class Bio::MAFFT::Report

MAFFT result parser class. MAFFT is a very fast multiple sequence alignment software.

Since a result of MAFFT is simply a multiple-fasta format, the significance of this class is to keep standard form and interface between Bio::ClustalW::Report.

Attributes

data[R]

sequence data. Returns an array of Bio::FastaFormat.

seqclass[R]

Sequence class (Bio::Sequence::AA, Bio::Sequence::NA, …)

Compatibility note: This method will be removed in the tufure.

Public Class Methods

new(str, seqclass = nil) click to toggle source

Creates a new Report object. str should be multi-fasta formatted text as a string.

Compatibility Note: the old usage (to get array of Bio::FastaFormat objects) is deprecated.

Compatibility Note 2: the argument seqclass is deprecated.

seqclass should be one of following: Class: Bio::Sequence::AA, Bio::Sequence::NA, … String: ‘PROTEIN’, ‘DNA’, …

Calls superclass method Bio::Alignment::MultiFastaFormat::new

    # File lib/bio/appl/mafft/report.rb
142 def initialize(str, seqclass = nil)
143   if str.is_a?(Array) then
144     warn "Array of Bio::FastaFormat objects will be no longer accepted."
145     @data = str
146   else
147     super(str)
148   end
149 
150   if seqclass then
151     warn "the 2nd argument (seqclass) will be no deprecated."
152     case seqclass
153     when /PROTEIN/i
154       @seqclass = Bio::Sequence::AA
155     when /[DR]NA/i
156       @seqclass = Bio::Sequence::NA
157     else
158       if seqclass.is_a?(Module) then
159         @seqclass = seqclass
160       else
161         @seqclass = nil
162       end
163     end
164   end
165 end

Public Instance Methods

align() click to toggle source

This method will be deprecated. Instead, please use alignment.

Gets an multiple alignment. Returns a Bio::Alignment object.

    # File lib/bio/appl/mafft/report.rb
185 def align
186   warn "Bio::MAFFT::Report#align is deprecated. Please use \'alignment\'."
187   alignment
188 end

alignment(method = nil) click to toggle source

Gets an multiple alignment. Returns a Bio::Alignment object.

Calls superclass method Bio::Alignment::MultiFastaFormat#alignment

    # File lib/bio/appl/mafft/report.rb
177 def alignment(method = nil)
178   super
179 end

to_a() click to toggle source

Compatibility note: Behavior of the method will be changed in the future.

Gets an array of the sequences. Returns an array of Bio::FastaFormat instances.

    # File lib/bio/appl/mafft/report.rb
206 def to_a
207   @data
208 end

to_fasta(*arg) click to toggle source

This will be deprecated. Instead, please use alignment.output_fasta.

Gets an fasta-format string of the sequences. Returns a string. Same as align.to_fasta. Please refer to Bio::Alignment#output_fasta for arguments.

    # File lib/bio/appl/mafft/report.rb
196 def to_fasta(*arg)
197   warn "Bio::MAFFT::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
198   alignment.output_fasta(*arg)
199 end