class Bio::Alignment::FactoryTemplate::FileInFileOutWithTree

Template class for alignment application factory. The program needs: input: file (cannot accept stdin), format = fasta format output: file (parser should be specified by DEFAULT_PARSER) Tree (*.dnd) output is also supported.

Attributes

output_dnd[R]

alignment guide tree generated by the program (*.dnd file)

Public Instance Methods

reset() click to toggle source
# File lib/bio/alignment.rb, line 2485
def reset
  @output_dnd = nil
  super
end

Private Instance Methods

_option_output_dndfile() click to toggle source

generates options specifying output tree file (*.dnd). returns an array of string

# File lib/bio/alignment.rb, line 2507
def _option_output_dndfile
  raise NotImplementedError
end
_query_local(fn_in, opt, data_stdin = nil) click to toggle source

Performs alignment

Calls superclass method Bio::Alignment::FactoryTemplate::WrapOutputTempfile#_query_local
# File lib/bio/alignment.rb, line 2492
def _query_local(fn_in, opt, data_stdin = nil)
  begin
    tf_dnd = _prepare_tempfile()
    opt = opt + _option_output_dndfile(tf_dnd.path)
    ret = super(fn_in, opt, data_stdin)
    tf_dnd.open
    @output_dnd = tf_dnd.read
  ensure
    tf_dnd.close(true) if tf_dnd
  end
  ret
end