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

NAME

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

SYNOPSIS

 use Bio::Phylo::Factory;
 my $fac = Bio::Phylo::Factory->new;

 my $matrix = $fac->create_matrix;
 my $taxa = $fac->create_taxa;

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

DESCRIPTION

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

the Bio::Phylo::Matrices::Matrix manpage

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

the Bio::Phylo::Forest manpage

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

the Bio::Phylo::Manual manpage

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

REVISION

 $Id: TaxaLinker.pm 841 2009-03-04 23:07:30Z rvos $
 Bio::Phylo::Taxa::TaxaLinker - Superclass for objects that link to taxa objects