class Bio::Blast::Report::Hit

Bio::Blast::Report::Hit

Attributes

accession [RW]

Accession

definition [RW]

Definition line of subject

hit_id [RW]

SeqId of subject

hsps [R]

Returns an Array of Bio::Blast::Report::Hsp objects.

len [RW]

Length of subject

num [RW]

Hit number

query_def [RW]

Compatible method with Bio::Fasta::Report::Hit class.

query_id [RW]

Compatible method with Bio::Fasta::Report::Hit class.

query_len [RW]

Compatible method with Bio::Fasta::Report::Hit class.

target_def [RW]

Definition line of subject

target_id [RW]

Accession

target_len [RW]

Length of subject

Public Class Methods

new ()

Source

    # File lib/bio/appl/blast/report.rb
261 def initialize
262   @hsps = []
263 end

Public Instance Methods

bit_score ()

Source

    # File lib/bio/appl/blast/report.rb
303 def bit_score;        @hsps.first.bit_score;        end

each () { |x| ... }

Source

    # File lib/bio/appl/blast/report.rb
280 def each
281   @hsps.each do |x|
282     yield x
283   end
284 end

Iterates on each Hsp object.

evalue ()

Source

    # File lib/bio/appl/blast/report.rb
302 def evalue;           @hsps.first.evalue;           end

Shortcut methods for the best Hsp, some are also compatible with Bio::Fasta::Report::Hit class.

identity ()

Source

    # File lib/bio/appl/blast/report.rb
304 def identity;         @hsps.first.identity;         end

lap_at ()

Source

    # File lib/bio/appl/blast/report.rb
316 def lap_at
317   [ query_start, query_end, target_start, target_end ]
318 end

midline ()

Source

    # File lib/bio/appl/blast/report.rb
310 def midline;          @hsps.first.midline;          end

overlap ()

Source

    # File lib/bio/appl/blast/report.rb
306 def overlap;          @hsps.first.align_len;        end

percent_identity ()

Source

    # File lib/bio/appl/blast/report.rb
305 def percent_identity; @hsps.first.percent_identity; end

query_end ()

Source

    # File lib/bio/appl/blast/report.rb
313 def query_end;        @hsps.first.query_to;         end

query_seq ()

Source

    # File lib/bio/appl/blast/report.rb
308 def query_seq;        @hsps.first.qseq;             end

query_start ()

Source

    # File lib/bio/appl/blast/report.rb
312 def query_start;      @hsps.first.query_from;       end

target_end ()

Source

    # File lib/bio/appl/blast/report.rb
315 def target_end;       @hsps.first.hit_to;           end

target_seq ()

Source

    # File lib/bio/appl/blast/report.rb
309 def target_seq;       @hsps.first.hseq;             end

target_start ()

Source

    # File lib/bio/appl/blast/report.rb
314 def target_start;     @hsps.first.hit_from;         end