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, line 245 def initialize(data, dummystr) if /\AQuery\=/ =~ data[0] then sc = StringScanner.new(data.shift) sc.skip(/\s*/) if sc.skip_until(/Query\= */) then q = [] begin q << sc.scan(/.*/) sc.skip(/\s*^ ?/) end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/) @query_len = sc[1].delete(',').to_i if r @query_def = q.join(' ') end end data.unshift(dummystr) super(data) end