Bio::Phylo::Taxa::TaxaLinker(3)

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>