class Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation

Inherits from DoubleStranded::CutLocations. Contains CutLocationPairInEnzymeNotation objects. Adds helper methods to convert from enzyme index notation to 0-based array index notation.

Public Instance Methods

complement_to_array_index() click to toggle source

Returns Array of locations of cuts on the complementary strand in 0-based array index notation.


Arguments

  • none

Returns

Array of locations of cuts on the complementary strand in 0-based array index notation.

# File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 39
def complement_to_array_index
  helper_for_to_array_index(self.complement)
end
primary_to_array_index() click to toggle source

Returns Array of locations of cuts on the primary strand in 0-based array index notation.


Arguments

  • none

Returns

Array of locations of cuts on the primary strand in 0-based array index notation.

# File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 28
def primary_to_array_index
  helper_for_to_array_index(self.primary)
end
to_array_index() click to toggle source

Returns the contents of the present CutLocationsInEnzymeNotation object as a CutLocations object with the contents converted from enzyme notation to 0-based array index notation.


Arguments

  • none

Returns

CutLocations

# File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 51
def to_array_index
  unless self.primary_to_array_index.size == self.complement_to_array_index.size
    err = "Primary and complement strand cut locations are not available in equal numbers.\n"
    err += "primary: #{self.primary_to_array_index.inspect}\n"
    err += "primary.size: #{self.primary_to_array_index.size}\n"
    err += "complement: #{self.complement_to_array_index.inspect}\n"
    err += "complement.size: #{self.complement_to_array_index.size}"
    raise IndexError, err
  end
  a = self.primary_to_array_index.zip(self.complement_to_array_index)
  CutLocations.new( *a.collect {|cl| CutLocationPair.new(cl)} )
end

Protected Instance Methods

helper_for_to_array_index(a) click to toggle source
# File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 68
def helper_for_to_array_index(a)
  minimum = (self.primary + self.complement).flatten
  minimum.delete(nil)
  minimum = minimum.sort.first

  return [] if minimum == nil  # no elements

  if minimum < 0
    calc = lambda do |n|
      unless n == nil
        n -= 1 unless n < 0
        n += minimum.abs
      end
      n
    end
  else
    calc = lambda do |n| 
      n -= 1 unless n == nil
      n
    end
  end

  a.collect(&calc)
end
validate_args(args) click to toggle source
# File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 93
def validate_args(args)
  args.each do |a|
    unless a.class == Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
      err = "Not a CutLocationPairInEnzymeNotation\n"
      err += "class: #{a.class}\n"
      err += "inspect: #{a.inspect}"
      raise TypeError, err
    end
  end
end