NAME

Bio::Phylo::Mediators::NodeMediator - Mediator class to manage links between nodes.

SYNOPSIS

 # no direct usage

DESCRIPTION

This module manages links between node objects. It is an implementation of the Mediator design pattern (e.g. see Relationship Manager Pattern, Mediator, Mediator Design Pattern).

Methods defined in this module are meant only for internal usage by Bio::Phylo.

METHODS

CONSTRUCTOR

new()

 Type    : Constructor
 Title   : new
 Usage   : my $mediator = Bio::Phylo::Taxa::NodeMediator->new;
 Function: Instantiates a Bio::Phylo::Taxa::NodeMediator
           object.
 Returns : A Bio::Phylo::Taxa::NodeMediator object (singleton).
 Args    : None.

METHODS

register()

 Type    : Method
 Title   : register
 Usage   : $mediator->register( $obj );
 Function: Stores an object in mediator's cache
 Returns : $self
 Args    : An object, $obj
 Comments: This method is called every time a node is instantiated.

unregister()

 Type    : Method
 Title   : unregister
 Usage   : $mediator->unregister( $obj );
 Function: Cleans up mediator's cache of $obj and $obj's relations
 Returns : $self
 Args    : An object, $obj
 Comments: This method is called every time a node ($obj) is destroyed.

set_link()

 Type    : Method
 Title   : set_link
 Usage   : $mediator->set_link( node => $obj1, $connection => $obj2 );
 Function: Creates link between objects
 Returns : $self
 Args    : node => a $node object
                   $connection => another $node object, where $connection is
                   *    parent
                   *    first_daughter
                   *    last_daughter
                   *    next_sister
                   *    previous_sister
 Comments: This method is called from within, for example, set_parent
           method calls. A call like $node1->set_parent( $node2 ),
           is internally rerouted to:

           $mediator->set_link( 
                node   => $node1,
                parent => $node2, 
           );

update_tree()

 Type    : Method
 Title   : update_tree
 Usage   : $mediator->update_tree( 
               keep   => $node1, 
               update => $node2,
           );
 Function: updates tree membership
 Returns : Linked object
 Args    : keep   => $node1 (node whose tree membership to retain)
           update => $node2 (node whose tree membership 
           is moved to that of $node1)

 Comments: This method is called so that $node2 and its descendants
                   becomes member of the same tree as $node1

get_link()

 Type    : Method
 Title   : get_link
 Usage   : $mediator->get_link( $connection => $node );
 Function: Retrieves relative of $node
 Returns : Relative of $node
 Args    : $connection => $node, where $connection can be:
                   *    parent_of
                   *    next_sister_of
                   *    previous_sister_of
                   *    first_daughter_of
                   *    last_daughter_of

SEE ALSO

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: TaxaMediator.pm 3386 2007-03-24 16:22:25Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.