Method: Bio::Locations#to_s

Defined in:
lib/bio/location.rb

#to_s ⇒ Object

String representation.

Note: In some cases, it fails to detect whether “complement(join(…))” or “join(complement(..))”, and whether “complement(order(…))” or “order(complement(..))”.

Returns

String



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# File 'lib/bio/location.rb', line 511

def to_s
  return '' if @locations.empty?
  complement_join = false
  locs = @locations
  if locs.size >= 2 and locs.inject(true) do |flag, loc|
      # check if each location is complement
      (flag && (loc.strand == -1) && !loc.xref_id)
    end and locs.inject(locs[0].from) do |pos, loc|
      if pos then
        (pos >= loc.from) ? loc.from : false
      else
        false
      end
    end then
    locs = locs.reverse
    complement_join = true
  end
  locs = locs.collect do |loc|
    lt = loc.lt ? '<' : ''
    gt = loc.gt ? '>' : ''
    str = if loc.from == loc.to then
            "#{lt}#{gt}#{loc.from.to_i}"
          elsif loc.carat then
            "#{lt}#{loc.from.to_i}^#{gt}#{loc.to.to_i}"
          else
            "#{lt}#{loc.from.to_i}..#{gt}#{loc.to.to_i}"
          end
    if loc.xref_id and !loc.xref_id.empty? then
      str = "#{loc.xref_id}:#{str}"
    end
    if loc.strand == -1 and !complement_join then
      str = "complement(#{str})"
    end
    if loc.sequence then
      str = "replace(#{str},\"#{loc.sequence}\")"
    end
    str
  end
  if locs.size >= 2 then
    op = (self.operator || 'join').to_s
    result = "#{op}(#{locs.join(',')})"
  else
    result = locs[0]
  end
  if complement_join then
    result = "complement(#{result})"
  end
  result
end