NAME

Bio::Phylo::Forest - The forest object, a set of phylogenetic trees.

SYNOPSIS

 use Bio::Phylo::Forest;
 my $trees = Bio::Phylo::Forest->new;

DESCRIPTION

The Bio::Phylo::Forest object models a set of trees. The object subclasses the Bio::Phylo::Listable object, so look there for more methods available to forest objects.

METHODS

CONSTRUCTOR

new
 Type    : Constructor
 Title   : new
 Usage   : my $trees = Bio::Phylo::Forest->new;
 Function: Instantiates a Bio::Phylo::Forest object.
 Returns : A Bio::Phylo::Forest object.
 Args    : None required, though see the superclass
           Bio::Phylo::Listable from which this
           object inherits.

MUTATORS

set_taxa()
 Type    : Mutator
 Title   : set_taxa
 Usage   : $forest->set_taxa( $taxa );
 Function: Links the invocant forest
           object to a taxa object.
           Individual terminal node
           objects are linked to
           individual taxon objects
           by name, i.e. by what is
           returned by $node->get_name
 Returns : $forest
 Args    : A Bio::Phylo::Taxa object.
 Comments: This method checks whether
           any of the nodes in the trees
           in the invocant link to
           Bio::Phylo::Taxa::Taxon objects
           not contained by $taxa. If found,
           these are set to undef and the
           following message is displayed:

           "Reset X references from nodes
           to taxa outside taxa block"

ACCESSORS

get_taxa()
 Type    : Accessor
 Title   : get_taxa
 Usage   : my $taxa = $forest->get_taxa;
 Function: Retrieves the taxa object
           linked to the invocant.
 Returns : Bio::Phylo::Taxa
 Args    : NONE

METHODS

to_cipres()
 Type    : Format converter
 Title   : to_cipres
 Usage   : my $cipresforest = $forest->to_cipres;
 Function: Turns the invocant forest object
           into a CIPRES CORBA compliant
           data structure
 Returns : ARRAYREF
 Args    : NONE
make_taxa()
 Type    : Utility method
 Title   : make_taxa
 Usage   : my $taxa = $forest->make_taxa;
 Function: Creates a Bio::Phylo::Taxa
           object from the terminal nodes
           in invocant.
 Returns : Bio::Phylo::Taxa
 Args    : NONE
 Comments: N.B.!: the newly created taxa
           object will replace all earlier
           references to other taxa and
           taxon objects.

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 forest object inherits from the Bio::Phylo::Listable object. The methods defined therein are applicable to forest objects.

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: Forest.pm,v 1.18 2006/04/12 22:38:22 rvosa Exp $

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.