view release on metacpan or  search on metacpan

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

           no values. This is because this entity basically represents a
           derived class, and we may simply be dealing with the base class.

 Example :
 Returns : The primary key of the newly inserted record.
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be inserted.
           A reference to an array of foreign key objects; if any of those
           foreign key values is NULL (some foreign keys may be nullable),
           then give the class name.


=cut

sub insert_object{
    my $self = shift;
    my ($adp,$obj,$fkobjs,$isdef) = @_;
    
    # this may come precomputed from the update_object() method below
    if(!defined($isdef)) {
	# no, not precomputed
	# obtain the object's slot values to be serialized
	my $slotvals = $adp->get_persistent_slot_values($obj, $fkobjs);
	# any value present?
	foreach (@$slotvals) { $isdef ||= $_; last if $isdef; }
    }
    return $self->SUPER::insert_object(@_) if $isdef;
    return -1;
}

=head2 update_object

 Title   : update_object
 Usage   :
 Function: See parent class. We need to override this here because
           there is no Biosequence object separate from PrimarySeq
           that would hold a primary key. Hence, store()s cannot
           recognize when the Biosequence for a Bioentry already
           exists and needs to be updated, or when it needs to be
           created. The way the code is currently wired, the presence
           of the primary key (stemming from the bioentry) will always
           trigger an update.

           So, what we need to do here is check whether the entry already
           exists and if not delegate to insert_object().
 Example :
 Returns : The number of updated rows
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
	    dbcontext(), and get_persistent_slots()).
	   The object to be updated.
           A reference to an array of foreign key objects; if any of those
           foreign key values is NULL (some foreign keys may be nullable),
           then give the class name.


=cut

sub update_object{
    my ($self,$adp,$obj,$fkobjs) = @_;

    # see whether there are any values defined at all
    my $slotvals = $adp->get_persistent_slot_values($obj, $fkobjs);
    my $isdef = 0;
    foreach (@$slotvals) { $isdef ||= $_; last if $isdef; }
    # in the majority of cases this actually will be an update indeed - so
    # let's just go ahead and try if there are any values to update
    my $rv = -1;
    if($isdef) {
	$rv = $self->SUPER::update_object($adp,$obj,$fkobjs);
	# if the number of affected rows was zero, then it needs to be
	# an insert
	if($rv && ($rv == 0)) {
	    # pass on the pre-computed $isdef (see the implementation above)
	    $rv = $self->insert_object($adp,$obj,$fkobjs,$isdef);
	}
    }
    # done
    return $rv;
}

=head2 get_biosequence

 Title   : get_biosequence
 Usage   :
 Function: Returns the actual sequence for a bioentry, or a substring of it.
 Example :
 Returns : A string (the sequence or subsequence)
 Args    : The calling persistence adaptor.
           The primary key of the bioentry for which to obtain the sequence.
           Optionally, start and end position if only a subsequence is to be
           returned (for long sequences, obtaining the subsequence from the
           database may be much faster than obtaining it from the complete
           in-memory string, because the latter has to be retrieved first).


=cut

sub get_biosequence{
    my ($self,$adp,$bioentryid,$start,$end) = @_;
    my ($sth, $cache_key, $row);
    my $seqstr;

    if(defined($start)) {
	# statement cached?
	$cache_key = "SELECT BIOSEQ SUBSTR".$adp.(defined($end) ?" 2POS":"");
	$sth = $adp->sth($cache_key);
	if(! $sth) {
	    # we need to create this
	    my $table = $self->table_name($adp);
	    my $seqcol = $self->slot_attribute_map($table)->{"seq"};
	    if(! $seqcol) {
		$self->throw("no mapping for column seq in table $table");
	    }
	    my $ukname = $self->foreign_key_name("Bio::PrimarySeqI");
	    my $sql = "SELECT DBMS_LOB.SUBSTR($seqcol, ";
	    if(defined($end)) {
		$sql .= "?, ?";
	    } else {