Class: Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair

Inherits:
Array
  • Object
show all
Defined in:
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb

Overview

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

Direct Known Subclasses

CutLocationPairInEnzymeNotation

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(*pair) ⇒ CutLocationPair

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



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# File 'lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb', line 48

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

Instance Attribute Details

#complementObject (readonly)

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'.



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# File 'lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb', line 29

def complement
  @complement
end

#primaryObject (readonly)

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'.



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# File 'lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb', line 24

def primary
  @primary
end