/ 
Bio-Phylo-0.16_RC1
River stage two • 9 direct dependents • 18 total dependents
/ Bio::Phylo::Taxa::Taxon

NAME

Bio::Phylo::Taxa::Taxon - The operational taxonomic unit.

SYNOPSIS

use Bio::Phylo::IO qw(parse);
use Bio::Phylo::Taxa;
use Bio::Phylo::Taxa::Taxon;

# array of names
my @apes = qw(
    Homo_sapiens
    Pan_paniscus
    Pan_troglodytes
    Gorilla_gorilla
);

# newick string
my $str = '(((Pan_paniscus,Pan_troglodytes),';
$str   .= 'Homo_sapiens),Gorilla_gorilla);';

# create tree object
my $tree = parse(
   -format => 'newick',
   -string => $str
)->first;

# instantiate taxa object
my $taxa = Bio::Phylo::Taxa->new;

# instantiate taxon objects, insert in taxa object
foreach( @apes ) {
   my $taxon = Bio::Phylo::Taxa::Taxon->new(
       -name => $_,
   );
   $taxa->insert($taxon);
}

# crossreference tree and taxa
$tree->crossreference($taxa);

# iterate over nodes
while ( my $node = $tree->next ) {

   # check references
   if ( $node->get_taxon ) {

       # prints crossreferenced tips
       print "match: ", $node->get_name, "\n";
   }
}

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 = Bio::Phylo::Taxa::Taxon->new;
Function: Instantiates a Bio::Phylo::Taxa::Taxon
          object.
Returns : A Bio::Phylo::Taxa::Taxon object.
Args    : none.

MUTATORS

set_data()
Type    : Mutator
Title   : set_data
Usage   : $taxon->set_data( $datum );
Function: Associates data with
          the current taxon.
Returns : Modified object.
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 : Modified object.
Args    : A Bio::Phylo::Forest::Node object
unset_datum()
Type    : Mutator
Title   : unset_datum
Usage   : $taxon->unset_datum($node);
Function: Disassociates datum from
          the invocant taxon (i.e.
          removes reference).
Returns : Modified object.
Args    : A Bio::Phylo::Matrix::Datum object
unset_node()
Type    : Mutator
Title   : unset_node
Usage   : $taxon->unset_node($node);
Function: Disassociates tree node from
          the invocant taxon (i.e.
          removes reference).
Returns : Modified object.
Args    : A Bio::Phylo::Forest::Node object

ACCESSORS

get_data()
Type    : Accessor
Title   : get_data
Usage   : @data = @{ $taxon->get_data };
Function: Retrieves data associated
          with the current taxon.
Returns : An ARRAY reference of
          Bio::Phylo::Matrices::Datum
          objects.
Args    : None.
get_nodes()
Type    : Accessor
Title   : get_nodes
Usage   : @nodes = @{ $taxon->get_nodes };
Function: Retrieves tree nodes associated
          with the current taxon.
Returns : An ARRAY reference of
          Bio::Phylo::Trees::Node objects
Args    : None.

DESTRUCTOR

DESTROY()
Type    : Destructor
Title   : DESTROY
Usage   : $phylo->DESTROY
Function: Destroys Phylo object
Alias   :
Returns : TRUE
Args    : none
Comments: You don't really need this,
          it is called automatically when
          the object goes out of scope.

SEE ALSO

Bio::Phylo

The taxon objects inherits from the Bio::Phylo object. The methods defined there are also applicable to the taxon object.

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: Taxon.pm 3319 2007-03-20 01:39:35Z 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.