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lib/Bio/DB/BioSQL/LocationAdaptor.pm  view on Meta::CPAN

 Function: Attaches foreign key objects to the given object as far as
           necessary.

           This method is called after find_by_XXX() queries, not for
           INSERTs or UPDATEs.

           LocationIs don''t really have a foreign key object attached
           -- it would be the SeqFeatureI if they had one.

 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The object to which to attach foreign key objects.
           A reference to an array of foreign key values, in the order
           of foreign keys returned by get_foreign_key_objects().


=cut

sub attach_foreign_key_objects{
    my ($self,$obj,$fks) = @_;
    my $ok = 1;

    # remote location reference?
    if($fks->[1]) {
	my $dbl = $self->_dblink_adaptor->find_by_primary_key($fks->[1]);
	$obj->is_remote(1);
	$obj->seq_id($dbl->namespace_string) if $dbl;
	$ok = $dbl && $ok;
    }

    return $ok;
}

=head2 store_children

 Title   : store_children
 Usage   :
 Function: Inserts or updates the child entities of the given object in the 
           datastore.

           Bio::LocationI may have qualifier/value pairs as children. This is
           not implemented yet.
 Example :
 Returns : TRUE on success, and FALSE otherwise
 Args    : The Bio::DB::PersistentObjectI implementing object for which the
           child objects shall be made persistent.


=cut

sub store_children{
    my ($self,$obj) = @_;

    return 1;
}

=head2 remove_children

 Title   : remove_children
 Usage   :
 Function: This method is to cascade deletes in maintained objects.

           We just return TRUE here.

 Example :
 Returns : TRUE on success and FALSE otherwise
 Args    : The persistent object that was just removed from the database.
           Additional (named) parameter, as passed to remove().


=cut

sub remove_children{
    return 1;
}

=head2 attach_children

 Title   : attach_children
 Usage   :
 Function: Possibly retrieve and attach child objects of the given object.

           This is needed when whole object trees are supposed to be built
           when a base object is queried for and returned. An example would
           be Bio::SeqI objects and all the annotation objects that hang off
           of it.

           This is called by the find_by_XXXX() methods once the base object
           has been built. 

           For Bio::LocationIs, we need to get the qualifier/value pairs
           possibly associated with it. Not implemented yet.
 Example :
 Returns : TRUE on success, and FALSE otherwise.
 Args    : The object for which to find and to which to attach the child
           objects.


=cut

sub attach_children{
    my ($self,$obj) = @_;

    return 1;
}

=head2 instantiate_from_row

 Title   : instantiate_from_row
 Usage   :
 Function: Instantiates the class this object is an adaptor for, and populates
           it with values from columns of the row.

           This implementation calls populate_from_row() to do the real job.
 Example :
 Returns : An object, or undef, if the row contains no values
 Args    : A reference to an array of column values. The first column is the
           primary key, the other columns are expected to be in the order 
           returned by get_persistent_slots().
           Optionally, a Bio::Factory::SequenceFactoryI compliant object to
           be used for creating the object.