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)

Source

   # 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

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

Public Instance Methods

alignment (method = nil)

Source

   # 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

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).

entries ()

Source

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

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