Class Bio::Sim4::Report::Hit
In: lib/bio/appl/sim4/report.rb
Parent: Object

Hit object of the sim4 result. Similar to Bio::Blast::Report::Hit but lacks many methods.

Methods

align   complement?   definition   each   exons   hit_id   hsps   introns   len   new   query_def   query_id   query_len   segmentpairs   target_def   target_id   target_len  

Attributes

seq1  [R]  Returns sequence informations of ‘seq1’. Returns a Bio::Sim4::Report::SeqDesc object. This would be Bio::Sim4 specific method.
seq2  [R]  Returns sequence informations of ‘seq2’. Returns a Bio::Sim4::Report::SeqDesc object. This would be Bio::Sim4 specific method.

Public Class methods

Parses part of sim4 result text and creates a new Hit object. It is designed to be called internally from Bio::Sim4::Report class. Users shall not use it directly.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 273
273:         def initialize(str)
274:           @data = str.split(/\n(?:\r?\n)+/)
275:           parse_seqdesc
276:         end

Public Instance methods

Returns alignments. Returns an Array of arrays. Each array contains sequence of seq1, midline, sequence of seq2, respectively. This would be a Bio::Sim4 specific method.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 432
432:         def align
433:           unless defined?(@align); parse_align; end
434:           @align
435:         end

Returns true if the hit reports ’-’(complemental) strand search result. Otherwise, return false or nil. This would be a Bio::Sim4 specific method.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 313
313:         def complement?
314:           @complement
315:         end
definition()

Alias for target_def

Iterates over each exon of the hit. Yields a Bio::Sim4::Report::SegmentPair object.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 470
470:         def each(&x) #:yields: segmentpair
471:           exons.each(&x)
472:         end

Returns exons of the hit. Each exon is a Bio::Sim4::Report::SegmentPair object.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 402
402:         def exons
403:           unless defined?(@exons); parse_segmentpairs; end
404:           @exons
405:         end
hit_id()

Alias for target_id

hsps()

Alias for exons

Returns introns of the hit. Some of them would contain untranscribed regions. Returns an array of Bio::Sim4::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)

[Source]

     # File lib/bio/appl/sim4/report.rb, line 422
422:         def introns
423:           unless defined?(@introns); parse_segmentpairs; end
424:           @introns
425:         end
len()

Alias for target_len

Definition of the query sequence Same as Bio::Sim4::Report#query_def.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 451
451:         def query_def;  seq1.definition; end

Identifier of the query sequence. Same as Bio::Sim4::Report#query_id.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 447
447:         def query_id;   seq1.entry_id;   end

Length of the query sequence. Same as Bio::Sim4::Report#query_len.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 443
443:         def query_len;  seq1.len;        end

Returns segment pairs (exons and introns) of the hit. Each segment pair is a Bio::Sim4::Report::SegmentPair object. Returns an array of Bio::Sim4::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)

[Source]

     # File lib/bio/appl/sim4/report.rb, line 412
412:         def segmentpairs
413:           unless defined?(@segmentpairs); parse_segmentpairs; end
414:           @segmentpairs
415:         end

Definition of the hit(target) sequence

[Source]

     # File lib/bio/appl/sim4/report.rb, line 460
460:         def target_def; seq2.definition; end

Identifier of the hit(target) sequence

[Source]

     # File lib/bio/appl/sim4/report.rb, line 457
457:         def target_id;  seq2.entry_id;   end

length of the hit(target) sequence

[Source]

     # File lib/bio/appl/sim4/report.rb, line 454
454:         def target_len; seq2.len;        end

[Validate]