NAME

Bio::Phylo::Mediators::TaxaMediator - Mediator for links between taxa and other objects

SYNOPSIS

# no direct usage

DESCRIPTION

This module manages links between taxon objects and other objects linked to them. 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).

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

METHODS

CONSTRUCTOR

new()

TaxaMediator constructor.

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

METHODS

register()

Stores argument in invocant's cache.

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

unregister()

Removes argument from invocant'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 an object is destroyed.

set_link()

Creates link between objects.

Type    : Method
Title   : set_link
Usage   : $mediator->set_link( -one => $obj1, -many => $obj2 );
Function: Creates link between objects
Returns : $self
Args    : -one  => $obj1 (source of a one-to-many relationship)
          -many => $obj2 (target of a one-to-many relationship)
Comments: This method is called from within, for example, set_taxa
          method calls. A call like $taxa->set_matrix( $matrix ),
          and likewise a call like $matrix->set_taxa( $taxa ), are 
          both internally rerouted to:

          $mediator->set_link( 
               -one  => $taxa, 
               -many => $matrix 
          );

get_link()

Retrieves link between objects.

Type    : Method
Title   : get_link
Usage   : $mediator->get_link( 
              -source => $obj, 
              -type   => _CONSTANT_,
          );
Function: Retrieves link between objects
Returns : Linked object
Args    : -source => $obj (required, the source of the link)
          -type   => a constant from Bio::Phylo::Util::CONSTANT

          (-type is optional, used to filter returned results in 
          one-to-many query).

Comments: This method is called from within, for example, get_taxa
          method calls. A call like $matrix->get_taxa()
          and likewise a call like $forest->get_taxa(), are 
          both internally rerouted to:

          $mediator->get_link( 
              -source => $self # e.g. $matrix or $forest           
          );

          A call like $taxa->get_matrices() is rerouted to:

          $mediator->get_link( -source => $taxa, -type => _MATRIX_ );

remove_link()

Removes link between objects.

Type    : Method
Title   : remove_link
Usage   : $mediator->remove_link( -one => $obj1, -many => $obj2 );
Function: Removes link between objects
Returns : $self
Args    : -one  => $obj1 (source of a one-to-many relationship)
          -many => $obj2 (target of a one-to-many relationship)

          (-many argument is optional)

Comments: This method is called from within, for example, 
          unset_taxa method calls. A call like $matrix->unset_taxa() 
          is rerouted to:

          $mediator->remove_link( -many => $matrix );

          A call like $taxa->unset_matrix( $matrix ); is rerouted to:

          $mediator->remove_link( -one => $taxa, -many => $matrix );

SEE ALSO

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63