class Bio::Sim4::Report::SegmentPair

Sequence segment pair of the sim4 result. Similar to Bio::Blast::Report::HSP but lacks many methods. For mRNA-genome mapping programs, unlike other homology search programs, the class is used not only for exons but also for introns. (Note that intron data would not be available according to run-time options of the program.)

Attributes

direction[R]

Returns directions of mapping. Maybe one of “->”, “<-”, “==” or “” or nil. This would be a Bio::Sim4 specific method.

midline[R]

Returns the “midline” of the segment pair. Returns nil if no alignment data are available.

percent_identity[R]

Returns percent identity of the segment pair.

seq1[R]

Returns segment informations of ‘seq1’. Returns a Bio::Sim4::Report::Segment object. These would be Bio::Sim4 specific methods.

seq2[R]

Returns segment informations of ‘seq2’. Returns a Bio::Sim4::Report::Segment object. These would be Bio::Sim4 specific methods.

Public Class Methods

both_intron(prev_e, e, aln) click to toggle source

Parses part of sim4 result text and creates a new SegmentPair object for regions which can not be aligned correctly. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.

    # File lib/bio/appl/sim4/report.rb
206 def self.both_intron(prev_e, e, aln)
207   self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]),
208            Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]),
209            aln[1])
210 end

new(seq1, seq2, midline = nil, percent_identity = nil, direction = nil) click to toggle source

Creates a new SegmentPair object. It is designed to be called internally from Bio::Sim4::Report::Hit object. Users shall not use it directly.

    # File lib/bio/appl/sim4/report.rb
139 def initialize(seq1, seq2, midline = nil,
140                percent_identity = nil, direction = nil)
141   @seq1 = seq1
142   @seq2 = seq2
143   @midline = midline
144   @percent_identity = percent_identity
145   @direction = direction
146 end

parse(str, aln) click to toggle source

Parses part of sim4 result text and creates a new SegmentPair object. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.

    # File lib/bio/appl/sim4/report.rb
172 def self.parse(str, aln)
173   /^(\d+)\-(\d+)\s*\((\d+)\-(\d+)\)\s*([\d\.]+)\%\s*([\-\<\>\=]*)/ =~ str
174   self.new(Segment.new($1, $2, aln[0]),
175            Segment.new($3, $4, aln[2]),
176            aln[1], $5, $6)
177 end

seq1_intron(prev_e, e, aln) click to toggle source

Parses part of sim4 result text and creates a new SegmentPair object when the seq1 is a intron. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.

    # File lib/bio/appl/sim4/report.rb
184 def self.seq1_intron(prev_e, e, aln)
185   self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]),
186            Segment.new(nil, nil, aln[2]),
187            aln[1])
188 end

seq2_intron(prev_e, e, aln) click to toggle source

Parses part of sim4 result text and creates a new SegmentPair object when seq2 is a intron. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.

    # File lib/bio/appl/sim4/report.rb
195 def self.seq2_intron(prev_e, e, aln)
196   self.new(Segment.new(nil, nil, aln[0]),
197            Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]),
198            aln[1])
199 end

Public Instance Methods

align_len() click to toggle source

Returns alignment length of the segment pair. Returns nil if no alignment data are available.

    # File lib/bio/appl/sim4/report.rb
238 def align_len
239   (@midline and @seq1.seq and @seq2.seq) ? @midline.length : nil
240 end

hit_from() click to toggle source

start position of the hit(target) (the first position is 1)

    # File lib/bio/appl/sim4/report.rb
227 def hit_from;   @seq2.from; end

hit_to() click to toggle source

end position of the hit(target) (including its position)

    # File lib/bio/appl/sim4/report.rb
230 def hit_to;     @seq2.to;   end

hseq() click to toggle source

hit(target) sequence (with gaps) of the alignment of the segment pair.

    # File lib/bio/appl/sim4/report.rb
234 def hseq;       @seq2.seq;  end

qseq() click to toggle source

query sequence (with gaps) of the alignment of the segment pair.

    # File lib/bio/appl/sim4/report.rb
224 def qseq;       @seq1.seq;  end

query_from() click to toggle source

start position of the query (the first position is 1)

    # File lib/bio/appl/sim4/report.rb
218 def query_from; @seq1.from; end

query_to() click to toggle source

end position of the query (including its position)

    # File lib/bio/appl/sim4/report.rb
221 def query_to;   @seq1.to;   end