class Bio::Phylip::PhylipFormat

This is phylip multiple alignment format parser. The two formats, interleaved and non-interleaved, are automatically determined.

Attributes

alignment_length [R]

alignment length

number_of_sequences [R]

number of sequences

Public Class Methods

new (str)

Source

   # File lib/bio/appl/phylip/alignment.rb
26 def initialize(str)
27   @data = str.strip.split(/(?:\r\n|\r|\n)/)
28   @first_line = @data.shift
29   @number_of_sequences, @alignment_length =
30     @first_line.to_s.strip.split(/\s+/).collect { |x| x.to_i }
31 end

create a new object from a string

Public Instance Methods

alignment ()

Source

   # File lib/bio/appl/phylip/alignment.rb
54 def alignment
55   unless defined? @alignment then
56     do_parse
57     a = Bio::Alignment.new
58     (0...@number_of_sequences).each do |i|
59       a.add_seq(@sequences[i], @sequence_names[i])
60     end
61     @alignment = a
62   end
63   @alignment
64 end

Gets the alignment. Returns a Bio::Alignment object.

interleaved? ()

Source

   # File lib/bio/appl/phylip/alignment.rb
42 def interleaved?
43   unless defined? @interleaved_flag then
44     if /\A +/ =~ @data[1].to_s then
45       @interleaved_flag = false
46     else
47       @interleaved_flag = true
48     end
49   end
50   @interleaved_flag
51 end

If the alignment format is “interleaved”, returns true. If not, returns false. It would mistake to determine if the alignment is very short.