Class: Bio::FinishM::HybridGraph::NodeArray

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/assembly/hybrid_velvet_graph.rb

Instance Method Summary collapse

Constructor Details

#initialize(bio_velvet_graph, bio_velvet_underground_graph, parent_graph) ⇒ NodeArray

Returns a new instance of NodeArray.



20
21
22
23
24
 
# File 'lib/assembly/hybrid_velvet_graph.rb', line 20

def initialize(bio_velvet_graph, bio_velvet_underground_graph, parent_graph)
  @bio_velvet_graph = bio_velvet_graph
  @bio_velvet_underground_graph = bio_velvet_underground_graph
  @parent_graph = parent_graph
end

Instance Method Details

#[](node_id) ⇒ Object 



30
31
32
33
34
35
 
# File 'lib/assembly/hybrid_velvet_graph.rb', line 30

def [](node_id)
  bio_velvet_node = @bio_velvet_graph.nodes[node_id]
  bio_velvet_node.short_reads = LazyShortReadArray.new(@bio_velvet_underground_graph.nodes[node_id])
  bio_velvet_node.parent_graph = @parent_graph
  return bio_velvet_node
end

#[]=(node_id, value) ⇒ Object 



26
27
28
 
# File 'lib/assembly/hybrid_velvet_graph.rb', line 26

def []=(node_id, value)
  raise "method not implemented"
end

#delete(node) ⇒ Object 



37
38
39
 
# File 'lib/assembly/hybrid_velvet_graph.rb', line 37

def delete(node)
  @bio_velvet_graph.nodes.delete node
end

#each(&block) ⇒ Object 



45
46
47
48
49
 
# File 'lib/assembly/hybrid_velvet_graph.rb', line 45

def each(&block)
  @bio_velvet_graph.nodes.each do |node|
    block.yield self[node.node_id]
  end
end

#length ⇒ Object 



41
42
43
 
# File 'lib/assembly/hybrid_velvet_graph.rb', line 41

def length
  @bio_velvet_graph.nodes.length
end