgumentError, "0-based index notation only.  Negative values are illegal."
  end

  if a == nil and b == nil
    raise ArgumentError, "Neither strand has a cut.  Ambiguous."
  end
end