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.

cpanm Bio::Phylo

perl -MCPAN -e shell
install Bio::Phylo