Class | Bio::Blast::Default::Report::Hit |
In: |
lib/bio/appl/blast/format0.rb
|
Parent: | Object |
Bio::Blast::Default::Report::Hit contains information about a hit. It may contain some Bio::Blast::Default::Report::HSP objects.
hsps | [R] | Hsp(high-scoring segment pair)s of the hit. Returns an array of Bio::Blast::Default::Report::HSP objects. |
Creates a new Hit object. It is designed to be called only internally from the Bio::Blast::Default::Report::Iteration class. Users should not call the method directly.
# File lib/bio/appl/blast/format0.rb, line 810 810: def initialize(data) 811: @f0hitname = data.shift 812: @hsps = [] 813: while r = data[0] and /\A\s+Score/ =~ r 814: @hsps << HSP.new(data) 815: end 816: @again = false 817: end
Returns definition of the hit.
# File lib/bio/appl/blast/format0.rb, line 885 885: def definition; parse_hitname; @definition; end
Iterates over each hsp(high-scoring segment pair) of the hit. Yields a Bio::Blast::Default::Report::HSP object.
# File lib/bio/appl/blast/format0.rb, line 825 825: def each 826: @hsps.each { |x| yield x } 827: end
Returns first hsp‘s e-value. (shown in hit list of BLAST result)
# File lib/bio/appl/blast/format0.rb, line 854 854: def evalue 855: unless defined?(@evalue) 856: if h = @hsps.first then 857: @evalue = h.evalue 858: end 859: end 860: @evalue 861: end
(PSI-BLAST) Returns true if the hit is found again in the iteration. Otherwise, returns false or nil.
# File lib/bio/appl/blast/format0.rb, line 832 832: def found_again? 833: @again 834: end
Returns an array which contains [ query_start, query_end, target_start, target_end ]. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 955 955: def lap_at 956: [ query_start, query_end, target_start, target_end ] 957: end
Returns length of the hit.
# File lib/bio/appl/blast/format0.rb, line 882 882: def len; parse_hitname; @len; end
Same as hsps.first.align_len. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 915 915: def overlap; hsp_first :align_len; end
Same as hsps.first.query_to. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 940 940: def query_end; hsp_first :query_to; end
Same as hsps.first.qseq. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 920 920: def query_seq; hsp_first :qseq; end
Same as hsps.first.query_from. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 935 935: def query_start; hsp_first :query_from; end
Same as hsps.first.hit_to. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 950 950: def target_end; hsp_first :hit_to; end
Same as hsps.first.hseq. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)
# File lib/bio/appl/blast/format0.rb, line 925 925: def target_seq; hsp_first :hseq; end