class Bio::Probcons::DEFAULT_PARSER

Data class for fasta-formatted multiple sequence alignment data, which is simply multiple entiries of fasta formatted sequences.

Constants

DELIMITER: delimiter for flatfile

Public Class Methods

new(str) click to toggle source

Creates a new data object. str should be a (multi-)fasta formatted string.

   # File lib/bio/appl/mafft/report.rb
46 def initialize(str)
47   ff = Bio::FlatFile.new(Bio::FastaFormat, StringIO.new(str))
48   @data = ff.to_a
49   @alignment = nil
50   @seq_method = nil
51 end

Public Instance Methods

alignment(method = nil) click to toggle source

Gets an multiple alignment. Returns a Bio::Alignment object. method should be one of :naseq, :aaseq, :seq, or nil (default). nil means to automatically determine nucleotide or amino acid.

This method returns previously parsed object if the same method is given (or guessed method is the same).

   # File lib/bio/appl/mafft/report.rb
60 def alignment(method = nil)
61   m = determine_seq_method(@data, method)
62   if !@alignment or m != @seq_method then
63     @seq_method = m
64     @alignment = do_parse(@data, @seq_method)
65   end
66   @alignment
67 end

entries() click to toggle source

Gets an array of the fasta formatted sequence objects. Returns an array of Bio::FastaFormat objects.

   # File lib/bio/appl/mafft/report.rb
71 def entries
72   @data
73 end