Class: Bio::AssemblyGraphAlgorithms::Dijkstra

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

Defined Under Namespace

Classes: DistancedOrientedNode

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#min_distances(graph, initial_oriented_node, options = {}) ⇒ Object

Return an array of DistancedOrientedNode objects, those reachable from the initial_oriented_node. options: :leash_length => max distance explored,

can be set to nil to search indefinitely

:ignore_directions: => true or false (default). If true, explore direction-independently.

i.e. if 1s->3s and 2s->3s, then include 2s in the returned set of min_distances
and continue exploring from 2s. Return each found node twice, once for each direction

:neighbour_finder => an object that responds to #neighbours(oriented_node) and

returns an array of Bio::FinishM::PairedEndNeighbourFinder::Neighbour objects
default: just search using OrientedNode#next_neighbours

:max_nodes => maximum number of nodes to return, to prevent out of control

exploring of the graph. If there is plenty of nodes to explore, then the
length of the returned hash is options[:max_nodes]+1 (+1 because the starting
node is included). It will probably be longer if :ignore_directions == true, in that
case the number of node_ids is constrained. It may also be longer if there is ties
at the edges of the constrained exploration.

Returns a Hash of [node_id, first_side] => distance



25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
 
# File 'lib/assembly/dijkstra.rb', line 25

def min_distances(graph, initial_oriented_node, options={})
  pqueue = DS::AnyPriorityQueue.new {|a,b| a < b}
  first = DistancedOrientedNode.new
  first.node = initial_oriented_node.node
  first.first_side = initial_oriented_node.first_side
  first.distance = 0
  pqueue.push first, first.distance

  to_return = {}
  first_node = true
  found_nodes = Set.new([first.node.node_id])

  while min_distanced_node = pqueue.shift

    # Add/overwrite the current one
    to_return[min_distanced_node.to_settable] = min_distanced_node.distance

    log.debug "Working from #{min_distanced_node.inspect}" if log.debug?

    if options[:leash_length] and min_distanced_node.distance > options[:leash_length]
      # we are passed leash length, and this is the nearest node. So we are finito.
      log.debug "passed the leash length, cutting short our travels" if log.debug?
      break
    end

    if options[:max_nodes] and found_nodes.length > options[:max_nodes]
      log.debug "passed max-nodes threshold and have #{found_nodes.length} nodes" if log.debug?
      # remove extras that may have been queued if we are over the limit
      distances_direction_agnostic = {}
      to_return.each do |key, distance|
        prev = distances_direction_agnostic[key[0]]
        if prev.nil? or prev > distance
          distances_direction_agnostic[key[0]] = distance
        end
      end
      if distances_direction_agnostic.length > options[:max_nodes]
        sorted = distances_direction_agnostic.to_a.sort{|a,b| a[1]<=>b[1]}
        # deal with ties i.e. at the edge there can be multiple neighbours
        last_distance = sorted[options[:max_nodes]][1]

        # only keep those nodes that are sufficiently close
        to_return.select! do |key, distance|
          distance <= last_distance
        end
      end
      break
    end

    # Queue nodes after this one
    current_distance = min_distanced_node.distance

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

    # explore each neighbour node
    neighbours.each do |onode|
      found_nodes << onode.node.node_id
      new_distance = current_distance
      if options[:neighbour_finder]
        # Don't use negative distances as this algorithm cannot handle it, and it is impossible
        # anyway
        if onode.distance > 0
          new_distance += onode.distance
        else
          new_distance += 0
        end
      end
      unless first_node
        new_distance += min_distanced_node.node.length_alone
      end

      if to_return[onode.to_settable] and to_return[onode.to_settable] <= new_distance
        # We already know a shorter path to this neighbour, so ignore it
        log.debug "Already seen this node at the same or shorter distance, going no further" if log.debug?
      else
        log.debug "Queuing new distance for neighbour: #{onode}: #{new_distance}" if log.debug?
        # new shortest distance found. queue it up
        distanced_node = DistancedOrientedNode.new
        distanced_node.node = onode.node
        distanced_node.first_side = onode.first_side
        distanced_node.distance = new_distance
        to_return[onode.to_settable] = new_distance
        pqueue.push distanced_node, new_distance

        if options[:ignore_directions]
          reverse = DistancedOrientedNode.new
          reverse.node = onode.node
          reverse.first_side = onode.reverse.first_side
          reverse.distance = new_distance
          to_return[onode.to_settable] = new_distance
          pqueue.push reverse, new_distance
        end
      end
    end

    first_node = false
  end

  # if ignore directions, then fixup the return so that each direction is included
  if options[:ignore_directions]
    new_to_return = {}
    to_return.each do |key, distance|
      keys = [
        Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST,
        Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST].collect do |direction|
          [key[0], direction]
        end
      new_distance = keys.collect{|k| to_return[k]}.reject{|d| d.nil?}.min
      keys.each do |key|
        new_to_return[key] = new_distance
      end
    end
    to_return = new_to_return
  end

  return to_return
end

#min_distances_from_many_nodes_in_both_directions(graph, nodes, options = {}) ⇒ Object 



167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
 
# File 'lib/assembly/dijkstra.rb', line 167

def min_distances_from_many_nodes_in_both_directions(graph, nodes, options={})
  all_min_distances = {}
  nodes.each do |node|
  [
    Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST,
    Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST,
    ].each do |direction|
      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(node, direction)
      min_distances = min_distances(graph, onode, options)
      min_distances.each do |node_direction, distance|
        current = all_min_distances[node_direction]
        unless current and current > distance
          all_min_distances[node_direction] = distance
        end
      end
    end
  end
  return all_min_distances
end

#min_distances_in_both_directions(graph, node, options = {}) ⇒ Object

like #min_distances except explores in both directions



149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
 
# File 'lib/assembly/dijkstra.rb', line 149

def min_distances_in_both_directions(graph, node, options={})
  all_min_distances = {}
  [
    Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST,
    Bio::Velvet::Graph::OrientedNodeTrail::END_IS_FIRST,
    ].each do |direction|
      onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode.new(node, direction)
      min_distances = min_distances(graph, onode, options)
      min_distances.each do |node_direction, distance|
        current = all_min_distances[node_direction]
        unless current and current > distance
          all_min_distances[node_direction] = distance
        end
      end
    end
  return all_min_distances
end