Method: Bio::MAFFT::Report#initialize

Defined in:
lib/bio/appl/mafft/report.rb

#initialize(str, seqclass = nil) ⇒ Report

Creates a new Report object. str should be multi-fasta formatted text as a string.

Compatibility Note: the old usage (to get array of Bio::FastaFormat objects) is deprecated.

Compatibility Note 2: the argument seqclass is deprecated.

seqclass should be one of following: Class: Bio::Sequence::AA, Bio::Sequence::NA, … String: ‘PROTEIN’, ‘DNA’, …



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# File 'lib/bio/appl/mafft/report.rb', line 142

def initialize(str, seqclass = nil)
  if str.is_a?(Array) then
    warn "Array of Bio::FastaFormat objects will be no longer accepted."
    @data = str
  else
    super(str)
  end

  if seqclass then
    warn "the 2nd argument (seqclass) will be no deprecated."
    case seqclass
    when /PROTEIN/i
      @seqclass = Bio::Sequence::AA
    when /[DR]NA/i
      @seqclass = Bio::Sequence::NA
    else
      if seqclass.is_a?(Module) then
        @seqclass = seqclass
      else
        @seqclass = nil
      end
    end
  end
end