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

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

make_taxa()

Creates a taxa block from the objects contents if none exists yet.

 Type    : Decorated interface method
 Title   : make_taxa
 Usage   : my $taxa = $obj->make_taxa
 Function: Creates a taxa block from the objects contents if none exists yet.
 Returns : $taxa
 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 and http://rutgervos.blogspot.com.

REVISION

 $Id: TaxaLinker.pm 604 2008-09-05 17:32:28Z rvos $