Class Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
In: lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
Parent: Array

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

Methods

init_with_array   new   validate_1   validate_2  

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 )

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

[Source]

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 48
48:   def initialize( *pair )
49:     a = b = nil
50: 
51:     if pair[0].kind_of? Array
52:       a,b = init_with_array( pair[0] )
53: 
54:     # no idea why this barfs without the second half during test/runner.rb
55:     # are there two Range objects running around?
56:     elsif pair[0].kind_of? Range or (pair[0].class.to_s == 'Range')
57:     #elsif pair[0].kind_of? Range
58:       a,b = init_with_array( [pair[0].first, pair[0].last] )
59: 
60:     elsif pair[0].kind_of? Integer or pair[0].kind_of? NilClass
61:       a,b = init_with_array( [pair[0], pair[1]] )
62: 
63:     else
64:       raise ArgumentError, "#{pair[0].class} is an invalid class type to initalize CutLocationPair."
65:     end
66: 
67:     super( [a,b] )
68:     @primary = a
69:     @complement = b
70:     return
71:   end

Protected Instance methods

init_with_array( ary )

[Source]

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 77
77:   def init_with_array( ary )
78:     validate_1(ary)
79:     a = ary.shift
80:     ary.empty? ? b = nil : b = ary.shift
81:     validate_2(a,b)
82:     [a,b]
83:   end
validate_1( ary )

[Source]

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 85
85:   def validate_1( ary )
86:     unless ary.size == 1 or ary.size == 2
87:       raise ArgumentError, "Must be one or two elements."
88:     end
89:   end
validate_2( a, b )

[Source]

    # File lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb, line 91
91:   def validate_2( a, b )
92:     if (a != nil and a < 0) or (b != nil and b < 0)
93:       raise ArgumentError, "0-based index notation only.  Negative values are illegal."
94:     end
95: 
96:     if a == nil and b == nil
97:       raise ArgumentError, "Neither strand has a cut.  Ambiguous."
98:     end
99:   end

[Validate]