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) using the Adaptor design pattern (e.g. see the page on the Portland Pattern Repository: http://www.c2.com/cgi/wiki?AdapterPattern). 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.

REVISION

$Id: Adaptor.pm 4265 2007-07-20 14:14:44Z rvosa $