/ 
Bio-Phylo-0.16_RC4
River stage two • 8 direct dependents • 17 total dependents
/ Bio::Phylo::Taxa::TaxaLinker

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.

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 3386 2007-03-24 16:22:25Z 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.