NAME

Bio::Phylo::Adaptor - Object adaptor for compatibility

SYNOPSIS

# load adaptor class
use Bio::Phylo::Adaptor;

# going to build Bio::Phylo tree
use Bio::Phylo::Forest::Tree;
my $tree = Bio::Phylo::Forest::Tree->new;

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

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

# $tree is now bioperl compatible
print "bioperl compatible!" if $bptree->isa('Bio::Tree::TreeI'); 

DESCRIPTION

The adaptor architecture is used to make Bio::Phylo objects compatible with other software (currently only bioperl). The compatibility mode can be defined globally at compile time by specifying:

use Bio::Phylo compat => 'Bioperl';

In which case all objects are instantiated as adapted objects automatically from within their respective constructors. Alternatively, adapted objects can be created by setting the $Bio::Phylo::COMPAT variable and passing 'raw' Bio::Phylo objects to the Bio::Phylo::Adaptor constructor.

METHODS

CONSTRUCTOR

new

Type    : Constructor
Title   : new
Usage   : my $adapted = Bio::Phylo::Adaptor->new($obj);
Function: Instantiates an adapted Bio::Phylo object.
Returns : An object compatible with whatever $Bio::Phylo::COMPAT
          is set to.
Args    : An object to adapt
Comments: This method depends on a correct setting of the global
          $Bio::Phylo::COMPAT setting.

SEE ALSO

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: Adaptor.pm 3386 2007-03-24 16:22:25Z 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.