Module Bio::Alignment::OriginalPrivate
In: lib/bio/alignment.rb  (CVS)

Methods

extract_key   extract_seq  

Public Instance methods

extract_key(obj)

Gets the name or the definition of the sequence from given object.

[Source]

# File lib/bio/alignment.rb, line 1498
      def extract_key(obj)
        sn = nil
        for m in [ :definition, :entry_id ]
          begin
            sn = obj.send(m)
          rescue NameError, ArgumentError
            sn = nil
          end
          break if sn
        end
        sn
      end
extract_seq(obj)

Gets the sequence from given object.

[Source]

# File lib/bio/alignment.rb, line 1478
      def extract_seq(obj)
        seq = nil
        if obj.is_a?(Bio::Sequence::NA) or obj.is_a?(Bio::Sequence::AA) then
          seq = obj
        else
          for m in [ :seq, :naseq, :aaseq ]
            begin
              seq = obj.send(m)
            rescue NameError, ArgumentError
              seq = nil
            end
            break if seq
          end
          seq = obj unless seq
        end
        seq
      end

[Validate]