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