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()
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Calls superclass method
Bio::Alignment::FactoryTemplate::Simple#reset
# File lib/bio/alignment.rb 2479 def reset 2480 @output_dnd = nil 2481 super 2482 end
Private Instance Methods
_option_output_dndfile()
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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)
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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