- SEE ALSO
- COPYRIGHT & LICENSE
Bio::Phylo::Forest - The forest object, a set of phylogenetic trees.
use Bio::Phylo::Forest; my $trees = Bio::Phylo::Forest->new;
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.
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.
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"
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
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
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.
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.
The forest object inherits from the Bio::Phylo::Listable object. The methods defined therein are applicable to forest objects.
Also see the manual: Bio::Phylo::Manual.
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
Please report any bugs or feature requests to
email@example.com, 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 $
Rutger A. Vos,
- web page: http://www.sfu.ca/~rvosa/
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 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.