NAME

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

SYNOPSIS

use Bio::Phylo::Taxa;
use Bio::Phylo::Taxa::Taxon;

# 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.

to_nexus()

Type    : Format convertor
Title   : to_nexus
Usage   : my $block = $taxa->to_nexus;
Function: Converts $taxa into a nexus taxa block.
Returns : Nexus taxa block (SCALAR).
Args    : -links => 1 (optional, adds 'TITLE' token)
Comments:

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 4193 2007-07-11 20:26:06Z 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.

cpanm Bio::Phylo

perl -MCPAN -e shell
install Bio::Phylo