Default::Report
Bio::Blast::WU::Report parses WU-BLAST default output and stores information in the data. It may contain a Bio::Blast::WU::Report::Iteration object. Because it inherits Bio::Blast::Default::Report, please also refer Bio::Blast::Default::Report.
Returns the name (filename or title) of the database.
# File lib/bio/appl/blast/wublast.rb, line 122 def db unless defined?(@db) if /Database *\: *(.*)/ =~ @f0database then a = $1.split(/^/) if a.size > 1 and /\ASearching\..+ done\s*\z/ =~ a[-1] then a.pop end if a.size > 1 and /\A +[\d\,]+ +sequences\; +[\d\,]+ total +letters\.?\s*\z/ =~ a[-1] then a.pop end @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ') end end #unless @db end
(WU-BLAST) Returns exit code for the execution. Returns an Integer or nil.
# File lib/bio/appl/blast/wublast.rb, line 79 def exit_code if defined? @exit_code then @exit_code else nil end end
(WU-BLAST) Returns the message bundled with the exit code output. The message will be shown when WU-BLAST ignores a fatal error due to the command line option “-nonnegok”, “-novalidctxok”, or “-shortqueryok”.
Returns a String or nil.
# File lib/bio/appl/blast/wublast.rb, line 93 def exit_code_message if defined? @exit_code_message then @exit_code_message else nil end end
Returns e-value threshold specified when BLAST was executed.
# File lib/bio/appl/blast/wublast.rb, line 50 def expect; parse_parameters; @parameters['E']; end
(WU-BLAST) Returns fatal error information. Returns nil or an array containing String.
# File lib/bio/appl/blast/wublast.rb, line 113 def fatal_errors if defined? @fatal_errors then @fatal_errors else nil end end
(WU-BLAST) Returns “NOTE:” information. Returns nil or an array containing String.
# File lib/bio/appl/blast/wublast.rb, line 103 def notes if defined? @notes then @notes else nil end end
Returns notice messages.
# File lib/bio/appl/blast/wublast.rb, line 62 def notice unless defined?(@notice) @notice = @f0notice.to_s.gsub(/\s+/, ' ').strip end #unless @notice end
Returns parameter matrix (???)
# File lib/bio/appl/blast/wublast.rb, line 44 def parameter_matrix parse_parameters @parameter_matrix end
Returns parameters (???)
# File lib/bio/appl/blast/wublast.rb, line 38 def parameters parse_parameters @parameters end
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