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)

Source

    # 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

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

Public Instance Methods

align ()

Source

    # 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

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

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

alignment (method = nil)

Source

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

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

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

to_a ()

Source

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

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.

to_fasta (*arg)

Source

    # 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

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.