Class: Bio::FinishM::PairedEndNeighbourFinder::Neighbour

Inherits:
Velvet::Graph::OrientedNodeTrail::OrientedNode show all
Defined in:
lib/assembly/paired_end_neighbour_finder.rb

Constant Summary collapse

PAIRED_END_CONNECTION = 
:paired_end_connection
DIRECT_CONNECTION = 
:direct_connection

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from Velvet::Graph::OrientedNodeTrail::OrientedNode

#==, #copy, #hash, #initialize, #next_neighbours, #node_id, #reverse, #reverse!, #starts_at_end?, #starts_at_start?, #to_shorthand

Constructor Details

This class inherits a constructor from Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode

Instance Attribute Details

#connection_type ⇒ Object

Returns the value of attribute connection_type.



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 160

def connection_type
  @connection_type
end

#distance ⇒ Object

Returns the value of attribute distance.



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 164

def distance
  @distance
end

#first_side ⇒ Object

Returns the value of attribute first_side.



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 163

def first_side
  @first_side
end

#node ⇒ Object

Returns the value of attribute node.



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 162

def node
  @node
end

#num_adjoining_reads ⇒ Object

Returns the value of attribute num_adjoining_reads.



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 165

def num_adjoining_reads
  @num_adjoining_reads
end

Instance Method Details

#inspect ⇒ Object Also known as: to_s 



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 171

def inspect
  "Neighbour #{object_id}: node=#{@node.node_id} first=#{@first_side} distance=#{@distance} num_adjoining_reads=#{@num_adjoining_reads} connection_type:#{@connection_type}"
end

#to_settable ⇒ Object 



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# File 'lib/assembly/paired_end_neighbour_finder.rb', line 167

def to_settable
  [@node.node_id, @first_side]
end