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 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