/ 
Bio-Phylo-0.01
River stage two • 8 direct dependents • 17 total dependents
/ Bio::Phylo::Taxa::Taxon

NAME

Bio::Phylo::Taxa::Taxon - An object-oriented module for managing a single taxon.

SYNOPSIS

my $taxon = Bio::Phylo::Taxa::Taxon->new(
   -name=>'Homo_sapiens',
   -desc=>'Canonical taxon'
);

DESCRIPTION

The taxon object models a single operational taxonomic unit. It is useful for cross-referencing datum objects and tree nodes.

METHODS

CONSTRUCTOR

new()
Type    : Constructor
Title   : new
Usage   : my $taxon = new Bio::Phylo::Taxa::Taxon;
Function: Initializes a Bio::Phylo::Taxa::Taxon object.
Returns : A Bio::Phylo::Taxa::Taxon object.
Args    : none.

MUTATORS

set_name()
Type    : Mutator
Title   : set_name
Usage   : $taxon->set_name($newname);
Function: Assigns a taxon's name.
Returns :
Args    : $newname must not contain [;|,|:|(|)]
set_desc()
Type    : Mutator
Title   : set_desc
Usage   : $taxon->set_desc($newdesc);
Function: Assigns a description of the current taxon.
Returns :
Args    : A SCALAR string of arbitrary length
set_data()
Type    : Mutator
Title   : set_data
Usage   : $taxon->set_data($datum);
Function: Associates data with the current taxon.
Returns :
Args    : Must be an object of type Bio::Phylo::Matrices::Datum
set_nodes()
Type    : Mutator
Title   : set_nodes
Usage   : $taxon->set_nodes($node);
Function: Associates tree nodes with the current taxon.
Returns :
Args    : A Bio::Phylo::Trees::Node object

ACCESSORS

get_name()
Type    : Accessor
Title   : get_name
Usage   : $name = $taxon->get_name();
Function: Retrieves a taxon's name.
Returns : SCALAR
Args    :
get_desc()
Type    : Accessor
Title   : get_desc
Usage   : $desc = $taxon->get_desc();
Function: Assigns a description of the current taxon.
Returns : SCALAR
Args    :
get_data()
Type    : Accessor
Title   : get_data
Usage   : @data = $taxon->get_data();
Function: Retrieves data associated with the current taxon.
Returns : An ARRAY of Bio::Phylo::Matrices::Datum objects.
Args    :
get_nodes()
Type    : Accessor
Title   : get_nodes
Usage   : @nodes = $taxon->get_nodes();
Function: Retrieves tree nodes associated with the current taxon.
Returns : An ARRAY of Bio::Phylo::Trees::Node objects
Args    :

CONTAINER

container
Type    : Internal method
Title   : container
Usage   : $taxon->container;
Function:
Returns : SCALAR
Args    :
container_type
Type    : Internal method
Title   : container_type
Usage   : $taxon->container_type;
Function:
Returns : SCALAR
Args    :

AUTHOR

Rutger Vos, <rvosa@sfu.ca>

BUGS

Please report any bugs or feature requests to bug-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

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