Class Bio::Blast::Default::Report::Iteration
In: lib/bio/appl/blast/format0.rb  (CVS)
Parent: Object

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.

Methods

converged?   each   hits   hits_for_pattern   hits_found_again   hits_newly_found   new   pattern   pattern_positions  

Attributes

database  [R]  name (title or filename) of the database
db_len  [R]  number of sequences in database
db_num  [R]  number of letters in database
eff_space  [R]  effective length of the database
entropy  [R]  entropy of the database
expect  [R]  e-value threshold specified when BLAST was executed
gapped_entropy  [R]  gapped entropy of the database
gapped_kappa  [R]  gapped kappa of the database
gapped_lambda  [R]  gapped lambda of the database
kappa  [R]  kappa of the database
lambda  [R]  lambda of the database
message  [R]  (PSI-BLAST) Messages of the iteration.
num  [R]  (PSI-BLAST) Iteration round number.
pattern_in_database  [R]  (PHI-BLAST) Number of occurrences of pattern in the database.
posted_date  [R]  posted date of the database

Public Class methods

new(data)

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.

[Source]

# File lib/bio/appl/blast/format0.rb, line 493
          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 = $1.to_i
              @f0message << r
              r = data.shift
            end
            if r and !(/\*{5} No hits found \*{5}/ =~ r) then
              @f0hitlist << r
              begin
                @f0hitlist << data.shift
              end until r = data[0] and /^\>/ =~ r
              if r and /^CONVERGED\!/ =~ r then
                r.sub!(/(.*\n)*^CONVERGED\!.*\n/) { |x| @f0hitlist << x; '' }
              end
              if defined?(@pattern_in_database) and r = data.first then
                #PHI-BLAST
                while /^\>/ =~ r
                  @hits << Hit.new(data)
                  r = data.first
                  break unless r
                  if /^Significant alignments for pattern/ =~ r
                    data.shift
                    r = data.first
                  end
                end
              else
                #not PHI-BLAST
                while r = data[0] and /^\>/ =~ r
                  @hits << Hit.new(data)
                end
              end
            end
            if /^CONVERGED\!\s*$/ =~ @f0hitlist[-1].to_s then
              @message = 'CONVERGED!'
              @flag_converged = true
            end
          end

Public Instance methods

converged?()

(PSI-BLAST) Returns true if the iteration is converged. Otherwise, returns false.

[Source]

# File lib/bio/appl/blast/format0.rb, line 574
          def converged?
            @flag_converged
          end
each() {|x| ...}

Iterates over each hit of the iteration. Yields a Bio::Blast::Default::Report::Hit object.

[Source]

# File lib/bio/appl/blast/format0.rb, line 566
          def each
            hits.each do |x|
              yield x
            end
          end
hits()

Returns the hits of the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.

[Source]

# File lib/bio/appl/blast/format0.rb, line 559
          def hits
            parse_hitlist
            @hits
          end
hits_for_pattern()

(PHI-BLAST) Returns hits for pattern. ????

[Source]

# File lib/bio/appl/blast/format0.rb, line 622
          def hits_for_pattern
            parse_hitlist
            @hits_for_pattern
          end
hits_found_again()

(PSI-BLAST) Returns hits which have been found again in the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.

[Source]

# File lib/bio/appl/blast/format0.rb, line 608
          def hits_found_again
            parse_hitlist
            @hits_found_again
          end
hits_newly_found()

(PSI-BLAST) Returns hits which have been newly found in the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.

[Source]

# File lib/bio/appl/blast/format0.rb, line 616
          def hits_newly_found
            parse_hitlist
            @hits_newly_found
          end
pattern()

(PHI-BLAST) Returns pattern string. Returns nil if it is not a PHI-BLAST result.

[Source]

# File lib/bio/appl/blast/format0.rb, line 580
          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 +(.+)$/) then
                  @pattern = sc[1] unless @pattern
                  sc.skip_until(/^ at position +(\d+)/)
                  @pattern_positions << sc[1].to_i
                end
              end
            end
            @pattern
          end
pattern_positions()

(PHI-BLAST) Returns pattern positions. Returns nil if it is not a PHI-BLAST result.

[Source]

# File lib/bio/appl/blast/format0.rb, line 599
          def pattern_positions
            #PHI-BLAST
            pattern
            @pattern_positions
          end

[Validate]