Class: Bio::AssemblyGraphAlgorithms::BubblyAssembler::DynamicProgrammingProblem

Inherits:
Object
  • Object
show all
Defined in:
lib/assembly/bubbly_assembler.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ DynamicProgrammingProblem

Returns a new instance of DynamicProgrammingProblem.



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# File 'lib/assembly/bubbly_assembler.rb', line 813

def initialize
  @path = []
  @ubiquitous_oriented_nodes = Set.new
end

Instance Attribute Details

#circular_path_detected ⇒ Object

Returns the value of attribute circular_path_detected.



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# File 'lib/assembly/bubbly_assembler.rb', line 811

def circular_path_detected
  @circular_path_detected
end

#distance ⇒ Object

Returns the value of attribute distance.



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# File 'lib/assembly/bubbly_assembler.rb', line 811

def distance
  @distance
end

#path ⇒ Object

Returns the value of attribute path.



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# File 'lib/assembly/bubbly_assembler.rb', line 811

def path
  @path
end

#ubiquitous_oriented_nodes ⇒ Object

Returns the value of attribute ubiquitous_oriented_nodes.



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# File 'lib/assembly/bubbly_assembler.rb', line 811

def ubiquitous_oriented_nodes
  @ubiquitous_oriented_nodes
end

#visited_oriented_nodes ⇒ Object

Returns the value of attribute visited_oriented_nodes.



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# File 'lib/assembly/bubbly_assembler.rb', line 811

def visited_oriented_nodes
  @visited_oriented_nodes
end

Instance Method Details

#to_s ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 822

def to_s
  ubiquitous_nodes = @ubiquitous_oriented_nodes.collect do |settabled|
    "#{settabled[0] }#{settabled[1] == Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST ? 's' : 'e'}"
  end
  return "DPP #{self.object_id}: #{@path.to_shorthand}/#{ubiquitous_nodes.join(',') }/#{distance}"
end

#to_settable ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 818

def to_settable
  @path[-1].to_settable
end

#to_shorthand ⇒ Object 



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# File 'lib/assembly/bubbly_assembler.rb', line 829

def to_shorthand
  ubiquitous_nodes = @ubiquitous_oriented_nodes.collect do |settabled|
    "#{settabled[0] }#{settabled[1] == Bio::Velvet::Graph::OrientedNodeTrail::START_IS_FIRST ? 's' : 'e'}"
  end
  "#{@path.to_shorthand}/#{ubiquitous_nodes.join(',') }/#{distance}"
end