Method: Bio::Alignment::EnumerableExtension#convert_unmatch

Defined in:
lib/bio/alignment.rb

#convert_unmatch(match_char = '.') ⇒ Object

This is the BioPerl’s AlignI::unmatch like method.

Changes second to last sequences’ sites match_char(default: ‘.’) to original sites’ characters.

Note that it is a destructive method.

For Hash, please use it carefully because the order of the sequences is inconstant.



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# File 'lib/bio/alignment.rb', line 690

def convert_unmatch(match_char = '.')
  #(BioPerl) AlignI::unmatch like method
  len = alignment_length
  firstseq = nil
  each_seq do |s|
    unless firstseq then
      firstseq = s
    else
      (0...len).each do |i|
        if s[i..i] == match_char then
          s[i..i] = (firstseq[i..i] or match_char)
        end
      end
    end
  end
  self
end