Class: Bio::Blast::Default::Report::Hit

new(data)

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.

[Source]

# File lib/bio/appl/blast/format0.rb, line 800
          def initialize(data)
            @f0hitname = data.shift
            @hsps = []
            while r = data[0] and /\A\s+Score/ =~ r
              @hsps << HSP.new(data)
            end
            @again = false
          end

bit_score()

Returns first hsp‘s bit score. (shown in hit list of BLAST result)

[Source]

# File lib/bio/appl/blast/format0.rb, line 833
          def bit_score
            unless defined?(@bit_score)
              if h = @hsps.first then
                @bit_score = h.bit_score
              end
            end
            @bit_score
          end

definition()

Returns definition of the hit.

[Source]

# File lib/bio/appl/blast/format0.rb, line 875
          def definition; parse_hitname; @definition; end

each() {|x| ...}

Iterates over each hsp(high-scoring segment pair) of the hit. Yields a Bio::Blast::Default::Report::HSP object.

[Source]

# File lib/bio/appl/blast/format0.rb, line 815
          def each
            @hsps.each { |x| yield x }
          end

evalue()

Returns first hsp‘s e-value. (shown in hit list of BLAST result)

[Source]

# File lib/bio/appl/blast/format0.rb, line 844
          def evalue
            unless defined?(@evalue)
              if h = @hsps.first then
                @evalue = h.evalue
              end
            end
            @evalue
          end

found_again?()

(PSI-BLAST) Returns true if the hit is found again in the iteration. Otherwise, returns false or nil.

[Source]

# File lib/bio/appl/blast/format0.rb, line 822
          def found_again?
            @again
          end

identity()

Same as hsps.first.identity. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 900
          def identity;      hsp_first :identity;     end

lap_at()

Returns an array which contains [ query_start, query_end, target_start, target_end ]. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 945
          def lap_at
            [ query_start, query_end, target_start, target_end ]
          end

len()

Returns length of the hit.

[Source]

# File lib/bio/appl/blast/format0.rb, line 872
          def len;        parse_hitname; @len;        end

midline()

Same as hsps.first.midline. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 920
          def midline;       hsp_first :midline;      end

overlap()

Same as hsps.first.align_len. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 905
          def overlap;       hsp_first :align_len;    end

query_end()

Same as hsps.first.query_to. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 930
          def query_end;     hsp_first :query_to;     end

query_seq()

Same as hsps.first.qseq. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 910
          def query_seq;     hsp_first :qseq;         end

query_start()

Same as hsps.first.query_from. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 925
          def query_start;   hsp_first :query_from;   end

score()

Returns first hsp‘s score.

[Source]

# File lib/bio/appl/blast/format0.rb, line 827
          def score
            (h = @hsps.first) ? h.score : nil
          end

target_def()

Alias for definition

target_end()

Same as hsps.first.hit_to. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 940
          def target_end;    hsp_first :hit_to;       end

target_id()

[Source]

# File lib/bio/appl/blast/format0.rb, line 877
          def target_id; definition[/^\s*(\S+)/, 1]; end

target_len()

Alias for len

target_seq()

Same as hsps.first.hseq. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 915
          def target_seq;    hsp_first :hseq;         end

target_start()

Same as hsps.first.hit_from. Returns nil if there are no hsp in the hit. (Compatibility method with FASTA)

[Source]

# File lib/bio/appl/blast/format0.rb, line 935
          def target_start;  hsp_first :hit_from;     end

Methods

Attributes

Public Class methods

Public Instance methods