Class: Wrnap::Rna::TreeStem

Inherits:
Tree::TreeNode
  • Object
show all
Extended by:
Forwardable
Includes:
Enumerable, MetaMissing
Defined in:
lib/wrnap/rna/tree.rb

Constant Summary collapse

STEM_NOTATION_REGEX = 
/^[pt]_?(\d+_)*\d+(_?[ijkl])?$/

Instance Method Summary collapse

Instance Method Details

#detached_copy ⇒ Object 



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# File 'lib/wrnap/rna/tree.rb', line 71

def detached_copy
  # The implementation of this in RubyTree explicitly returns a new Tree::TreeNode instance rather than self.class.new, so we
  # maintain ducktyping by intercepting the method.
  self.class.new(@name, @content ? @content.clone : nil)
end

#in(sequence) ⇒ Object 



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# File 'lib/wrnap/rna/tree.rb', line 23

def in(sequence)
  sequence[i..j]
end

#postorder_traversal {|_self| ... } ⇒ Object

Yields:

  • (_self)

Yield Parameters:



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# File 'lib/wrnap/rna/tree.rb', line 83

def postorder_traversal(&block)
  return enum_for(:postorder_traversal) unless block_given?
  children.each { |child| child.postorder_traversal(&block) }
  yield self
end

#preorder_traversal {|_self| ... } ⇒ Object

Yields:

  • (_self)

Yield Parameters:



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# File 'lib/wrnap/rna/tree.rb', line 77

def preorder_traversal(&block)
  return enum_for(:preorder_traversal) unless block_given?
  yield self
  children.map { |child| child.preorder_traversal(&block) }
end

#unpaired_regions ⇒ Object 



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# File 'lib/wrnap/rna/tree.rb', line 27

def unpaired_regions
  Wrnap.debugger { "Collecting unpaired regions for %s" % [root.content.name] }
  
  postorder_traversal.inject([]) do |array, node|
    array.tap do
      if node.is_leaf?
        array << Loop.new(node.k + 1, node.l - 1)
      end
      
      if node != self
        if node.is_only_child?
          Wrnap.debugger { "Interior node: %s, parent: %s" % [node.content.inspect, node.parent.content.inspect] }
    
          if node.i - node.parent.k > 0
            Wrnap.debugger { "Left bulge." }
            array << Loop.new(node.parent.k + 1, node.i - 1)
          end
    
          if node.parent.l - node.j > 0
            Wrnap.debugger { "Right bulge." }
            array << Loop.new(node.j + 1, node.parent.l - 1)
          end
        else
          node_index = node.parent.children.each_with_index.find { |child, _| child == node }.last
        
          if node.is_last_sibling?
            Wrnap.debugger { "Leaf node, last child: %s" % node.content.inspect }
            array << Loop.new(node.j + 1, node.parent.l - 1)
          else
            if node.is_first_sibling?
              Wrnap.debugger { "Leaf node, first child: %s" % node.content.inspect }
              array << Loop.new(node.parent.k + 1, node.i - 1) 
            end
          
            Wrnap.debugger { "Connecting node, middle child: %s" % node.content.inspect }
            alexa = node.siblings[node_index]
            array << Loop.new(node.j + 1, alexa.i - 1)
          end
        end
      end            
    end
  end
end