Module: Bio::BioAlignment::PhylipOutput

Defined in:
lib/bio-alignment/format/phylip.rb

Class Method Summary collapse

Class Method Details

.header(alignment) ⇒ Object

Calculate header info from alignment and return as string



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# File 'lib/bio-alignment/format/phylip.rb', line 5

def PhylipOutput::header alignment
  "#{alignment.size} #{alignment[0].length}\n"
end

.to_paml(seq, size = 60) ⇒ Object

Output sequence PAML style and return as a multi-line string



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# File 'lib/bio-alignment/format/phylip.rb', line 10

def PhylipOutput::to_paml seq, size=60
  buf = seq.id+"\n"
  coding = if seq.kind_of?(CodonSequence) 
           seq.to_nt
         else
           seq.to_s
         end
  coding.scan(/.{1,#{size}}/).each do | section |
    buf += section + "\n"
  end
  buf
end