Method: Bio::Alignment::OriginalAlignment#to_fasta_array

Defined in:
lib/bio/alignment.rb

#to_fasta_array(*arg) ⇒ Object

Convert to fasta format and returns an array of strings.

It will be obsoleted.



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# File 'lib/bio/alignment.rb', line 2096

def to_fasta_array(*arg)
  #(original)
  width = nil
  if arg[0].is_a?(Integer) then
    width = arg.shift
  end
  options = (arg.shift or {})
  width = options[:width] unless width
  if options[:avoid_same_name] then
    na = __clustal_avoid_same_name(self.keys, 30)
  else
    na = self.keys.collect { |k| k.to_s.gsub(/[\r\n\x00]/, ' ') }
  end
  a = self.collect do |s|
    ">#{na.shift}\n" +
      if width then
        s.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
      else
        s.to_s + "\n"
      end
  end
  a
end