Bio::Blast::Default::Report::Iteration stores information about a iteration. It may contain some Bio::Blast::Default::Report::Hit objects. Note that a PSI-BLAST (blastpgp command) result usually contain multiple iterations in it, and a normal BLAST (blastall command) result usually contain one iteration in it.
Creates a new Iteration object. It is designed to be called only internally from the Bio::Blast::Default::Report class. Users shall not use the method directly.
# File lib/bio/appl/blast/format0.rb, line 485 def initialize(data) @f0stat = [] @f0dbstat = AlwaysNil.instance @f0hitlist = [] @hits = [] @num = 1 r = data.shift @f0message = [ r ] r.gsub!(/^Results from round (\d+).*\z/) { |x| @num = $1.to_i @f0message << x '' } r = data.shift while /^Number of occurrences of pattern in the database is +(\d+)/ =~ r # PHI-BLAST @pattern_in_database = $1.to_i @f0message << r r = data.shift end if /^Results from round (\d+)/ =~ r then @num = $1.to_i @f0message << r r = data.shift end if r and !(/\*{5} No hits found \*{5}/ =~ r) then @f0hitlist << r begin @f0hitlist << data.shift end until r = data[0] and /^\>/ =~ r if r and /^CONVERGED\!/ =~ r then r.sub!(/(.*\n)*^CONVERGED\!.*\n/) { |x| @f0hitlist << x; '' } end if defined?(@pattern_in_database) and r = data.first then #PHI-BLAST while /^\>/ =~ r @hits << Hit.new(data) r = data.first break unless r while /^Significant alignments for pattern/ =~ r data.shift r = data.first end end else #not PHI-BLAST while r = data[0] and /^\>/ =~ r @hits << Hit.new(data) end end end if /^CONVERGED\!\s*$/ =~ @f0hitlist[-1].to_s then @message = 'CONVERGED!' @flag_converged = true end end
(PSI-BLAST) Returns true if the iteration is converged. Otherwise, returns false.
# File lib/bio/appl/blast/format0.rb, line 566 def converged? @flag_converged end
Iterates over each hit of the iteration. Yields a Bio::Blast::Default::Report::Hit object.
# File lib/bio/appl/blast/format0.rb, line 558 def each hits.each do |x| yield x end end
Returns the hits of the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.
# File lib/bio/appl/blast/format0.rb, line 551 def hits parse_hitlist @hits end
(PHI-BLAST) Returns hits for pattern. ????
# File lib/bio/appl/blast/format0.rb, line 614 def hits_for_pattern parse_hitlist @hits_for_pattern end
(PSI-BLAST) Returns hits which have been found again in the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.
# File lib/bio/appl/blast/format0.rb, line 600 def hits_found_again parse_hitlist @hits_found_again end
(PSI-BLAST) Returns hits which have been newly found in the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.
# File lib/bio/appl/blast/format0.rb, line 608 def hits_newly_found parse_hitlist @hits_newly_found end
(PHI-BLAST) Returns pattern string. Returns nil if it is not a PHI-BLAST result.
# File lib/bio/appl/blast/format0.rb, line 572 def pattern #PHI-BLAST if !defined?(@pattern) and defined?(@pattern_in_database) then @pattern = nil @pattern_positions = [] @f0message.each do |r| sc = StringScanner.new(r) if sc.skip_until(/^ *pattern +([^\s]+)/) then @pattern = sc[1] unless @pattern sc.skip_until(/(?:^ *| +)at position +(\d+) +of +query +sequence/) @pattern_positions << sc[1].to_i end end end @pattern end
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