Class: Codon

Inherits:
Object
  • Object
show all
Defined in:
lib/genetic_code.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(seq) ⇒ Codon

Returns a new instance of Codon.



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# File 'lib/genetic_code.rb', line 101

def initialize seq
  @seq = seq
  @aa = GeneticCode.aa_for seq
  @aliases = @aa.codons
end

Instance Attribute Details

#aa ⇒ Object (readonly)

Returns the value of attribute aa.



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# File 'lib/genetic_code.rb', line 100

def aa
  @aa
end

#aliases ⇒ Object (readonly)

Returns the value of attribute aliases.



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# File 'lib/genetic_code.rb', line 100

def aliases
  @aliases
end

#seq ⇒ Object (readonly)

Returns the value of attribute seq.



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# File 'lib/genetic_code.rb', line 100

def seq
  @seq
end

Class Method Details

.[](seq) ⇒ Object 



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# File 'lib/genetic_code.rb', line 89

def [] seq
  @codons ||= {}
  @codons[seq] ||= build_codon seq
end

.build_codon(seq) ⇒ Object 



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# File 'lib/genetic_code.rb', line 94

def build_codon seq
  return nil unless seq.is_a?(Symbol) && seq.to_s =~ /^[ATGC]{3}$/
  new seq
end

Instance Method Details

#compute_degeneracy ⇒ Object 



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# File 'lib/genetic_code.rb', line 119

def compute_degeneracy
  3.times.map do |i|
    [ "A", "T", "G", "C" ].count do |n|
      mut = seq.to_s
      mut[i] = n
      @aliases.include? mut.to_sym
    end
  end
end

#degeneracy ⇒ Object 



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# File 'lib/genetic_code.rb', line 107

def degeneracy
  @degeneracy ||= compute_degeneracy
end

#distance_to(codon) ⇒ Object 



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# File 'lib/genetic_code.rb', line 111

def distance_to codon
  s1 = seq.to_s
  s2 = codon.seq.to_s
  3.times.count do |i|
    s1[i] != s2[i]
  end
end