Sha256: 44c6bbebceff730d0709b8d39b3e879b4e6911919f2702cfeb6168e9e0bea95f
Contents?: true
Size: 1.93 KB
Versions: 8
Compression:
Stored size: 1.93 KB
Contents
# A velvet Graph where the nodes and arcs are in Ruby, but the NodedReads are in C
class Bio::FinishM::HybridGraph < Bio::Velvet::Graph
include Bio::FinishM::Logging
attr_accessor :bio_velvet_underground_graph
def initialize(bio_velvet_graph, bio_velvet_underground_graph)
@bio_velvet_underground_graph = bio_velvet_underground_graph
@nodes = NodeArray.new(bio_velvet_graph, bio_velvet_underground_graph, self)
@hash_length = bio_velvet_graph.hash_length
@number_of_nodes = bio_velvet_graph.number_of_nodes
@number_of_sequences = bio_velvet_graph.number_of_sequences
@arcs = bio_velvet_graph.arcs
end
class NodeArray
include Enumerable
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
def []=(node_id, value)
raise "method not implemented"
end
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
def delete(node)
@bio_velvet_graph.nodes.delete node
end
def length
@bio_velvet_graph.nodes.length
end
def each(&block)
@bio_velvet_graph.nodes.each do |node|
block.yield self[node.node_id]
end
end
end
# Hold pointers to short reads, but don't actually create them until required.
# Utilizes method_missing to pick up calls made to the underlying object
class LazyShortReadArray
@short_reads = nil
def method_missing(m, *args, &block)
read_short_reads.send(m, *args, &block)
end
def read_short_reads
@short_reads ||= @parent_node.short_reads
end
def initialize(node)
@parent_node = node
end
end
end
Version data entries
8 entries across 8 versions & 1 rubygems