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

Methods

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

[Source]

     # File lib/bio/appl/blast/report.rb, line 255
255:     def initialize
256:       @hsps = []
257:     end

Public Instance methods

[Source]

     # File lib/bio/appl/blast/report.rb, line 297
297:     def bit_score;        @hsps.first.bit_score;        end

Iterates on each Hsp object.

[Source]

     # File lib/bio/appl/blast/report.rb, line 274
274:     def each
275:       @hsps.each do |x|
276:         yield x
277:       end
278:     end

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 296
296:     def evalue;           @hsps.first.evalue;           end

[Source]

     # File lib/bio/appl/blast/report.rb, line 298
298:     def identity;         @hsps.first.identity;         end

[Source]

     # File lib/bio/appl/blast/report.rb, line 310
310:     def lap_at
311:       [ query_start, query_end, target_start, target_end ]
312:     end

[Source]

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

[Source]

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

[Source]

     # File lib/bio/appl/blast/report.rb, line 299
299:     def percent_identity; @hsps.first.percent_identity; end

[Source]

     # File lib/bio/appl/blast/report.rb, line 307
307:     def query_end;        @hsps.first.query_to;         end

[Source]

     # File lib/bio/appl/blast/report.rb, line 302
302:     def query_seq;        @hsps.first.qseq;             end

[Source]

     # File lib/bio/appl/blast/report.rb, line 306
306:     def query_start;      @hsps.first.query_from;       end

[Source]

     # File lib/bio/appl/blast/report.rb, line 309
309:     def target_end;       @hsps.first.hit_to;           end

[Source]

     # File lib/bio/appl/blast/report.rb, line 303
303:     def target_seq;       @hsps.first.hseq;             end

[Source]

     # File lib/bio/appl/blast/report.rb, line 308
308:     def target_start;     @hsps.first.hit_from;         end

[Validate]