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

new(data, dummystr)

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 244
244:         def initialize(data, dummystr)
245:           if /\AQuery\=/ =~ data[0] then
246:             sc = StringScanner.new(data.shift)
247:             sc.skip(/\s*/)
248:             if sc.skip_until(/Query\= */) then
249:               q = []
250:               begin
251:                 q << sc.scan(/.*/)
252:                 sc.skip(/\s*^ ?/)
253:               end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
254:               @query_len = sc[1].delete(',').to_i if r
255:               @query_def = q.join(' ')
256:             end
257:           end
258:           data.unshift(dummystr)
259:           
260:           super(data)
261:         end

[Validate]