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

new(str)

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

align()

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

complement?()

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

each() {|segmentpair| ...}

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

exons()

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

introns()

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

query_def()

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

query_id()

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

query_len()

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

segmentpairs()

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

target_def()

Definition of the hit(target) sequence

[Source]

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

target_id()

Identifier of the hit(target) sequence

[Source]

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

target_len()

length of the hit(target) sequence

[Source]

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

[Validate]