Class: Bio::Velvet::Graph::Arc

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#begin_node_direction ⇒ Object

true for forwards direction, false for reverse



480
481
482
 
# File 'lib/bio-velvet/graph.rb', line 480

def begin_node_direction
  @begin_node_direction
end

#begin_node_id ⇒ Object

Returns the value of attribute begin_node_id.



477
478
479
 
# File 'lib/bio-velvet/graph.rb', line 477

def begin_node_id
  @begin_node_id
end

#end_node_direction ⇒ Object

true for forwards direction, false for reverse



480
481
482
 
# File 'lib/bio-velvet/graph.rb', line 480

def end_node_direction
  @end_node_direction
end

#end_node_id ⇒ Object

Returns the value of attribute end_node_id.



477
478
479
 
# File 'lib/bio-velvet/graph.rb', line 477

def end_node_id
  @end_node_id
end

#multiplicity ⇒ Object

Returns the value of attribute multiplicity.



477
478
479
 
# File 'lib/bio-velvet/graph.rb', line 477

def multiplicity
  @multiplicity
end

Instance Method Details

#begin_node_forward? ⇒ Boolean 



493
494
495
 
# File 'lib/bio-velvet/graph.rb', line 493

def begin_node_forward?
  @begin_node_direction
end

#connects_beginning_to_beginning?(first_node_id, second_node_id) ⇒ Boolean

Returns true if this arc connects the start of the first node to the start of the second node, else false



524
525
526
527
528
529
 
# File 'lib/bio-velvet/graph.rb', line 524

def connects_beginning_to_beginning?(first_node_id, second_node_id)
  (first_node_id == @begin_node_id and second_node_id == @end_node_id and
    @begin_node_direction == false and @end_node_direction == true) or
    (first_node_id == @end_node_id and second_node_id = @begin_node_id and
    @begin_node_direction == false and @end_node_direction == true)
end

#connects_beginning_to_end?(first_node_id, second_node_id) ⇒ Boolean

Returns true if this arc connects the start of the first node to the start of the second node, else false



533
534
535
536
537
538
 
# File 'lib/bio-velvet/graph.rb', line 533

def connects_beginning_to_end?(first_node_id, second_node_id)
  (first_node_id == @begin_node_id and second_node_id == @end_node_id and
    @begin_node_direction == false and @end_node_direction == false) or
    (first_node_id == @end_node_id and second_node_id = @begin_node_id and
    @begin_node_direction == true and @end_node_direction == true)
end

#connects_end_to_beginning?(first_node_id, second_node_id) ⇒ Boolean

Returns true if this arc connects the end of the first node to the start of the second node, else false



503
504
505
506
507
508
509
510
511
 
# File 'lib/bio-velvet/graph.rb', line 503

def connects_end_to_beginning?(first_node_id, second_node_id)
  # ARC $START_NODE $END_NODE $MULTIPLICITY
  #Note: this one line implicitly represents an arc from node A to B and
  #another, with same multiplicity, from -B to -A.
  (first_node_id == @begin_node_id and second_node_id == @end_node_id and
    @begin_node_direction == true and @end_node_direction == true) or
    (first_node_id == @end_node_id and second_node_id = @begin_node_id and
    @begin_node_direction == false and @end_node_direction == false)
end

#connects_end_to_end?(first_node_id, second_node_id) ⇒ Boolean

Returns true if this arc connects the end of the first node to the end of the second node, else false



515
516
517
518
519
520
 
# File 'lib/bio-velvet/graph.rb', line 515

def connects_end_to_end?(first_node_id, second_node_id)
  (first_node_id == @begin_node_id and second_node_id == @end_node_id and
    @begin_node_direction == true and @end_node_direction == false) or
    (first_node_id == @end_node_id and second_node_id = @begin_node_id and
    @begin_node_direction == true and @end_node_direction == false)
end

#connects_to_beginning?(node_id) ⇒ Boolean

Return true if this arc connects the beginning of the node, else false



542
543
544
545
 
# File 'lib/bio-velvet/graph.rb', line 542

def connects_to_beginning?(node_id)
  (node_id == @begin_node_id and !@begin_node_direction) or
  (node_id == @end_node_id and @end_node_direction)
end

#connects_to_end?(node_id) ⇒ Boolean

Return true if this arc connects the end of the node, else false



549
550
551
552
 
# File 'lib/bio-velvet/graph.rb', line 549

def connects_to_end?(node_id)
  (node_id == @begin_node_id and @begin_node_direction) or
  (node_id == @end_node_id and !@end_node_direction)
end

#directions_opposing? ⇒ Boolean 



482
483
484
485
486
487
488
489
490
491
 
# File 'lib/bio-velvet/graph.rb', line 482

def directions_opposing?
  if (@begin_node_direction == true and @end_node_direction == false) or
    (@begin_node_direction == false and @end_node_direction == true)
    return true
  elsif [true,false].include?(@begin_node_direction) and [true,false].include?(@end_node_direction)
    return false
  else
    raise Exception, "Node directions not set! Cannot tell whether directions are opposing"
  end
end

#end_node_forward? ⇒ Boolean 



497
498
499
 
# File 'lib/bio-velvet/graph.rb', line 497

def end_node_forward?
  @end_node_forward
end

#to_s ⇒ Object 



554
555
556
557
558
559
560
561
562
563
564
 
# File 'lib/bio-velvet/graph.rb', line 554

def to_s
  str = ''
  str += '-' if @begin_node_direction == false
  str += @begin_node_id.to_s
  str += ' '
  str += '-' if @end_node_direction == false
  str += @end_node_id.to_s
  str += ' '
  str += @multiplicity.to_s
  str
end