module Bio::RestrictionEnzyme::CutSymbol

Usage

#require 'bio/util/restriction_enzyme/cut_symbol'
require 'cut_symbol'
include Bio::RestrictionEnzyme::CutSymbol

cut_symbol                            # => "^"
set_cut_symbol('|')                   # => "|"
cut_symbol                            # => "|"
escaped_cut_symbol                    # => "\\|"
re_cut_symbol                         # => /\|/
set_cut_symbol('^')                   # => "^"
"abc^de" =~ re_cut_symbol             # => 3
"abc^de" =~ re_cut_symbol_adjacent    # => nil
"abc^^de" =~ re_cut_symbol_adjacent   # => 3
"a^bc^^de" =~ re_cut_symbol_adjacent  # => 4
"a^bc^de" =~ re_cut_symbol_adjacent   # => nil

Public Instance Methods

cut_symbol() click to toggle source

Get the token that's used as the cut symbol in a restriction enzyme sequece


Arguments

  • none

Returns

glyph

   # File lib/bio/util/restriction_enzyme/cut_symbol.rb
53 def cut_symbol; CutSymbol__.cut_symbol; end
escaped_cut_symbol() click to toggle source

Get the token that's used as the cut symbol in a restriction enzyme sequece with a back-slash preceding it.


Arguments

  • none

Returns

\glyph

   # File lib/bio/util/restriction_enzyme/cut_symbol.rb
62 def escaped_cut_symbol; CutSymbol__.escaped_cut_symbol; end
re_cut_symbol() click to toggle source

A Regexp of the cut_symbol.


Arguments

  • none

Returns

RegExp

   # File lib/bio/util/restriction_enzyme/cut_symbol.rb
80 def re_cut_symbol
81   %r"#{escaped_cut_symbol}"
82 end
re_cut_symbol_adjacent() click to toggle source

Used to check if multiple cut symbols are next to each other.


Arguments

  • none

Returns

RegExp

   # File lib/bio/util/restriction_enzyme/cut_symbol.rb
70 def re_cut_symbol_adjacent
71   %r"#{escaped_cut_symbol}{2}"
72 end
set_cut_symbol(glyph) click to toggle source

Set the token to be used as the cut symbol in a restriction enzyme sequece

Starts as +^+ character


Arguments

  • glyph: The single character to be used as the cut symbol in an enzyme sequence

Returns

glyph

   # File lib/bio/util/restriction_enzyme/cut_symbol.rb
43 def set_cut_symbol(glyph)
44   CutSymbol__.cut_symbol = glyph
45 end