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()

 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()

 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()

 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()

 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.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: TaxaLinker.pm 4175 2007-07-11 02:13:51Z rvosa $

AUTHOR

Rutger A. Vos,

email: rvosa@sfu.ca

web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.