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() click to toggle source

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() click to toggle source

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