class Bio::Alignment::FactoryTemplate::FileInFileOut
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)
Private Instance Methods
_option_input_stdin()
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generates options specifying that input is taken from stdin. returns an array of string
# File lib/bio/alignment.rb 2458 def _option_input_stdin 2459 raise 'input is always a file' 2460 end
_option_output_stdout()
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generates options specifying output to stdout. returns an array of string
# File lib/bio/alignment.rb 2464 def _option_output_stdout 2465 raise 'output is always a file' 2466 end