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 792 792: def initialize(data) 793: @f0hitname = data.shift 794: @hsps = [] 795: while r = data[0] and /\A\s+Score/ =~ r 796: @hsps << HSP.new(data) 797: end 798: @again = false 799: end
Returns definition of the hit.
# File lib/bio/appl/blast/format0.rb, line 867 867: 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 807 807: def each 808: @hsps.each { |x| yield x } 809: end
Returns first hsp‘s e-value. (shown in hit list of BLAST result)
# File lib/bio/appl/blast/format0.rb, line 836 836: def evalue 837: unless defined?(@evalue) 838: if h = @hsps.first then 839: @evalue = h.evalue 840: end 841: end 842: @evalue 843: 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 814 814: def found_again? 815: @again 816: 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 937 937: def lap_at 938: [ query_start, query_end, target_start, target_end ] 939: end
Returns length of the hit.
# File lib/bio/appl/blast/format0.rb, line 864 864: 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 897 897: 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 922 922: 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 902 902: 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 917 917: 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 932 932: 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 907 907: def target_seq; hsp_first :hseq; end