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, line 2485 def reset @output_dnd = nil super 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, line 2507 def _option_output_dndfile raise NotImplementedError 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, 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