class Bio::Blast::WU::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.

Public Instance Methods

db() click to toggle source

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 *\: *(.*)/m =~ @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
exit_code() click to toggle source

(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
exit_code_message() click to toggle source

(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
expect() click to toggle source

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
fatal_errors() click to toggle source

(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
notes() click to toggle source

(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
notice() click to toggle source

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
parameter_matrix() click to toggle source

Returns parameter matrix (???)

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

Returns parameters (???)

# File lib/bio/appl/blast/wublast.rb, line 38
def parameters
  parse_parameters
  @parameters
end
query_record_number() click to toggle source

(WU-BLAST) Returns record number of the query. It may only be available for reports with multiple queries. Returns an Integer or nil.

# File lib/bio/appl/blast/wublast.rb, line 72
def query_record_number
  format0_parse_query
  @query_record_number
end
warnings() click to toggle source

Returns warning messages.

# 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