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

 Title   : attach_foreign_key_objects
 Usage   :
 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.

           PrimarySeqIs have a BioNamespace as foreign key.
 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) = @_;
    
    # retrieve namespace by primary key
    my $nsadp = $self->_bionamespace_adaptor();
    my $ns = $nsadp->find_by_primary_key($fks->[0]);
    if($ns) {
	$obj->namespace($ns->namespace()) if $ns->namespace();
	$obj->authority($ns->authority()) if $ns->authority();
	return 1;
    }
    return 0;
}

=head2 store_children

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

           Bio::PrimarySeqI has a sequence as child.
 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) = @_;

    # delegate to Biosequence adaptor
    return $self->_bioseq_adaptor()->store($obj);
}

=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::PrimarySeqIs, we need to get the biosequence attributes
           as well.
 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) = @_;

    my $adp = $self->_bioseq_adaptor();
    # This will find the biosequence by its foreign key to bioentry, since
    # that's the UK. Subsequently, it will populate the biosequence-specific
    # slots of $obj with the found record.
    my $o = $adp->find_by_unique_key($obj);
    # on success, $o == $obj, and $o == undef otherwise
    # however, some SeqI objects may legally lack any of those attributes
    # and hence may not have an entry here, so we'll have to be permissive
    return 1; #$o ? 1 : 0;
}

=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.