class Bio::Sim4::Report::Hit

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

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) click to toggle source

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
273 def initialize(str)
274   @data = str.split(/\n(?:\r?\n)+/)
275   parse_seqdesc
276 end

Public Instance Methods

align() click to toggle source

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
432 def align
433   unless defined?(@align); parse_align; end
434   @align
435 end
complement?() click to toggle source

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
313 def complement?
314   @complement
315 end
definition()
Alias for: target_def
each() { |segmentpair| ... } click to toggle source

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

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

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

    # File lib/bio/appl/sim4/report.rb
402 def exons
403   unless defined?(@exons); parse_segmentpairs; end
404   @exons
405 end
Also aliased as: hsps
hit_id()
Alias for: target_id
hsps()
Alias for: exons
introns() click to toggle source

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
422 def introns
423   unless defined?(@introns); parse_segmentpairs; end
424   @introns
425 end
len()
Alias for: target_len
query_def() click to toggle source

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

    # File lib/bio/appl/sim4/report.rb
451 def query_def;  seq1.definition; end
query_id() click to toggle source

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

    # File lib/bio/appl/sim4/report.rb
447 def query_id;   seq1.entry_id;   end
query_len() click to toggle source

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

    # File lib/bio/appl/sim4/report.rb
443 def query_len;  seq1.len;        end
segmentpairs() click to toggle source

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
412 def segmentpairs
413   unless defined?(@segmentpairs); parse_segmentpairs; end
414   @segmentpairs
415 end
target_def() click to toggle source

Definition of the hit(target) sequence

    # File lib/bio/appl/sim4/report.rb
460 def target_def; seq2.definition; end
Also aliased as: definition
target_id() click to toggle source

Identifier of the hit(target) sequence

    # File lib/bio/appl/sim4/report.rb
457 def target_id;  seq2.entry_id;   end
Also aliased as: hit_id
target_len() click to toggle source

length of the hit(target) sequence

    # File lib/bio/appl/sim4/report.rb
454 def target_len; seq2.len;        end
Also aliased as: len