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 collapse
-
#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.
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# File 'lib/bio/appl/blast/wublast.rb', line 200 def initialize(data) @f0stat = [] @f0dbstat = Default::Report::AlwaysNil.instance @f0hitlist = [] @hits = [] @num = 1 @f0message = [] @f0warnings = [] return unless r = data.shift @f0hitlist << r 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.
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# File 'lib/bio/appl/blast/wublast.rb', line 223 def warnings @f0warnings end |