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

Inherits:
Default::Report show all
Defined in:
lib/bio/appl/blast/wublast.rb

Overview

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.

Direct Known Subclasses

Report_TBlast

Defined Under Namespace

Classes: F0dbstat, HSP, Hit, Iteration

Constant Summary

Constants inherited from Default::Report

Default::Report::DELIMITER, Default::Report::DELIMITER_OVERRUN

Instance Attribute Summary

Attributes inherited from Default::Report

#db_len, #db_num, #eff_space, #entry_overrun, #gap_extend, #gap_open, #iterations, #matrix, #num_hits, #posted_date, #sc_match, #sc_mismatch

Instance Method Summary collapse

Methods inherited from Default::Report

#converged?, #db, #each_hit, #each_iteration, #entropy, #gapped_entropy, #gapped_kappa, #gapped_lambda, #hits, #initialize, #kappa, #lambda, #message, open, #pattern, #pattern_positions, #program, #query_def, #query_len, #reference, #references, #to_s, #version, #version_date, #version_number

Constructor Details

This class inherits a constructor from Bio::Blast::Default::Report

Instance Method Details

#expect ⇒ Object

Returns e-value threshold specified when BLAST was executed.



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# File 'lib/bio/appl/blast/wublast.rb', line 50

def expect; parse_parameters; @parameters['E']; end

#notice ⇒ Object

Returns notice messages.



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# 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 ⇒ Object

Returns parameter matrix (???)



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# File 'lib/bio/appl/blast/wublast.rb', line 44

def parameter_matrix
  parse_parameters
  @parameter_matrix
end

#parameters ⇒ Object

Returns parameters (???)



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# File 'lib/bio/appl/blast/wublast.rb', line 38

def parameters
  parse_parameters
  @parameters
end

#warnings ⇒ Object

Returns warning messages.



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# 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