Class Bio::Sim4::Report::SegmentPair
In: lib/bio/appl/sim4/report.rb
Parent: Object

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.)

Methods

align_len   both_intron   hit_from   hit_to   hseq   new   parse   qseq   query_from   query_to   seq1_intron   seq2_intron  

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

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.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 206
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

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

[Source]

     # File lib/bio/appl/sim4/report.rb, line 139
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

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.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 172
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

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.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 184
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

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.

[Source]

     # File lib/bio/appl/sim4/report.rb, line 195
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

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

[Source]

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

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

[Source]

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

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

[Source]

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

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

[Source]

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

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

[Source]

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

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

[Source]

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

end position of the query (including its position)

[Source]

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

[Validate]