Class Bio::Blast::RPSBlast::Report::Iteration
In: lib/bio/appl/blast/rpsblast.rb
Parent: Bio::Blast::Default::Report::Iteration

Iteration class for RPS-Blast. Though RPS-Blast does not iterate like PSI-BLAST, it aims to store a result of single query sequence.

Normally, the instance of the class is generated by Bio::Blast::RPSBlast::Report object.

Methods

new  

Attributes

query_def  [R]  definition of the query
query_len  [R]  length of the query sequence

Public Class methods

Creates a new Iteration object. It is designed to be called only internally from the Bio::Blast::RPSBlast::Report class. Users shall not use the method directly.

[Source]

     # File lib/bio/appl/blast/rpsblast.rb, line 245
245:         def initialize(data, dummystr)
246:           if /\AQuery\=/ =~ data[0] then
247:             sc = StringScanner.new(data.shift)
248:             sc.skip(/\s*/)
249:             if sc.skip_until(/Query\= */) then
250:               q = []
251:               begin
252:                 q << sc.scan(/.*/)
253:                 sc.skip(/\s*^ ?/)
254:               end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
255:               @query_len = sc[1].delete(',').to_i if r
256:               @query_def = q.join(' ')
257:             end
258:           end
259:           data.unshift(dummystr)
260:           
261:           super(data)
262:         end

[Validate]