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 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

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

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.

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