Class Bio::MAFFT::Report
In: lib/bio/appl/mafft/report.rb
Parent: Bio::Alignment::MultiFastaFormat

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.

Methods

align   alignment   new   to_a   to_fasta  

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)

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’, …

[Source]

     # File lib/bio/appl/mafft/report.rb, line 142
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()

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

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

[Source]

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

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

[Source]

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

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.

[Source]

     # File lib/bio/appl/mafft/report.rb, line 206
206:       def to_a
207:         @data
208:       end
to_fasta(*arg)

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.

[Source]

     # File lib/bio/appl/mafft/report.rb, line 196
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

[Validate]