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
2479 def reset
2480   @output_dnd = nil
2481   super
2482 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
2501 def _option_output_dndfile
2502   raise NotImplementedError
2503 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
2486 def _query_local(fn_in, opt, data_stdin = nil)
2487   begin
2488     tf_dnd = _prepare_tempfile()
2489     opt = opt + _option_output_dndfile(tf_dnd.path)
2490     ret = super(fn_in, opt, data_stdin)
2491     tf_dnd.open
2492     @output_dnd = tf_dnd.read
2493   ensure
2494     tf_dnd.close(true) if tf_dnd
2495   end
2496   ret
2497 end