NAME

Bio::Phylo::Taxa::TaxaLinker - Superclass for objects that link to taxa objects.

SYNOPSIS

use Bio::Phylo::Matrices::Matrix;
use Bio::Phylo::Taxa;

my $matrix = Bio::Phylo::Matrices::Matrix->new;
my $taxa = Bio::Phylo::Taxa->new;

if ( $matrix->isa('Bio::Phylo::Taxa::TaxaLinker') ) {
   $matrix->set_taxa( $taxa );
}

DESCRIPTION

This module is a superclass for objects that link to Bio::Phylo::Taxa objects.

METHODS

CONSTRUCTOR

new()

TaxaLinker constructor.

Type    : Constructor
Title   : new
Usage   : # no direct usage
Function: 
Returns :
Args    :

MUTATORS

set_taxa()

Associates invocant with Bio::Phylo::Taxa argument.

Type    : Mutator
Title   : set_taxa
Usage   : $obj->set_taxa( $taxa );
Function: Links the invocant object
          to a taxa object.
Returns : Modified $obj
Args    : A Bio::Phylo::Taxa object.

unset_taxa()

Removes association between invocant and Bio::Phylo::Taxa object.

Type    : Mutator
Title   : unset_taxa
Usage   : $obj->unset_taxa();
Function: Removes the link between invocant object and taxa
Returns : Modified $obj
Args    : NONE

ACCESSORS

get_taxa()

Retrieves association between invocant and Bio::Phylo::Taxa object.

Type    : Accessor
Title   : get_taxa
Usage   : my $taxa = $obj->get_taxa;
Function: Retrieves the Bio::Phylo::Taxa
          object linked to the invocant.
Returns : Bio::Phylo::Taxa
Args    : NONE
Comments: This method returns the Bio::Phylo::Taxa
          object to which the invocant is linked.
          The returned object can therefore contain
          *more* taxa than are actually in the matrix.

check_taxa()

Performs sanity check on taxon relationships.

Type    : Interface method
Title   : check_taxa
Usage   : $obj->check_taxa
Function: Performs sanity check on taxon relationships
Returns : $obj
Args    : NONE

SEE ALSO

Bio::Phylo::Matrices::Matrix

The matrix object subclasses Bio::Phylo::Taxa::TaxaLinker.

Bio::Phylo::Forest

The forest object subclasses Bio::Phylo::Taxa::TaxaLinker.

Bio::Phylo::Manual

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

REVISION

$Id: TaxaLinker.pm 4265 2007-07-20 14:14:44Z rvosa $