class Bio::Blast::RPSBlast::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.

Attributes

query_def[R]

definition of the query

query_len[R]

length of the query sequence

Public Class Methods

new(data, dummystr) click to toggle source

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.

Calls superclass method Bio::Blast::Default::Report::Iteration::new

    # File lib/bio/appl/blast/rpsblast.rb
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