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lib/Bio/Phylo/Mediators/TaxaMediator.pm  view on Meta::CPAN

    sub set_link {
        my $self = shift;
        my %opt  = @_;
        my ( $one, $many ) = ( $opt{'-one'}, $opt{'-many'} );
        my ( $one_id, $many_id ) = ( $one->get_id, $many->get_id );
        $one_to_one{$many_id} = $one_id;
        $one_to_many{$one_id} = {} unless $one_to_many{$one_id};

        # once other objects start referring to the taxon we want
        # these references to keep the taxon "alive" until all other
        # objects pointing to it have gone out of scope, in which
        # case the reference must be weakened again, so that it
        # might get cleaned up also
        if (isweak($object[$one_id]) ) {
            my $strong = $object[$one_id];
            $object[$one_id] = $strong;
        }
        
        $one_to_many{$one_id}->{$many_id} = $many->_type;
        return $self;

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

        # 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};
			}
        }