Bio::Network::Interaction - describes a protein-protein interaction
# Add an interaction with some attributes use Bio::Network::Interaction; my $interx = Bio::Network::Interaction->new(-weight => $score, -id => $id); $gr->add_interaction(-nodes => [($node1,$node2)], -interaction => $interx); # Retrieve an interaction using an identifier my $interaction = $gr->get_interaction_by_id($id); my $id = $interaction->primary_id; my $wt = $interaction->weight; my @nodes = $interaction->nodes;
This class contains information about a bi-molecular interaction. At present it just contains data about a weight (optional) and an identifier. Subclasses could hold more specific information. A pair of nodes can have more than one Interaction object associated with it.
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Name : new Purpose : Constructor for an Interaction object Usage : my $interx = Bio::Network::Interaction->new(-id => $id); Returns : A new Bio::Network::Interaction object Arguments : -id => interaction id -weight (optional) => weight score
Name : weight Purpose : Get or set a weight or score Usage : my $weight = $interx->weight() or $interx->weight(3) Returns : a number Arguments : Nothing or a number
Name : primary_id Purpose : Get or set the primary_id Usage : my $id = $interx->primary_id() or $interx->primary_id("SIB4") Returns : A string identifier Arguments : Nothing or an identifier
Name : nodes Purpose : Get the pair of nodes for an Interaction Usage : my $count = $interx->nodes or my @nodes = $interx->nodes Returns : Gets an array of 2 Nodes or a count of the number of Nodes Arguments : Notes : Getting a count of the number of Nodes in an Interaction will almost always return 2, but there is a formal possibility that a Node could interact with itself, returning 1
Title : annotation Usage : my $annotation = $ix->annotation or $ix->annotation($annotation) Function: Gets or sets the annotation Returns : Bio::AnnotationCollectionI object Args : None or Bio::AnnotationCollectionI object
Name : object_id Purpose : Alias to primary_id Usage : my $id = $edge->object_id() Notes : Deprecated