class Bio::Sim4::Report::Hit

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

Attributes

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)

Source

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

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.

Public Instance Methods

align ()

Source

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

complement? ()

Source

    # File lib/bio/appl/sim4/report.rb
313 def complement?
314   @complement
315 end

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

definition ()

Alias for: target_def

each () { |segmentpair| ... }

Source

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

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

exons ()

Source

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

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

Also aliased as: hsps

hit_id ()

Alias for: target_id

hsps ()

Alias for: exons

introns ()

Source

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

len ()

Alias for: target_len

query_def ()

Source

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

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

query_id ()

Source

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

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

query_len ()

Source

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

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

segmentpairs ()

Source

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

target_def ()

Source

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

Definition of the hit(target) sequence

Also aliased as: definition

target_id ()

Source

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

Identifier of the hit(target) sequence

Also aliased as: hit_id

target_len ()

Source

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

length of the hit(target) sequence

Also aliased as: len