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BioPerl-Network-1.006902
River stage zero No dependents
/ Bio::Network::Interaction

NAME

Bio::Network::Interaction - describes a protein-protein interaction

SYNOPSIS

# 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;

DESCRIPTION

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.

FEEDBACK

Mailing Lists

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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

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/

AUTHORS

Brian Osborne bosborne at alum.mit.edu Richard Adams richard.adams@ed.ac.uk

Maintained by Brian Osborne

new

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

weight

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

primary_id

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

nodes

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

annotation

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

See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information

object_id

Name      : object_id
Purpose   : Alias to primary_id
Usage     : my $id = $edge->object_id()
Notes     : Deprecated