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

Returns the name (filename or title) of the database.

     # File lib/bio/appl/blast/wublast.rb, line 122
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()

(WU-BLAST) Returns exit code for the execution. Returns an Integer or nil.

[Source]

    # File lib/bio/appl/blast/wublast.rb, line 79
79:         def exit_code
80:           if defined? @exit_code then
81:             @exit_code
82:           else
83:             nil
84:           end
85:         end

exit_code_message()

(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.

[Source]

    # File lib/bio/appl/blast/wublast.rb, line 93
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()

Returns e-value threshold specified when BLAST was executed.

[Source]

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

fatal_errors()

(WU-BLAST) Returns fatal error information. Returns nil or an array containing String.

[Source]

     # File lib/bio/appl/blast/wublast.rb, line 113
113:         def fatal_errors
114:           if defined? @fatal_errors then
115:             @fatal_errors
116:           else
117:             nil
118:           end
119:         end

notes()

(WU-BLAST) Returns "NOTE:" information. Returns nil or an array containing String.

[Source]

     # File lib/bio/appl/blast/wublast.rb, line 103
103:         def notes
104:           if defined? @notes then
105:             @notes
106:           else
107:             nil
108:           end
109:         end

notice()

Returns notice messages.

[Source]

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

parameter_matrix()

Returns parameter matrix (???)

[Source]

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

parameters()

Returns parameters (???)

[Source]

    # File lib/bio/appl/blast/wublast.rb, line 38
38:         def parameters
39:           parse_parameters
40:           @parameters
41:         end

query_record_number()

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

[Source]

    # File lib/bio/appl/blast/wublast.rb, line 72
72:         def query_record_number
73:           format0_parse_query
74:           @query_record_number
75:         end

warnings()

Returns warning messages.

[Source]

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

Methods

Classes and Modules

Public Instance methods