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

 Function: We override this here in order to omit the insert if there are
           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) = @_;
    
    # obtain the object's slot values to be serialized
    my $slotvals = $adp->get_persistent_slot_values($obj, $fkobjs);
    # any value present?
    my $isdef = $slotvals->[0];
    for(my $i = 1; $i < @$slotvals; $i++) {
	$isdef ||= $slotvals->[$i];
	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) = @_;
    
    my $cache_key = 'SELECT UK '.ref($self);
    my $sth = $adp->sth($cache_key);
    if(! $sth) {
	# create and prepare sql
	my $table = $self->table_name($adp);
	my $ukname = $self->foreign_key_name("Bio::PrimarySeqI");
	my $sql = "SELECT $ukname FROM $table WHERE $ukname = ?";
	$adp->debug("preparing SELECT statement: $sql\n");
	$sth = $adp->dbh()->prepare($sql);
	# and cache it
	$adp->sth($cache_key, $sth);
    }
    # bind parameters
    $sth->bind_param(1, $obj->primary_key(), SQL_INTEGER);
    # execute and fetch
    $sth->execute();
    my $row = $sth->fetchall_arrayref();
    if(@$row) {
	# exists already, this is an update
	return $self->SUPER::update_object($adp,$obj,$fkobjs);
    } else {
	# doesn't exist yet, this is in fact an insert
	return $self->insert_object($adp,$obj,$fkobjs);
    }
}

=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) = @_;

    # statement cached?
    my $cache_key = defined($start) 
        ? "SELECT BIOSEQ SUBSTR ".(defined($end) ? "2POS " : "").ref($adp)
        : "SELECT BIOSEQ ".ref($adp);
    my $sth = $adp->sth($cache_key);
    if(! $sth) {
        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");