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

Inherits:

Default::Report::Iteration

• Object
• Default::Report::Iteration
• Bio::Blast::WU::Report::Iteration

Defined in:

lib/bio/appl/blast/wublast.rb

Overview

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.

Instance Attribute Summary

Attributes inherited from Default::Report::Iteration

#database, #db_len, #db_num, #eff_space, #entropy, #expect, #gapped_entropy, #gapped_kappa, #gapped_lambda, #kappa, #lambda, #message, #num, #pattern_in_database, #posted_date

Instance Method Summary

• #initialize(data) ⇒ Iteration constructor

  Creates a new Iteration object.

• #warnings ⇒ Object

  Returns warning messages.

Methods inherited from Default::Report::Iteration

#converged?, #each, #hits, #hits_for_pattern, #hits_found_again, #hits_newly_found, #pattern, #pattern_positions

Constructor Details

#initialize(data) ⇒ Iteration

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', line 319

def initialize(data)
  @f0stat = []
  @f0dbstat = Default::Report::AlwaysNil.instance
  @f0hitlist = []
  @hits = []
  @num = 1
  @f0message = []
  @f0warnings = []
  return unless r = data.first
  return if /\AParameters\:$/ =~ r
  return if /\AEXIT CODE *\d+/ =~ r
  @f0hitlist << data.shift
  return unless r = data.shift
  unless /\*{3} +NONE +\*{3}/ =~ r then
    @f0hitlist << r
    while r = data.first and /^WARNING\: / =~ r
      @f0warnings << data.shift
    end
    while r = data.first and /^\>/ =~ r
      @hits << Hit.new(data)
    end
  end #unless
end

Instance Method Details

#warnings ⇒ Object

Returns warning messages.

# File 'lib/bio/appl/blast/wublast.rb', line 344

def warnings
  @f0warnings
end