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.

Public Class Methods

new(data) click to toggle source

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.

    # File lib/bio/appl/blast/wublast.rb
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() click to toggle source

Returns warning messages.

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