Class: Bio::Blast::WU::Report::Iteration

Iteration class for WU-BLAST report. Though WU-BLAST does not iterate like PSI-BLAST, Bio::Blast::WU::Report::Iteration aims to keep compatibility with Bio::Blast::Default::Report::* classes. It may contain some Bio::Blast::WU::Report::Hit objects. Because it inherits Bio::Blast::Default::Report::Iteration, please also refer Bio::Blast::Default::Report::Iteration.

Methods

new warnings

Public Class methods

new(data)

Creates a new Iteration object. It is designed to be called only internally from the Bio::Blast::WU::Report class. Users shall not use the method directly.

[Source]

     # File lib/bio/appl/blast/wublast.rb, line 319
319:           def initialize(data)
320:             @f0stat = []
321:             @f0dbstat = Default::Report::AlwaysNil.instance
322:             @f0hitlist = []
323:             @hits = []
324:             @num = 1
325:             @f0message = []
326:             @f0warnings = []
327:             return unless r = data.first
328:             return if /\AParameters\:$/ =~ r
329:             return if /\AEXIT CODE *\d+/ =~ r
330:             @f0hitlist << data.shift
331:             return unless r = data.shift
332:             unless /\*{3} +NONE +\*{3}/ =~ r then
333:               @f0hitlist << r
334:               while r = data.first and /^WARNING\: / =~ r
335:                 @f0warnings << data.shift
336:               end
337:               while r = data.first and /^\>/ =~ r
338:                 @hits << Hit.new(data)
339:               end
340:             end #unless
341:           end

Public Instance methods

warnings()

Returns warning messages.

[Source]

     # File lib/bio/appl/blast/wublast.rb, line 344
344:           def warnings
345:             @f0warnings
346:           end