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NAME

Bio::Phylo::Taxa - An object-oriented module for managing taxa.

SYNOPSIS

# A mesquite-style default
# taxa block for 10 taxa.
my $taxa = Bio::Phylo::Taxa->new;
for my $i ( 1 .. 10 ) {
my $taxon = Bio::Phylo::Taxa::Taxon->new(
'-name' => 'taxon_' . $i,
);
$taxa->insert( $taxon );
}

DESCRIPTION

The Bio::Phylo::Taxa object models a set of operational taxonomic units. The object subclasses the Bio::Phylo::Listable object, and so the filtering methods of that class are available.

A taxa object can link to multiple forest and matrix objects.

METHODS

CONSTRUCTOR

new()
Type : Constructor
Title : new
Usage : my $taxa = Bio::Phylo::Taxa->new;
Function: Instantiates a Bio::Phylo::Taxa object.
Returns : A Bio::Phylo::Taxa object.
Args : none.

MUTATORS

set_forest()
Type : Mutator
Title : set_forest
Usage : $taxa->set_forest( $forest );
Function: Associates forest with the
invocant taxa object (i.e.
creates reference).
Returns : Modified object.
Args : A Bio::Phylo::Forest object
Comments: A taxa object can link to multiple
forest and matrix objects.
set_matrix()
Type : Mutator
Title : set_matrix
Usage : $taxa->set_matrix($matrix);
Function: Associates matrix with the
invocant taxa object (i.e.
creates reference).
Returns : Modified object.
Args : A Bio::Phylo::Matrices::Matrix object
Comments: A taxa object can link to multiple
forest and matrix objects.
unset_forest()
Type : Mutator
Title : unset_forest
Usage : $taxa->unset_forest($forest);
Function: Disassociates forest from the
invocant taxa object (i.e.
removes reference).
Returns : Modified object.
Args : A Bio::Phylo::Forest object
unset_matrix()
Type : Mutator
Title : unset_matrix
Usage : $taxa->unset_matrix($matrix);
Function: Disassociates matrix from the
invocant taxa object (i.e.
removes reference).
Returns : Modified object.
Args : A Bio::Phylo::Matrices::Matrix object

ACCESSORS

get_forests()
Type : Accessor
Title : get_forests
Usage : @forests = @{ $taxa->get_forests };
Function: Retrieves forests associated
with the current taxa object.
Returns : An ARRAY reference of
Bio::Phylo::Forest objects.
Args : None.
get_matrices()
Type : Accessor
Title : get_matrices
Usage : @matrices = @{ $taxa->get_matrices };
Function: Retrieves matrices associated
with the current taxa object.
Returns : An ARRAY reference of
Bio::Phylo::Matrices::Matrix objects.
Args : None.
get_ntax()
Type : Accessor
Title : get_ntax
Usage : my $ntax = $taxa->get_ntax;
Function: Retrieves the number of taxa for the invocant.
Returns : INT
Args : None.
Comments:

METHODS

merge_by_name()
Type : Method
Title : merge_by_name
Usage : $taxa->merge_by_name($other_taxa);
Function: Merges two taxa objects such that
internally different taxon objects
with the same name become a single
object with the combined references
to datum objects and node objects
contained by the two.
Returns : A merged Bio::Phylo::Taxa object.
Args : A Bio::Phylo::Taxa object.

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::Listable

The Bio::Phylo::Taxa object inherits from the Bio::Phylo::Listable object. Look there for more methods applicable to the taxa 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: Taxa.pm 1721 2006-07-20 03:43:06Z rvosa $

AUTHOR

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