Class: Bio::Alignment::MultiFastaFormat

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/mafft/report.rb

Overview

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

Direct Known Subclasses

MAFFT::Report

Constant Summary collapse

DELIMITER =

delimiter for flatfile

RS = nil

Instance Method Summary collapse

Constructor Details

#initialize(str) ⇒ MultiFastaFormat

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



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# File 'lib/bio/appl/mafft/report.rb', line 46

def initialize(str)
  ff = Bio::FlatFile.new(Bio::FastaFormat, StringIO.new(str))
  @data = ff.to_a
  @alignment = nil
  @seq_method = nil
end

Instance Method Details

#alignment(method = nil) ⇒ Object

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).



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# File 'lib/bio/appl/mafft/report.rb', line 60

def alignment(method = nil)
  m = determine_seq_method(@data, method)
  if !@alignment or m != @seq_method then
    @seq_method = m
    @alignment = do_parse(@data, @seq_method)
  end
  @alignment
end

#entries ⇒ Object

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



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# File 'lib/bio/appl/mafft/report.rb', line 71

def entries
  @data
end