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Bio::Phylo::Mediators::TaxaMediator(3) |
User Contributed Perl Documentation |
Bio::Phylo::Mediators::TaxaMediator(3) |
Bio::Phylo::Mediators::TaxaMediator - Mediator for links between taxa and other
objects
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.
- 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.
- 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 );
There is a mailing list at
<https://groups.google.com/forum/#!forum/bio-phylo> for any user or
developer questions and discussions.
- Bio::Phylo::Manual
- Also see the manual: Bio::Phylo::Manual and
<http://rutgervos.blogspot.com>.
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>
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