Hit object of the sim4 result. Similar to Bio::Blast::Report::Hit but lacks many methods.
Returns sequence informations of ‘seq1’. Returns a Bio::Sim4::Report::SeqDesc object. This would be Bio::Sim4 specific method.
Returns sequence informations of ‘seq2’. Returns a Bio::Sim4::Report::SeqDesc object. This would be Bio::Sim4 specific method.
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.
# File lib/bio/appl/sim4/report.rb, line 273 def initialize(str) @data = str.split(/\n(?:\r?\n)+/) parse_seqdesc end
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.
# File lib/bio/appl/sim4/report.rb, line 432 def align unless defined?(@align); parse_align; end @align end
Returns true if the hit reports ‘-’(complemental) strand search result. Otherwise, return false or nil. This would be a Bio::Sim4 specific method.
# File lib/bio/appl/sim4/report.rb, line 313 def complement? @complement end
Iterates over each exon of the hit. Yields a Bio::Sim4::Report::SegmentPair object.
# File lib/bio/appl/sim4/report.rb, line 470 def each(&x) #:yields: segmentpair exons.each(&x) end
Returns exons of the hit. Each exon is a Bio::Sim4::Report::SegmentPair object.
# File lib/bio/appl/sim4/report.rb, line 402 def exons unless defined?(@exons); parse_segmentpairs; end @exons end
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.)
# File lib/bio/appl/sim4/report.rb, line 422 def introns unless defined?(@introns); parse_segmentpairs; end @introns end
Definition of the query sequence Same as Bio::Sim4::Report#query_def.
# File lib/bio/appl/sim4/report.rb, line 451 def query_def; seq1.definition; end
Identifier of the query sequence. Same as Bio::Sim4::Report#query_id.
# File lib/bio/appl/sim4/report.rb, line 447 def query_id; seq1.entry_id; end
Length of the query sequence. Same as Bio::Sim4::Report#query_len.
# File lib/bio/appl/sim4/report.rb, line 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.)
# File lib/bio/appl/sim4/report.rb, line 412 def segmentpairs unless defined?(@segmentpairs); parse_segmentpairs; end @segmentpairs end
Definition of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 460 def target_def; seq2.definition; end
Identifier of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 457 def target_id; seq2.entry_id; end
length of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 454 def target_len; seq2.len; end
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