Class: Bio::Spidey::Report::Hit

new(data, d0)

Creates a new Hit object. It is designed to be called internally from Bio::Spidey::Report::* classes. Users shall not call it directly.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 290
290:         def initialize(data, d0)
291:           @data = data
292:           @d0 = d0
293:         end

align()

Returns alignments. Returns an Array of arrays. This would be a Bio::Spidey specific method.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 465
465:         def align
466:           unless defined?(@align); parse_align; end
467:           @align
468:         end

complement?()

Returns true if the result reports ‘Reverse complement’. Otherwise, return false or nil. This would be a Bio::Spidey specific method.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 330
330:         def complement?
331:           unless defined?(@complement); parse_strand; end
332:           @complement
333:         end

definition()

Alias for target_def

each() {|segmentpair| ...}

Iterates over each exon of the hit. Yields Bio::Spidey::Report::SegmentPair object.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 555
555:         def each(&x) #:yields: segmentpair
556:           exons.each(&x)
557:         end

exons()

Returns exons of the hit. Returns an array of Bio::Spidey::Report::SegmentPair object.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 437
437:         def exons
438:           unless defined?(@exons); parse_segmentpairs; end
439:           @exons
440:         end

genomic()

Returns sequence informations of the ‘Genomic’. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 373
373:         def genomic
374:           unless defined?(@genomic)
375:             @genomic = SeqDesc.parse(@d0.find { |x| /^Genomic\:/ =~ x })
376:           end
377:           @genomic
378:         end

hit_id()

Alias for target_id

hsps()

Alias for exons

introns()

Returns introns of the hit. Some of them would contain untranscribed regions. Returns an array of Bio::Spidey::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)

[Source]

     # File lib/bio/appl/spidey/report.rb, line 447
447:         def introns
448:           unless defined?(@introns); parse_segmentpairs; end
449:           @introns
450:         end

len()

Alias for target_len

missing_mrna_ends()

Returns missing mRNA ends of the hit.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 363
363:         def missing_mrna_ends
364:           unless defined?(@missing_mrna_ends)
365:             @missing_mrna_ends = field_fetch('Missing mRNA ends', @d0)
366:           end
367:           @missing_mrna_ends
368:         end

mrna()

Returns sequence informations of the mRNA. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 383
383:         def mrna
384:           unless defined?(@mrna)
385:             @mrna = SeqDesc.parse(@d0.find { |x| /^mRNA\:/ =~ x })
386:           end
387:           @mrna
388:         end

number_of_exons()

Returns number of exons in the hit.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 336
336:         def number_of_exons
337:           unless defined?(@number_of_exons)
338:             @number_of_exons = field_fetch('Number of exons', @d0).to_i
339:           end
340:           @number_of_exons
341:         end

number_of_splice_sites()

Returns number of splice sites of the hit.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 344
344:         def number_of_splice_sites
345:           unless defined?(@number_of_splice_sites)
346:             @number_of_splice_sites = 
347:               field_fetch('Number of splice sites', @d0).to_i
348:           end
349:           @number_of_splice_sites
350:         end

percent_identity()

Returns overall percent identity of the hit.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 353
353:         def percent_identity
354:           unless defined?(@percent_identity)
355:             x = field_fetch('overall percent identity', @d0)
356:             @percent_identity = 
357:               (/([\d\.]+)\s*\%/ =~ x.to_s) ? $1 : nil
358:           end
359:           @percent_identity
360:         end

query_def()

Definition of the mRNA (query). Same as Bio::Spidey::Report#query_def.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 536
536:         def query_def;  mrna.definition; end

query_id()

Identifier of the mRNA (query). Same as Bio::Spidey::Report#query_id.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 532
532:         def query_id;   mrna.entry_id;   end

query_len()

Length of the mRNA (query) sequence. Same as Bio::Spidey::Report#query_len.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 528
528:         def query_len;  mrna.len;        end

segmentpairs()

Returns segment pairs (exons and introns) of the hit. Each segment pair is a Bio::Spidey::Report::SegmentPair object. Returns an array of Bio::Spidey::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)

[Source]

     # File lib/bio/appl/spidey/report.rb, line 457
457:         def segmentpairs
458:           unless defined?(@segmentparis); parse_segmentpairs; end
459:           @segmentpairs
460:         end

strand()

Returns strand information of the hit. Returns ‘plus’, ‘minus’, or nil. This would be a Bio::Spidey specific method.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 322
322:         def strand
323:           unless defined?(@strand); parse_strand; end
324:           @strand
325:         end

target_def()

Definition of the genomic (target) sequence.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 545
545:         def target_def; genomic.definition; end

target_id()

Identifier of the genomic (target) sequence.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 542
542:         def target_id;  genomic.entry_id;   end

target_len()

The genomic (target) sequence length.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 539
539:         def target_len; genomic.len;        end

Methods

Public Class methods

Public Instance methods