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, line 2464
def _option_input_stdin
  raise 'input is always a file'
end
_option_output_stdout() click to toggle source

generates options specifying output to stdout. returns an array of string

# File lib/bio/alignment.rb, line 2470
def _option_output_stdout
  raise 'output is always a file'
end