Class Bio::Blast::WU::Report
In: lib/bio/appl/blast/wublast.rb  (CVS)
Parent: 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.

Methods

expect   notice   parameter_matrix   parameters   warnings  

Classes and Modules

Class Bio::Blast::WU::Report::HSP
Class Bio::Blast::WU::Report::Hit
Class Bio::Blast::WU::Report::Iteration

Public Instance methods

expect()

Returns e-value threshold specified when BLAST was executed.

[Source]

# File lib/bio/appl/blast/wublast.rb, line 50
        def expect; parse_parameters; @parameters['E']; end
notice()

Returns notice messages.

[Source]

# 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
parameter_matrix()

Returns parameter matrix (???)

[Source]

# File lib/bio/appl/blast/wublast.rb, line 44
        def parameter_matrix
          parse_parameters
          @parameter_matrix
        end
parameters()

Returns parameters (???)

[Source]

# File lib/bio/appl/blast/wublast.rb, line 38
        def parameters
          parse_parameters
          @parameters
        end
warnings()

Returns warning messages.

[Source]

# File lib/bio/appl/blast/wublast.rb, line 53
        def warnings
          unless defined?(@warnings)
            @warnings = @f0warnings
            iterations.each { |x| @warnings.concat(x.warnings) }
          end
          @warnings
        end

[Validate]