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.
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. |
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’, …
# 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
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, line 185 185: def align 186: warn "Bio::MAFFT::Report#align is deprecated. Please use \'alignment\'." 187: alignment 188: end
Gets an multiple alignment. Returns a Bio::Alignment object.
# File lib/bio/appl/mafft/report.rb, line 177 177: def alignment(method = nil) 178: super 179: 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.
# File lib/bio/appl/mafft/report.rb, line 206 206: def to_a 207: @data 208: 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.
# 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