# File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 40
40:   def complement_to_array_index
41:     helper_for_to_array_index(self.complement)
42:   end

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 29
29:   def primary_to_array_index
30:     helper_for_to_array_index(self.primary)
31:   end

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 52
52:   def to_array_index
53:     unless self.primary_to_array_index.size == self.complement_to_array_index.size
54:       err = "Primary and complement strand cut locations are not available in equal numbers.\n"
55:       err += "primary: #{self.primary_to_array_index.inspect}\n"
56:       err += "primary.size: #{self.primary_to_array_index.size}\n"
57:       err += "complement: #{self.complement_to_array_index.inspect}\n"
58:       err += "complement.size: #{self.complement_to_array_index.size}"
59:       raise IndexError, err
60:     end
61:     a = self.primary_to_array_index.zip(self.complement_to_array_index)
62:     CutLocations.new( *a.collect {|cl| CutLocationPair.new(cl)} )
63:   end

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 69
69:   def helper_for_to_array_index(a)
70:     minimum = (self.primary + self.complement).flatten
71:     minimum.delete(nil)
72:     minimum = minimum.sort.first
73: 
74:     return [] if minimum == nil  # no elements
75: 
76:     if minimum < 0
77:       calc = lambda do |n|
78:         unless n == nil
79:           n -= 1 unless n < 0
80:           n += minimum.abs
81:         end
82:         n
83:       end
84:     else
85:       calc = lambda do |n| 
86:         n -= 1 unless n == nil
87:         n
88:       end
89:     end
90: 
91:     a.collect(&calc)
92:   end

     # File lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb, line 94
 94:   def validate_args(args)
 95:     args.each do |a|
 96:       unless a.class == Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
 97:         err = "Not a CutLocationPairInEnzymeNotation\n"
 98:         err += "class: #{a.class}\n"
 99:         err += "inspect: #{a.inspect}"
100:         raise TypeError, err
101:       end
102:     end
103:   end