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Contents
require 'ds'
require 'set'
class Bio::AssemblyGraphAlgorithms::SequenceHasher
include Bio::FinishM::Logging
#
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
class DistancedOrientedNodeTrail < Bio::Velvet::Graph::OrientedNodeTrail
attr_accessor :distance
def copy
o = DistancedOrientedNodeTrail.new
o.trail = Array.new(@trail.collect{|onode| onode.copy})
o.distance = @distance
return o
end
def to_s
"DistancedOrientedTrail: #{object_id}: #{to_shorthand} distance=#{@distance}"
end
end
end
Version data entries
8 entries across 8 versions & 1 rubygems