class Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation

Stores the cut location in thier enzyme index notation

May be initialized with a series of cuts or an enzyme pattern marked with cut symbols.

Enzyme index notation

1..n, value before 1 is -1

example
-3][-1][2][4][5

Negative values are used to indicate when a cut may occur at a specified distance before the sequence begins. This would be padded with 'n' nucleotides to represent wildcards.

Notes:

Attributes

max[R]

Last cut, in enzyme-index notation

min[R]

First cut, in enzyme-index notation

Public Class Methods

new(*a) click to toggle source

Constructor for CutLocationsInEnzymeNotation


Arguments

  • a: Locations of cuts represented as a string with cuts or an array of values

Examples:

  • n^ng^arraxt^n

  • 2

  • -1, 5

  • -1, 5
Returns

nothing

Calls superclass method
# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 58
def initialize(*a)
  a.flatten! # in case an array was passed as an argument

  if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol
    # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n'
    s = a[0]
    a = []
    i = -( s.tr(cut_symbol, '') =~ %r{[^n]} )  # First character that's not 'n'
    s.each_byte { |c| (a << i; next) if c.chr == cut_symbol; i += 1 }
    a.collect! { |n| n <= 0 ? n-1 : n } # 0 is not a valid enzyme index, decrement from 0 and all negative
  else
    a.collect! { |n| n.to_i } # Cut locations are always integers
  end

  validate_cut_locations( a )
  super(a)
  self.sort!
  @min = self.first
  @max = self.last
  self.freeze
end

Public Instance Methods

to_array_index() click to toggle source

Transform the cut locations from enzyme index notation to 0-based index notation.

input -> output
[  1, 2, 3 ] -> [ 0, 1, 2 ]
[  1, 3, 5 ] -> [ 0, 2, 4 ]
[ -1, 1, 2 ] -> [ 0, 1, 2 ]
[ -2, 1, 3 ] -> [ 0, 2, 4 ]

Arguments

  • none

Returns

Array of cuts in 0-based index notation

# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 93
def to_array_index
  return [] if @min == nil
  if @min < 0
    calc = lambda do |n| 
      n -= 1 unless n < 0
      n + @min.abs
    end
  else
    calc = lambda { |n| n - 1 }
  end
  self.collect(&calc)
end

Protected Instance Methods

validate_cut_locations( input_cut_locations ) click to toggle source
# File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb, line 110
def validate_cut_locations( input_cut_locations )
  unless input_cut_locations == input_cut_locations.uniq
    err = "The cut locations supplied contain duplicate values.  Redundant / undefined meaning.\n"
    err += "cuts: #{input_cut_locations.inspect}\n"
    err += "unique: #{input_cut_locations.uniq.inspect}"
    raise ArgumentError, err
  end

  if input_cut_locations.include?(nil)
    err = "The cut locations supplied contained a nil.  nil has no index for enzyme notation, alternative meaning is 'no cut'.\n"
    err += "cuts: #{input_cut_locations.inspect}"
    raise ArgumentError, err
  end

  if input_cut_locations.include?(0)
    err = "The cut locations supplied contained a '0'.  '0' has no index for enzyme notation, alternative meaning is 'no cut'.\n"
    err += "cuts: #{input_cut_locations.inspect}"
    raise ArgumentError, err
  end

end