Class: Bio::Velvet::Underground::Graph

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-velvet_underground/graph.rb

Defined Under Namespace

Classes: ArcArray, Node, NodeArray, NodedRead

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(graph_struct) ⇒ Graph

Use parse_from_file, not #new



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# File 'lib/bio-velvet_underground/graph.rb', line 10

def initialize(graph_struct)
  @internal_graph_struct = graph_struct
end

Instance Attribute Details

#internal_graph_struct ⇒ Object

Returns the value of attribute internal_graph_struct.



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# File 'lib/bio-velvet_underground/graph.rb', line 7

def internal_graph_struct
  @internal_graph_struct
end

Class Method Details

.parse_from_file(path) ⇒ Object

Read in a graph from a file



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# File 'lib/bio-velvet_underground/graph.rb', line 15

def self.parse_from_file(path)
  # First read the first line of the file to determine which underground velvet library to load
  hash_length = nil
  CSV.foreach(path, :col_sep => "\t") do |row|
    raise "Badly formatted graph file" if row.length < 3
    hash_length = row[2].to_i
    if hash_length < 1 or hash_length > Bio::Velvet::Underground.max_kmers.max
      raise "unable to load velvet shared library for kmer length `#{hash_length}'"
    end
    break
  end
  raise "No lines in graph file `#{path}', is it really a velvet LastGraph-type file?" if hash_length.nil?

  # setup FFI in the underground base class with the correct kmer length
  Bio::Velvet::Underground.attach_shared_library(:kmer => hash_length)

  # Using the loaded velvet library, do the actual import of the graph
  pointer = Bio::Velvet::Underground.importGraph path
  struct = Bio::Velvet::Underground::GraphStruct.new pointer
  Graph.new struct
end

Instance Method Details

#hash_length ⇒ Object 



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# File 'lib/bio-velvet_underground/graph.rb', line 45

def hash_length
  @internal_graph_struct[:wordLength]
end

#node_count ⇒ Object 



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# File 'lib/bio-velvet_underground/graph.rb', line 41

def node_count
  @internal_graph_struct[:nodeCount]
end

#nodes ⇒ Object 



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# File 'lib/bio-velvet_underground/graph.rb', line 37

def nodes
  @nodes ||= NodeArray.new self #cache node array
end