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lib/Bio/Phylo/NeXML/Writable.pm  view on Meta::CPAN

 Serializes object to JSON string

 Type    : Serializer
 Title   : to_json()
 Usage   : print $obj->to_json();
 Function: Serializes object to JSON string
 Returns : String 
 Args    : None
 Comments:

=cut

    sub to_json {
		looks_like_class('Bio::Phylo::NeXML::XML2JSON')->new->convert( shift->to_xml );
    }    

	sub _json_data {
		my $self   = shift;
		my %meta   = map { $_->get_predicate => $_->get_object } @{ $self->get_meta };
		my %result = %{ $self->SUPER::_json_data };
		$result{$_} = $meta{$_} for keys %meta;
		$result{'name'} = $self->get_name if $self->get_name;
		$result{'link'} = $self->get_link if $self->get_link;
		return \%result;
	}

=item to_cdao()

Serializes object to CDAO RDF/XML string

 Type    : Serializer
 Title   : to_cdao()
 Usage   : print $obj->to_cdao();
 Function: Serializes object to CDAO RDF/XML string
 Returns : String 
 Args    : None
 Comments:

=cut	
	
	sub to_cdao {
		return unparse(
			'-phylo'  => shift,
			'-format' => 'cdao',
		);
	}

    sub _cleanup : Destructor {
        my $self = shift;
        
        # this deserves an explanation. the issue is as follows: for the package
        # bio-phylo-megatree we have node objects that are persisted in a database
        # and accessed through an object-relational mapping provided by DBIx::Class.
        # these node objects are created and destroyed on the fly as a set of node
        # records (i.e. a tree) is traversed. this is the whole point of the package,
        # because it means large trees don't ever have to be kept in memory. however,
        # as a consequence, every time one of those ORM-backed nodes goes out of scope, 
        # this destructor is called and all the @fields are cleaned up again. this 
        # precludes computation and caching of node coordinates (or any other semantic 
        # annotation) on such ORM-backed objects. the terrible, terrible fix for now is 
        # to just assume that i) these annotations need to stay alive ii) we're not going 
        # to have ID clashes (!!!!!), so iii) we just don't clean up after ourselves. 
        # as a note to my future self: it would be a good idea to have a triple store-like 
        # table to store the annotations, so they are persisted in the same way as the
        # node objects, bypassing this malarkey.        
        if ( not $self->isa('DBIx::Class::Core') ) {
			my $id = $self->get_id;
			for my $field (@fields) {
				delete $field->{$id};
			}
        }
    }

=back

=cut

    # podinherit_insert_token

=head1 SEE ALSO

There is a mailing list at L<https://groups.google.com/forum/#!forum/bio-phylo> 
for any user or developer questions and discussions.

Also see the manual: L<Bio::Phylo::Manual> and L<http://rutgervos.blogspot.com>.

=head1 CITATION

If you use Bio::Phylo in published research, please cite it:

B<Rutger A Vos>, B<Jason Caravas>, B<Klaas Hartmann>, B<Mark A Jensen>
and B<Chase Miller>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
I<BMC Bioinformatics> B<12>:63.
L<http://dx.doi.org/10.1186/1471-2105-12-63>

=cut

}
1;