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?'