Class: Bio::AssemblyGraphAlgorithms::SequenceHasher

Inherits:
Object
  • Object
show all
Includes:
FinishM::Logging
Defined in:
lib/assembly/sequence_hasher.rb

Defined Under Namespace

Classes: DistancedOrientedNodeTrail

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#extend_overlap(graph, oriented_onode, overlap, options = {}) ⇒ Object 



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# File 'lib/assembly/sequence_hasher.rb', line 8

def extend_overlap(graph, oriented_onode, overlap, options={})
  trails = []

  current_path = DistancedOrientedNodeTrail.new
  current_path.add_oriented_node oriented_onode
  current_path.distance = 0

  stack = DS::Stack.new
  stack.push current_path

  # While there is more on the stack
  while current_path = stack.pop

    current_distance = current_path.distance

    if current_distance >= overlap
      # Found all the sequence we need
      trails.push current_path
      next
    end

    # Find neighbouring nodes
    neighbours = nil
    if options[:neighbour_finder]
      neighbours = options[:neighbour_finder].neighbours(oriented_onode)
    else
      neighbours = oriented_node.next_neighbours(graph)
    end

    neighbours.each do |onode|
      new_distance = current_distance
      if options[:neighbour_finder]
        if onode.distance
          new_distance += onode.distance
        else
          new_distance += 0
        end
      end
      new_distance += onode.node.length_alone

      new_path = current_path.copy
      new_path.add_oriented_node onode
      new_path.distance = new_distance
      stack.push new_path
    end
  end
end