Bio::DB::BioSQL::Pg BiosequenceAdaptorDriver
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Summary
Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver
DBI qw ( :sql_types )
Inherit
Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver
Synopsis
Give standard usage here
Description
Describe the object here
Methods
insert_objectDescriptionCode
update_objectDescriptionCode
get_biosequenceDescriptionCode
Methods description
insert_objectcode    nextTop
 Title   : insert_object
Usage :
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, $sth), dbcontext(), and get_persistent_slots()). The object to be inserted. A reference to an array of foreign key objects; if any of those foreign key values is NULL (some foreign keys may be nullable), then give the class name.
update_objectcodeprevnextTop
 Title   : update_object
Usage :
Function: See parent class. We need to override this here because there is
no Biosequence object separate from PrimarySeq that would hold a
primary key. Hence, store()s cannot recognize when the Biosequence
for a Bioentry already exists and needs to be updated, or when it
needs to be created. The way the code is currently wired, the
presence of the primary key (stemming from the bioentry) will always
trigger an update.
So, what we need to do here is check whether the entry already exists and if not delegate to insert_object(). Example : Returns : The number of updated rows Args : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object (basically, it needs to implement dbh(), sth($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.
get_biosequencecodeprevnextTop
 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).
Methods code
insert_objectdescriptionprevnextTop
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 $isdef; return -1;
}
update_objectdescriptionprevnextTop
sub update_object {
    my ($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); }
}
get_biosequencedescriptionprevnextTop
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"); # we need to create this
my $sql = defined($start) ? "SELECT SUBSTRING($seqcol FROM ?".(defined($end) ? " FOR ?" : "") . ") FROM $table WHERE $ukname = ?" : "SELECT $seqcol FROM $table WHERE $ukname = ?"; $adp->debug("preparing SELECT statement: $sql\n"); $sth = $adp->dbh()->prepare($sql); # cache it
if ($sth) { $adp->sth($cache_key, $sth); } else { $self->throw("failed to prepare SQL statement '$sql': " .$adp->dbh->errstr); } } # bind parameters
my $i = 1; if (defined($start)) { # note that the SQL type specification is absolutely necessary
# here as otherwise the server will complain about an escaped string
$sth->bind_param($i, $start, SQL_INTEGER); $i++; if (defined($end)) { $sth->bind_param($i, $end-$start+1, SQL_INTEGER); $i++; } } $sth->bind_param($i, $bioentryid, SQL_INTEGER); # execute and fetch
$adp->debug(substr(ref($self),rindex(ref($self),"::")+2) .": executing SELECT SUBSTRING with (" .(defined($start) ? "$start;" : "") .(defined($end) ? ($end-$start+1).";" : "") .$bioentryid.")\n") if $adp->verbose > 0; if (! $sth->execute()) { $self->throw("error while executing query $cache_key with values (" .(defined($start) ? "$start;" : "") .(defined($end) ? ($end-$start+1).";" : "") .$bioentryid."):\n" .$sth->errstr." (".$sth->state.")"); } my $row = $sth->fetchall_arrayref(); return (@$row ? $row->[0]->[0] : undef); } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
 
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
AUTHOR - Yves BastideTop
Email ybastide at irisa.fr
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _