Class: Bio::FinishM::HybridGraph

Inherits:
Velvet::Graph show all
Includes:
Logging
Defined in:
lib/assembly/hybrid_velvet_graph.rb

Overview

A velvet Graph where the nodes and arcs are in Ruby, but the NodedReads are in C

Defined Under Namespace

Classes: LazyShortReadArray, NodeArray

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Logging

#log

Methods inherited from Velvet::Graph

#depth_first_search, #neighbours_of, #neighbours_of_node_id

Constructor Details

#initialize(bio_velvet_graph, bio_velvet_underground_graph) ⇒ HybridGraph

Returns a new instance of HybridGraph.



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# File 'lib/assembly/hybrid_velvet_graph.rb', line 7

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

Instance Attribute Details

#bio_velvet_underground_graph ⇒ Object

Returns the value of attribute bio_velvet_underground_graph.



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# File 'lib/assembly/hybrid_velvet_graph.rb', line 5

def bio_velvet_underground_graph
  @bio_velvet_underground_graph
end