Class: Bio::MAFFT::Report

Inherits:
Alignment::MultiFastaFormat show all
Defined in:
lib/bio/appl/mafft/report.rb

Overview

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.

Constant Summary

Constants inherited from Alignment::MultiFastaFormat

Alignment::MultiFastaFormat::DELIMITER

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from Alignment::MultiFastaFormat

#entries

Constructor Details

#initialize(str, seqclass = nil) ⇒ Report

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’, …



142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
 
# File 'lib/bio/appl/mafft/report.rb', line 142

def initialize(str, seqclass = nil)
  if str.is_a?(Array) then
    warn "Array of Bio::FastaFormat objects will be no longer accepted."
    @data = str
  else
    super(str)
  end

  if seqclass then
    warn "the 2nd argument (seqclass) will be no deprecated."
    case seqclass
    when /PROTEIN/i
      @seqclass = Bio::Sequence::AA
    when /[DR]NA/i
      @seqclass = Bio::Sequence::NA
    else
      if seqclass.is_a?(Module) then
        @seqclass = seqclass
      else
        @seqclass = nil
      end
    end
  end
end

Instance Attribute Details

#data ⇒ Object (readonly)

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



168
169
170
 
# File 'lib/bio/appl/mafft/report.rb', line 168

def data
  @data
end

#seqclass ⇒ Object (readonly)

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

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



173
174
175
 
# File 'lib/bio/appl/mafft/report.rb', line 173

def seqclass
  @seqclass
end

Instance Method Details

#align ⇒ Object

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

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



185
186
187
188
 
# File 'lib/bio/appl/mafft/report.rb', line 185

def align
  warn "Bio::MAFFT::Report#align is deprecated. Please use \'alignment\'."
  alignment
end

#alignment(method = nil) ⇒ Object

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



177
178
179
 
# File 'lib/bio/appl/mafft/report.rb', line 177

def alignment(method = nil)
  super
end

#to_a ⇒ Object

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.



206
207
208
 
# File 'lib/bio/appl/mafft/report.rb', line 206

def to_a
  @data
end

#to_fasta(*arg) ⇒ Object

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.



196
197
198
199
 
# File 'lib/bio/appl/mafft/report.rb', line 196

def to_fasta(*arg)
  warn "Bio::MAFFT::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'"
  alignment.output_fasta(*arg)
end