Class Bio::Phylip::PhylipFormat
In: lib/bio/appl/phylip/alignment.rb
Parent: Object

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

Methods

alignment   interleaved?   new  

Attributes

alignment_length  [R]  alignment length
number_of_sequences  [R]  number of sequences

Public Class methods

new(str)

create a new object from a string

[Source]

    # File lib/bio/appl/phylip/alignment.rb, line 26
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

Public Instance methods

alignment()

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

[Source]

    # File lib/bio/appl/phylip/alignment.rb, line 54
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
interleaved?()

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

[Source]

    # File lib/bio/appl/phylip/alignment.rb, line 42
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

[Validate]