Method: Bio::Alignment::OriginalAlignment#do_align

Defined in:
lib/bio/alignment.rb

#do_align(factory) ⇒ Object

Performs multiple alignment by using external program.



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# File 'lib/bio/alignment.rb', line 2070

def do_align(factory)
  a0 = self.class.new
  (0...self.size).each { |i| a0.store(i, self.order(i)) }
  r = factory.query(a0)
  a1 = r.alignment
  a0.keys.each do |k|
    unless a1[k.to_s] then
      raise 'alignment result is inconsistent with input data'
    end
  end
  a2 = self.new
  a0.keys.each do |k|
    a2.store(self.keys[k], a1[k.to_s])
  end
  a2
end