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 http://www.atug.com/andypatterns/RM.htm, http://home.earthlink.net/~huston2/dp/mediator.html, http://sern.ucalgary.ca/courses/SENG/443/W02/assignments/Mediator/).

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

METHODS

CONSTRUCTOR

new()

NodeMediator constructor.

 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()

Stores an object in mediator's cache.

 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()

Removes argument from mediator's cache.

 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()

Creates link between arguments.

 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()

Updates tree membership.

 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()

Retrieves relative of argument.

 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.