module Bio::BioAlignment::PhylipOutput
Public Class Methods
header(alignment)
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Calculate header info from alignment and return as string
# 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)
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Output sequence PAML style and return as a multi-line string
# 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