Class: Bioinform::ComplementableAlphabet

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

Overview

alphabets for DNA/RNA (which do have complements)

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(alphabet, complements) ⇒ ComplementableAlphabet

ComplementableAlphabet.new(, [:T,:G,:C,:A])

Raises:



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# File 'lib/bioinform/alphabet.rb', line 10

def initialize(alphabet, complements)
  @alphabet = alphabet.map{|letter| letter.upcase.to_sym }
  @complement_alphabet = complements.map{|letter| letter.upcase.to_sym }

  @complements_by_letters = Support.various_key_value_case_types( Hash[ @alphabet.zip(@complement_alphabet) ] )

  @index_by_letter = Support.various_key_case_types(Support.element_indices(@alphabet))
  raise Error, "Complement's complement should be original letter"  unless valid?
end

Instance Attribute Details

#alphabet ⇒ Object (readonly)

Returns the value of attribute alphabet.



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# File 'lib/bioinform/alphabet.rb', line 7

def alphabet
  @alphabet
end

#complement_alphabet ⇒ Object (readonly)

Returns the value of attribute complement_alphabet.



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# File 'lib/bioinform/alphabet.rb', line 7

def complement_alphabet
  @complement_alphabet
end

Instance Method Details

#==(other) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 57

def ==(other)
  @alphabet == other.alphabet && @complement_alphabet == other.complement_alphabet
end

#complement_index(index) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 52

def complement_index(index)
  letter = @complement_alphabet[index] || raise(Error, "Unknown letter-index #{index}")
  @index_by_letter[letter]
end

#complement_letter(letter) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 48

def complement_letter(letter)
  @complements_by_letters[letter] || raise(Error, "Unknown letter #{letter}")
end

#each_letter(&block) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 32

def each_letter(&block)
  @alphabet.each(&block)
end

#each_letter_index(&block) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 36

def each_letter_index(&block)
  @alphabet.each_index(&block)
end

#index_by_letter(letter) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 44

def index_by_letter(letter)
  @index_by_letter[letter] || raise(Error, "Unknown letter #{letter}")
end

#letter_by_index(index) ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 40

def letter_by_index(index)
  @alphabet[index] || raise(Error, "Unknown letter-index #{index}")
end

#size ⇒ Object 



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# File 'lib/bioinform/alphabet.rb', line 28

def size
  @alphabet.size
end