Summary

Bio::Graph::Edge - encapsulation of an interaction between 2 Bio::Seq objects

Package variables

Inherit

Bio::IdentifiableI Bio::Root::Root

Synopsis

  ## get an interaction between two nodes ##

  my $edge  = $gr->edge( $gr->nodes_by_id('P12345'),
                         $gr->nodes_by_id('P23456'));
  my $id    = $edge->object_id();
  my $wt    = $edge->weight();
  my @nodes = $edge->nodes();

Description

This class contains information about a bimolecular interaction.
At present it just contains data about its component node, a weight
(if set) and an identifier. Subclasses could hold more specific
information.

Methods

Methods description

 Name       : new
 Purpose    : constructor for an edge object
 Usage      : my $edge = Bio::Graph::Edge->new(nodes => [$node1,$node2]
                                               id => $id);
              $graph->add_edge($edge);
 Returns    : a new Bio::Graph::Edge object 
 Arguments  : hash nodes            => array reference of 2 nodes
                   id               => edge id
                   weight(optional) => weight score.

 Name      : weight
 Purpose   : get/setter for weight score
 Usage     : my $weight = $edge->weight();
 Returns   : anumber
 Arguments : void/ a number

 Name      : object_id
 Purpose   : get/setter for object_id
 Usage     : my $id = $edge->object_id();
 Returns   : a string identifier
 Arguments : void/ an identifier

 Name      : nodes
 Purpose   : get/setter for nodes
 Usage     : my @nodes = $edge->nodes();
 Returns   : a 2 element list of nodes /void
 Arguments : void/ a 2 element list of nodes.

Methods code

sub new {

      ##array based, not hash based ##..., therefore does not use 
      #Bio::Root::Root->new().

	my ($caller, @args) = @_;
	my $class  = ref ($caller) || $caller;
	my $self    = [];
	bless ($self, $class);

	my ($weight, $id, $nodes) = $self->_rearrange([qw( WEIGHT ID NODES)], @args);
	$self->[0] = $nodes->[0];
	$self->[1] = $nodes->[1];
	$self->[2] = defined($weight)?$weight:undef; 
	$self->[3] = defined($id)?$id:undef; 
	return $self;

}

sub weight {

	my $self = shift;
	if (@_) {$self->[2] = shift;}
	return defined($self->[2])?$self->[2]:undef;

}

sub object_id {

	my $self            = shift;
	if (@_) {
		my $v  = shift;
		if (ref ($v)) {
			$self->throw ("Edge ID must be a text value, not a [".
							ref($v). "].");
			} 
		$self->[3] = shift;
	}
	return defined($self->[3])?$self->[3]:undef;

}

sub nodes {

	my ($self, @args) = @_;
	if (@args >= 2 ) {
		$self->[0] =  $args[0];
		$self->[1] =  $args[1];
		}
	return ($self->[0], $self->[1]);

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Email richard.adams@ed.ac.uk