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Bio-Phylo-0.17_RC1
River stage two • 9 direct dependents • 18 total dependents
8 ++
/ Bio::Phylo::Adaptor::Bioperl::Tree

NAME

Bio::Phylo::Adaptor::Bioperl::Tree - Adaptor class for bioperl compatibility

SYNOPSIS

 use Bio::Phylo::Adaptor;

 # some way to get a tree
 use Bio::Phylo::IO;
 my $string = '((A,B),C);';
 my $forest = Bio::Phylo::IO->parse(
    -format => 'newick',
    -string => $string
 );
 my $tree = $forest->first;

 $Bio::Phylo::COMPAT = 'Bioperl';

 my $bptree = Bio::Phylo::Adaptor->new( $tree );

 print "compatible!" if $bptree->isa('Bio::Tree::TreeI');

DESCRIPTION

This class wraps Bio::Phylo tree objects to give them an interface compatible with bioperl.

METHODS

get_nodes()
 Title   : get_nodes
 Usage   : my @nodes = $tree->get_nodes()
 Function: Return list of Tree::NodeI objects
 Returns : array of Tree::NodeI objects
 Args    : (named values) hash with one value 
           order => 'b|breadth' first order or 'd|depth' first order
get_root_node()
 Title   : get_root_node
 Usage   : my $node = $tree->get_root_node();
 Function: Get the Top Node in the tree, in this implementation
           Trees only have one top node.
 Returns : Bio::Tree::NodeI object
 Args    : none
number_nodes()
 Title   : number_nodes
 Usage   : my $size = $tree->number_nodes
 Function: Returns the number of nodes
 Example :
 Returns : 
 Args    :
total_branch_length()
 Title   : total_branch_length
 Usage   : my $size = $tree->total_branch_length
 Function: Returns the sum of the length of all branches
 Returns : integer
 Args    : none
height()
 Title   : height
 Usage   : my $height = $tree->height
 Function: Gets the height of tree - this LOG_2($number_nodes)
           WARNING: this is only true for strict binary trees.  The TreeIO
           system is capable of building non-binary trees, for which this
           method will currently return an incorrect value!!
 Returns : integer
 Args    : none
id()
 Title   : id
 Usage   : my $id = $tree->id();
 Function: An id value for the tree
 Returns : scalar
 Args    :
score()
 Title   : score
 Usage   : $obj->score($newval)
 Function: Sets the associated score with this tree
           This is a generic slot which is probably best used 
           for log likelihood or other overall tree score
 Returns : value of score
 Args    : newvalue (optional)
get_leaf_nodes()
 Title   : get_leaf_nodes
 Usage   : my @leaves = $tree->get_leaf_nodes()
 Function: Returns the leaves (tips) of the tree
 Returns : Array of Bio::Tree::NodeI objects
 Args    : none

SEE ALSO

Bio::Tree::TreeI

Bio::Phylo::Adaptor::Bioperl::Tree is an adaptor that makes Bio::Phylo trees compatible with the Bio::Tree::TreeI interface.

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: Tree.pm 4162 2007-07-11 01:35:39Z rvosa $

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.