Class Bio::Blast::Report::Hit
In: lib/bio/appl/blast/report.rb
Parent: Object

Methods

bit_score   each   evalue   identity   lap_at   midline   new   overlap   percent_identity   query_end   query_seq   query_start   target_end   target_seq   target_start  

External Aliases

accession -> target_id
  Compatible method with Bio::Fasta::Report::Hit class.
definition -> target_def
  Compatible method with Bio::Fasta::Report::Hit class.
len -> target_len
  Compatible method with Bio::Fasta::Report::Hit class.

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.

Public Class methods

new()

[Source]

     # File lib/bio/appl/blast/report.rb, line 251
251:     def initialize
252:       @hsps = []
253:     end

Public Instance methods

bit_score()

[Source]

     # File lib/bio/appl/blast/report.rb, line 293
293:     def bit_score;        @hsps.first.bit_score;        end
each() {|x| ...}

Iterates on each Hsp object.

[Source]

     # File lib/bio/appl/blast/report.rb, line 270
270:     def each
271:       @hsps.each do |x|
272:         yield x
273:       end
274:     end
evalue()

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

[Source]

     # File lib/bio/appl/blast/report.rb, line 292
292:     def evalue;           @hsps.first.evalue;           end
identity()

[Source]

     # File lib/bio/appl/blast/report.rb, line 294
294:     def identity;         @hsps.first.identity;         end
lap_at()

[Source]

     # File lib/bio/appl/blast/report.rb, line 306
306:     def lap_at
307:       [ query_start, query_end, target_start, target_end ]
308:     end
midline()

[Source]

     # File lib/bio/appl/blast/report.rb, line 300
300:     def midline;          @hsps.first.midline;          end
overlap()

[Source]

     # File lib/bio/appl/blast/report.rb, line 296
296:     def overlap;          @hsps.first.align_len;        end
percent_identity()

[Source]

     # File lib/bio/appl/blast/report.rb, line 295
295:     def percent_identity; @hsps.first.percent_identity; end
query_end()

[Source]

     # File lib/bio/appl/blast/report.rb, line 303
303:     def query_end;        @hsps.first.query_to;         end
query_seq()

[Source]

     # File lib/bio/appl/blast/report.rb, line 298
298:     def query_seq;        @hsps.first.qseq;             end
query_start()

[Source]

     # File lib/bio/appl/blast/report.rb, line 302
302:     def query_start;      @hsps.first.query_from;       end
target_end()

[Source]

     # File lib/bio/appl/blast/report.rb, line 305
305:     def target_end;       @hsps.first.hit_to;           end
target_seq()

[Source]

     # File lib/bio/appl/blast/report.rb, line 299
299:     def target_seq;       @hsps.first.hseq;             end
target_start()

[Source]

     # File lib/bio/appl/blast/report.rb, line 304
304:     def target_start;     @hsps.first.hit_from;         end

[Validate]