Module: IntervalList

Included in:
GTF, GTF::Gene, SegFile
Defined in:
lib/intervals.rb,
lib/intervals.rb,
lib/intervals.rb,
lib/intervals.rb

Overview

Operations that can be defined on a pair of intervals, yielding a new set of intervals

- overlap(b) = intersection between a and b, nil if no overlap
- a.union(b) = union between a and b, nil if no overlap
- a.diff(b) = set of regions of b that do not include a, { b } if no overlap

Operations that can be defined on interval b and set a

- a.overlap(b) - set of intervals in a that overlap b

Operations on a set of intervals a

- flatten - collapses overlapping intervals
-

Defined Under Namespace

Modules: Interval Classes: Set, Tree, TreeNode

Instance Method Summary collapse

Instance Method Details

#add_interval(int) ⇒ Object 



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# File 'lib/intervals.rb', line 135

def add_interval int
  # don't bother if the tree hasn't been built yet
  @interval_set << int if @interval_set
end

#flatten ⇒ Object 



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# File 'lib/intervals.rb', line 105

def flatten
  current_span = nil
  flat = []
  each do |interval|
    if current_span && current_span.overlaps?(interval)
      current_span.stop = interval.stop
    else
      # you reached a new span
      if current_span
        yield current_span if block_given?
        flat.push current_span
      end
      current_span = interval.clone
    end
  end
  if current_span
    yield current_span if block_given?
    flat.push current_span
  end
  present flat
end

#interval_set ⇒ Object 



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# File 'lib/intervals.rb', line 140

def interval_set
  # create a new set of intervals
  @interval_set ||= IntervalList::Set.new self.to_a
end

#nearest(interval) ⇒ Object 



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# File 'lib/intervals.rb', line 100

def nearest interval
  return nil unless interval_set[interval.seqname]
  interval_set[interval.seqname].nearest interval
end

#overlap(interval) ⇒ Object 



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# File 'lib/intervals.rb', line 95

def overlap interval
  return present([]) unless interval_set[interval.seqname]
  present(interval_set[interval.seqname].overlap interval)
end

#present(obj) ⇒ Object 



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# File 'lib/intervals.rb', line 127

def present obj
  if respond_to? :wrap
    wrap obj
  else
    obj
  end
end