Class: SequenceLogo::SequenceWithSNP

Inherits:
Object
  • Object
show all
Defined in:
lib/sequence_logo/data_models/sequence_with_snp.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(left, allele_variants, right, options = {}) ⇒ SequenceWithSNP

Returns a new instance of SequenceWithSNP.



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 7

def initialize(left, allele_variants, right, options = {})
  raise unless Sequence.valid_sequence?(left)
  raise unless Sequence.valid_sequence?(right)
  raise unless allele_variants.all?{|letter| %w[A C G T].include?(letter.upcase) }
  @left, @allele_variants, @right = left, allele_variants, right
  @name = options[:name] || (left + '_' + allele_variants.join('-') + '_' + right)
end

Instance Attribute Details

#allele_variants ⇒ Object (readonly)

Returns the value of attribute allele_variants.



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 6

def allele_variants
  @allele_variants
end

#left ⇒ Object (readonly)

Returns the value of attribute left.



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 6

def left
  @left
end

#name ⇒ Object (readonly)

Returns the value of attribute name.



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 6

def name
  @name
end

#right ⇒ Object (readonly)

Returns the value of attribute right.



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 6

def right
  @right
end

Class Method Details

.from_string(sequence, options = {}) ⇒ Object 



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 15

def self.from_string(sequence, options = {})
  left, mid, right = sequence.split(/[\[\]]/)
  allele_variants = mid.split('/')
  SequenceWithSNP.new(left, allele_variants, right, options)
end

Instance Method Details

#length ⇒ Object 



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 21

def length
  left.length + 1 + right.length
end

#render(canvas_factory) ⇒ Object 



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 31

def render(canvas_factory)
  canvas = LogoCanvas.new(canvas_factory)
  canvas.background(canvas_factory.background_fill)
  left.each_char{|letter| canvas.add_letter(letter) }
  canvas.add_position_ordered(snp_position_heights)
  right.each_char{|letter| canvas.add_letter(letter) }
  canvas.image
end

#revcomp ⇒ Object 



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# File 'lib/sequence_logo/data_models/sequence_with_snp.rb', line 25

def revcomp
  SequenceWithSNP.new(Sequence.revcomp(right),
                      allele_variants.map{|letter| Sequence.complement(letter) },
                      Sequence.revcomp(left))
end