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

           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.


=cut

sub instantiate_from_row{
    my ($self,$row,$fact) = @_;
    my $obj;

    if($row && @$row) {
	if(! $fact) {
	    # we need to create at least Bio::SeqI implementing objects here;
	    # as a default catch-all we upgrade that to Bio::Seq::RichSeqI
	    $fact = Bio::Seq::SeqFactory->new(-type => "Bio::Seq::RichSeq");
	}
	$obj = $fact->create_object();
	$self->populate_from_row($obj, $row);
    }

    return $obj;
}

=head2 populate_from_row

 Title   : populate_from_row
 Usage   :
 Function: Populates an object with values from columns of the row.

 Example :
 Returns : The object populated, or undef, if the row contains no values
 Args    : The object to be populated.
           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().


=cut

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

    $obj = $self->SUPER::populate_from_row($obj,$rows);
    if($obj && $rows && @$rows && $obj->isa("Bio::Seq::RichSeqI")) {
	$obj->division($rows->[6]) if $rows->[6];
    }
    return $obj;
}

=head2 remove_children

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

           We need to undefine the primary keys of all contained
           feature objects 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{
    my $self = shift;
    my $obj = shift;

    # features
    foreach my $feat ($obj->top_SeqFeatures()) {
	if($feat->isa("Bio::DB::PersistentObjectI")) {
	    $feat->primary_key(undef);
	    # cascade to feature's children
	    $self->_feat_adaptor->remove_children($feat);
	}
    }
    # annotation collection
    my $ac = $obj->annotation();
    if($ac->isa("Bio::DB::PersistentObjectI")) {
	$ac->primary_key(undef);
	$ac->adaptor()->remove_children($ac);
    }
    # done
    return 1;
}

=head1 Internal methods

 These are mostly private or 'protected.' Methods which are in the
 latter class have this explicitly stated in their
 documentation. 'Protected' means you may call these from derived
 classes, but not from outside.

 Most of these methods cache certain adaptors or otherwise reduce call
 path and object creation overhead. There's no magic here.

=cut

=head2 _feat_adaptor

 Title   : _feat_adaptor
 Usage   : $obj->_feat_adaptor($newval)
 Function: Get/set cached persistence adaptor for a Bio::SeqFeatureI object

           In OO speak, consider the access class of this method protected.
           I.e., call from descendants, but not from outside.
 Example : 
 Returns : value of _feat_adaptor (a Bio::DB::PersistenceAdaptorI
	   instance)
 Args    : new value (a Bio::DB::PersistenceAdaptorI instance, optional)


=cut

sub _feat_adaptor{
    my ($self,$adp) = @_;
    if( defined $adp) {
	$self->{'_feat_adaptor'} = $adp;
    }
    if(! exists($self->{'_feat_adaptor'})) {
	$self->{'_feat_adaptor'} =
	    $self->db()->get_object_adaptor("Bio::SeqFeatureI");
    }
    return $self->{'_feat_adaptor'};
}


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