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
122 def db
123   unless defined?(@db)
124     if /Database *\: *(.*)/m =~ @f0database then
125       a = $1.split(/^/)
126       if a.size > 1 and /\ASearching\..+ done\s*\z/ =~ a[-1] then
127         a.pop
128       end
129       if a.size > 1 and /\A +[\d\,]+ +sequences\; +[\d\,]+ total +letters\.?\s*\z/ =~ a[-1] then
130         a.pop
131       end
132       @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
133     end
134   end #unless
135   @db
136 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
79 def exit_code
80   if defined? @exit_code then
81     @exit_code
82   else
83     nil
84   end
85 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
93 def exit_code_message
94   if defined? @exit_code_message then
95     @exit_code_message
96   else
97     nil
98   end
99 end

expect() click to toggle source

Returns e-value threshold specified when BLAST was executed.

   # File lib/bio/appl/blast/wublast.rb
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
113 def fatal_errors
114   if defined? @fatal_errors then
115     @fatal_errors
116   else
117     nil
118   end
119 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
103 def notes
104   if defined? @notes then
105     @notes
106   else
107     nil
108   end
109 end

notice() click to toggle source

Returns notice messages.

   # File lib/bio/appl/blast/wublast.rb
62 def notice
63   unless defined?(@notice)
64     @notice = @f0notice.to_s.gsub(/\s+/, ' ').strip
65   end #unless
66   @notice
67 end

parameter_matrix() click to toggle source

Returns parameter matrix (???)

   # File lib/bio/appl/blast/wublast.rb
44 def parameter_matrix
45   parse_parameters
46   @parameter_matrix
47 end

parameters() click to toggle source

Returns parameters (???)

   # File lib/bio/appl/blast/wublast.rb
38 def parameters
39   parse_parameters
40   @parameters
41 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
72 def query_record_number
73   format0_parse_query
74   @query_record_number
75 end

warnings() click to toggle source

Returns warning messages.

   # File lib/bio/appl/blast/wublast.rb
53 def warnings
54   unless defined?(@warnings)
55     @warnings = @f0warnings
56     iterations.each { |x| @warnings.concat(x.warnings) }
57   end
58   @warnings
59 end