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.
query_def | [R] | definition of the query |
query_len | [R] | length of the query sequence |
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.
# 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