# File lib/bio/appl/psort/report.rb, line 36
def self.default_parser(output_report)
  rpt = self.new
  rpt.raw = output_report
  query_info = output_report.scan(%r^Query Information\n\n(.+?)\n\n/)[0][0].split(%r\n/)
  result_info = output_report.scan(%r^Result Information\n\n(.+?)\n\n\*/)[0][0]
  step1 = output_report.scan(%r^\*\*\* Reasoning Step: 1\n\n(.+?)\n\n/)[0][0]
  step2 = output_report.scan(%r^\*\*\* Reasoning Step: 2\n\n(.+?)\n\n/)[0][0]
  final_result = output_report.scan(%r\n\n----- Final Results -----\n\n(.+?)\n\n\n/)[0][0]

  rpt.entry_id = query_info[2].scan(%r^>(\S+) */).to_s
  rpt.origin   = query_info[0].scan(%rORIGIN (\w+)/).to_s
  rpt.sequence = Bio::Sequence::AA.new(query_info[3..query_info.size].to_s)
  # rpt.reasoning

  rpt.final_result = final_result.split(%r\n/).map {|x|
    x = x.strip.split(%r---/).map {|y| y.strip }
    { 'prediction' => x[0], 
      'certainty'  => x[1].scan(%rCertainty= (\d\.\d{3})/).to_s,
      'comment'    => x[1].scan(%r\((\w+)\)/).to_s
    }
  }
  return rpt
end

# File lib/bio/appl/psort/report.rb, line 72
def initialize(entry_id = '', origin = '', title = '', sequence = '',
               result_info = '', reasoning = {}, final_result = [])
  @entry_id = entry_id
  @origin = origin
  @title = title
  @sequence = sequence
  @result_info = result_info
  @reasoning = reasoning
  @final_result = final_result
  @raw = ''
end

# File lib/bio/appl/psort/report.rb, line 31
def self.parser(output_report)
  self.default_parser(output_report)
end