Link documentation.

Object oriented graph system which is based on Node and Link objects. There is
no 'graph' object, the graph is constructed out of Nodes and Links, and the
graph is 'walked' from Node to Link to Node. Can be used to represent any graph
structure from DAGs (directed acyclic graph) to Trees to undirected cyclic Graphs.
The system is fully connected so from any object in the graph one can 'walk' to
any other. Links contain pointers to the nodes on either side (called neighbors),
and each Node contains a list of the links it is connected to.
Nodes also keep hashes of their neighbors for fast 'set theory' operations.
This graph system is used as the foundation for the Nested-set
(Compara::NestedSet) system for storing trees in the compara database.
System has a simple API based on creating Nodes and then linking them together:
my $node1 = new Bio::EnsEMBL::Compara::Graph::Node;
my $node2 = new Bio::EnsEMBL::Compara::Graph::Node;
new Bio::EnsEMBL::Compara::Graph::Link($node1, $node2, $distance_between);
And to 'disconnect' nodes, one just breaks a link;
my $link = $node1->link_for_neighbor($node2);
$link->dealloc;
Convenience methods to simplify this process
$node1->create_link_to_node($node2, $distance_between);
$node2->unlink_neighbor($node1);

sub copy {

  my $self = shift;
  
  my ($node1, $node2) = $self->get_nodes;
  my $mycopy = new Bio::EnsEMBL::Compara::Graph::Link($node1, $node2);
  $mycopy->distance_between($self->distance_between);

  return $mycopy;

}

sub dealloc {

  my $self = shift;
  
  $self->{'_link_node1'}->_unlink_node_in_hash($self->{'_link_node2'});
  $self->{'_link_node2'}->_unlink_node_in_hash($self->{'_link_node1'});

  $self->{'_link_node1'} = undef;
  $self->{'_link_node2'} = undef;
  
  #printf("DEALLOC link refcount:%d ", $self->refcount);
}


# copy system is based that the nodes make the copies
# and the link just links (retains)

}

sub distance_between {

  my $self = shift;
  $self->{'_distance_between'} = shift if(@_);
  $self->{'_distance_between'} = 0.0 unless(defined($self->{'_distance_between'}));
  return $self->{'_distance_between'};

}

sub equals {

  my $self = shift;
  my $other = shift;
#  throw("arg must be a [Bio::EnsEMBL::Compara::Graph::Link] not a [$other]")
#        unless($other and $other->isa('Bio::EnsEMBL::Compara::Graph::Link')); # BEWARE speed up change uncommented
  return 1 if($self->obj_id eq $other->obj_id); # BEWARE speed up change below
  # return 1 if($self->{'_cgobject_id'} eq $other->{'_cgobject_id'});
  return 0;

}

sub get_neighbor {

  my $self = shift;
  my $node = shift;
  
  return $self->{'_link_node2'} if($node->equals($self->{'_link_node1'}));
  return $self->{'_link_node1'} if($node->equals($self->{'_link_node2'}));
  return undef;

}

sub new {

  my $class = shift;
  my $node1 = shift;
  my $node2 = shift;
  my $dist = shift;

  throw("arg1 must be a [Bio::EnsEMBL::Compara::Graph::Node] not a [$node1]")
        unless(defined($node1) and $node1->isa('Bio::EnsEMBL::Compara::Graph::Node'));
  throw("arg2 must be a [Bio::EnsEMBL::Compara::Graph::Node] not a [$node2]")
        unless(defined($node2) and $node2->isa('Bio::EnsEMBL::Compara::Graph::Node'));

  my $self = $class->SUPER::new;
  bless $self, "Bio::EnsEMBL::Compara::Graph::Link";

  $self->{'_link_node1'} = $node1;
  $self->{'_link_node2'} = $node2;
  
  $node1->_add_neighbor_link_to_hash($node2, $self);
  $node2->_add_neighbor_link_to_hash($node1, $self);
  
  $self->distance_between($dist) if(defined($dist));
  return $self;

}

sub print_link {

  my $self  = shift;
  printf("link(%s): (%s)-- %1.5f --(%s)\n", 
      $self->obj_id, 
      $self->{'_link_node1'}->node_id,
      $self->distance_between,
      $self->{'_link_node2'}->node_id,
    );
}


1;

}

copy	No description	Code
dealloc	No description	Code
distance_between	Description	Code
equals	No description	Code
get_neighbor	Description	Code
get_nodes	Description	Code
new	Description	Code
print_link	No description	Code