module Bio::BioAlignment::Coerce
Public Class Methods
fetch_id(seq)
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Make BioRuby's entry_id compatible with id
# File lib/bio-alignment/coerce.rb, line 5 def Coerce::fetch_id seq if seq.respond_to?(:id) seq.id elsif seq.respond_to?(:entry_id) seq.entry_id else "id?" end end
fetch_seq(seq)
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Coerce
BioRuby's sequence objects to return the sequence itself
# File lib/bio-alignment/coerce.rb, line 16 def Coerce::fetch_seq seq if seq.respond_to?(:seq) seq.seq else seq end end
fetch_seq_string(seq)
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Coerce
sequence objects into a string
# File lib/bio-alignment/coerce.rb, line 25 def Coerce::fetch_seq_string seq s = fetch_seq(seq) if s.respond_to?(:join) s.join else s.to_s end end
to_elements(seq)
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Coerce
sequence objects into elements
# File lib/bio-alignment/coerce.rb, line 35 def Coerce::to_elements seq if seq.respond_to?(:to_elements) seq.to_elements else Elements.new(fetch_id(seq),fetch_seq(seq)) end end