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:

0 is invalid as it does not refer to any index
nil is not allowed here as it has no meaning
nil values are kept track of in DoubleStranded::CutLocations as they need a reference point on the correlating strand. In DoubleStranded::CutLocations nil represents no cut or a partial digestion.

Attributes

max [R]

Last cut, in enzyme-index notation

min [R]

First cut, in enzyme-index notation

Public Class Methods

new (*a)

Source

   # File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
58 def initialize(*a)
59   a.flatten! # in case an array was passed as an argument
60 
61   if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol
62     # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n'
63     s = a[0]
64     a = []
65     i = -( s.tr(cut_symbol, '') =~ %r{[^n]} )  # First character that's not 'n'
66     s.each_byte { |c| (a << i; next) if c.chr == cut_symbol; i += 1 }
67     a.collect! { |n| n <= 0 ? n-1 : n } # 0 is not a valid enzyme index, decrement from 0 and all negative
68   else
69     a.collect! { |n| n.to_i } # Cut locations are always integers
70   end
71 
72   validate_cut_locations( a )
73   super(a)
74   self.sort!
75   @min = self.first
76   @max = self.last
77   self.freeze
78 end

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

Public Instance Methods

to_array_index ()

Source

    # File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
 93 def to_array_index
 94   return [] if @min == nil
 95   if @min < 0
 96     calc = lambda do |n| 
 97       n -= 1 unless n < 0
 98       n + @min.abs
 99     end
100   else
101     calc = lambda { |n| n - 1 }
102   end
103   self.collect(&calc)
104 end

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

Protected Instance Methods

validate_cut_locations ( input_cut_locations )

Source

    # File lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
110 def validate_cut_locations( input_cut_locations )
111   unless input_cut_locations == input_cut_locations.uniq
112     err = "The cut locations supplied contain duplicate values.  Redundant / undefined meaning.\n"
113     err += "cuts: #{input_cut_locations.inspect}\n"
114     err += "unique: #{input_cut_locations.uniq.inspect}"
115     raise ArgumentError, err
116   end
117 
118   if input_cut_locations.include?(nil)
119     err = "The cut locations supplied contained a nil.  nil has no index for enzyme notation, alternative meaning is 'no cut'.\n"
120     err += "cuts: #{input_cut_locations.inspect}"
121     raise ArgumentError, err
122   end
123 
124   if input_cut_locations.include?(0)
125     err = "The cut locations supplied contained a '0'.  '0' has no index for enzyme notation, alternative meaning is 'no cut'.\n"
126     err += "cuts: #{input_cut_locations.inspect}"
127     raise ArgumentError, err
128   end
129 
130 end