in 'bio/alignment.rb': ### def self.extract_seq(s) seq = nil if seq.is_a?(Bio::Sequence) then seq = s else for m in [ :seq, :naseq, :aaseq ] begin seq = s.send(m) rescue NameError, ArgumentError seq = nil end break if seq end seq = s unless seq end seq end ### Should 'seq.is_a?' be 's.is_a?'